Starting phenix.real_space_refine on Fri Feb 6 17:59:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n1v_24124/02_2026/7n1v_24124.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n1v_24124/02_2026/7n1v_24124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n1v_24124/02_2026/7n1v_24124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n1v_24124/02_2026/7n1v_24124.map" model { file = "/net/cci-nas-00/data/ceres_data/7n1v_24124/02_2026/7n1v_24124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n1v_24124/02_2026/7n1v_24124.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 116 5.16 5 C 17126 2.51 5 N 4360 2.21 5 O 5345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26947 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8530 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 52, 'TRANS': 1036} Chain breaks: 5 Chain: "B" Number of atoms: 8545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8545 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 52, 'TRANS': 1038} Chain breaks: 5 Chain: "C" Number of atoms: 8572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 8572 Classifications: {'peptide': 1094} Link IDs: {'PTRANS': 53, 'TRANS': 1040} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.20, per 1000 atoms: 0.23 Number of scatterers: 26947 At special positions: 0 Unit cell: (154.288, 156.763, 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 116 16.00 O 5345 8.00 N 4360 7.00 C 17126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.01 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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 Atom "HETATM26903 O5 NAG C1405 .*. O " rejected from bonding due to valence issues. Atom "HETATM26749 O5 NAG B1403 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 234 " " NAG A1406 " - " ASN A 282 " " NAG A1407 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 657 " " NAG A1410 " - " ASN A 709 " " NAG A1411 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " 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 B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6134 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 49 sheets defined 27.6% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.615A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.834A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.993A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.405A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 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: 3.969A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.504A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 837 removed outlier: 3.559A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA A 829 " --> pdb=" O LYS A 825 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.770A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.273A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.804A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.102A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.026A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 344 removed outlier: 4.022A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.651A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.504A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.696A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.890A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.585A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.891A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.438A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.735A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.584A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.537A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.611A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.801A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.016A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.692A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.669A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.522A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 635 through 639 Processing helix chain 'C' and resid 737 through 744 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: 3.825A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.419A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.820A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.815A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.656A 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 941 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 965 removed outlier: 4.000A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.693A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1161 removed outlier: 3.811A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.631A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.095A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.033A 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: 13.174A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.444A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.378A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.704A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.852A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.503A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.083A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.562A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.811A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.430A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.960A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.361A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.864A 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: 7.729A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.036A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.130A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.077A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.522A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.522A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.642A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.872A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.877A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.386A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.904A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.061A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.310A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.503A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE4, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.206A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.770A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.630A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.638A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.819A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.966A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.253A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.230A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3081 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: 6.82 Time building geometry restraints manager: 3.28 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: 4795 1.32 - 1.45: 7069 1.45 - 1.57: 15533 1.57 - 1.70: 0 1.70 - 1.83: 146 Bond restraints: 27543 Sorted by residual: bond pdb=" N ARG A1000 " pdb=" CA ARG A1000 " ideal model delta sigma weight residual 1.459 1.405 0.054 1.20e-02 6.94e+03 2.06e+01 bond pdb=" CA ARG A1000 " pdb=" C ARG A1000 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.26e-02 6.30e+03 1.78e+01 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.495 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C ARG B1014 " pdb=" O ARG B1014 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.16e-02 7.43e+03 1.68e+01 bond pdb=" C1 FUC d 3 " pdb=" O5 FUC d 3 " ideal model delta sigma weight residual 1.400 1.479 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 27538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 32868 2.76 - 5.51: 4436 5.51 - 8.27: 153 8.27 - 11.02: 5 11.02 - 13.78: 2 Bond angle restraints: 37464 Sorted by residual: angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 108.45 122.23 -13.78 1.26e+00 6.30e-01 1.20e+02 angle pdb=" N ARG A1107 " pdb=" CA ARG A1107 " pdb=" C ARG A1107 " ideal model delta sigma weight residual 112.87 122.90 -10.03 1.20e+00 6.94e-01 6.99e+01 angle pdb=" OD1 ASN C1074 " pdb=" CG ASN C1074 " pdb=" ND2 ASN C1074 " ideal model delta sigma weight residual 122.60 114.69 7.91 1.00e+00 1.00e+00 6.26e+01 angle pdb=" OD1 ASN A1074 " pdb=" CG ASN A1074 " pdb=" ND2 ASN A1074 " ideal model delta sigma weight residual 122.60 114.84 7.76 1.00e+00 1.00e+00 6.03e+01 angle pdb=" N ARG A 983 " pdb=" CA ARG A 983 " pdb=" C ARG A 983 " ideal model delta sigma weight residual 111.36 119.63 -8.27 1.09e+00 8.42e-01 5.75e+01 ... (remaining 37459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.25: 16882 25.25 - 50.51: 577 50.51 - 75.76: 100 75.76 - 101.02: 42 101.02 - 126.27: 21 Dihedral angle restraints: 17622 sinusoidal: 8087 harmonic: 9535 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 170.98 -77.98 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -139.07 53.07 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CA THR B 95 " pdb=" C THR B 95 " pdb=" N GLU B 96 " pdb=" CA GLU B 96 " ideal model delta harmonic sigma weight residual -180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 17619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.608: 4498 0.608 - 1.216: 6 1.216 - 1.823: 2 1.823 - 2.431: 0 2.431 - 3.039: 3 Chirality restraints: 4509 Sorted by residual: chirality pdb=" C1 NAG C1401 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1401 " pdb=" O5 NAG C1401 " both_signs ideal model delta sigma weight residual False -2.40 0.64 -3.04 2.00e-01 2.50e+01 2.31e+02 chirality pdb=" C1 NAG C1405 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1405 " pdb=" O5 NAG C1405 " both_signs ideal model delta sigma weight residual False -2.40 0.38 -2.78 2.00e-01 2.50e+01 1.94e+02 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 0.13 -2.53 2.00e-01 2.50e+01 1.60e+02 ... (remaining 4506 not shown) Planarity restraints: 4768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " -0.179 2.00e-02 2.50e+03 1.99e-01 4.95e+02 pdb=" CG ASN B 165 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " 0.328 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " -0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " -0.148 2.00e-02 2.50e+03 1.61e-01 3.26e+02 pdb=" CG ASN C 709 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " 0.272 2.00e-02 2.50e+03 pdb=" C1 NAG C1407 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.132 2.00e-02 2.50e+03 1.34e-01 2.23e+02 pdb=" CG ASN B 61 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.199 2.00e-02 2.50e+03 pdb=" C1 NAG B1401 " 0.165 2.00e-02 2.50e+03 ... (remaining 4765 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 16 2.40 - 3.03: 14790 3.03 - 3.65: 38432 3.65 - 4.28: 61784 4.28 - 4.90: 99670 Nonbonded interactions: 214692 Sorted by model distance: nonbonded pdb=" O THR A 124 " pdb=" CE1 PHE A 175 " model vdw 1.776 3.340 nonbonded pdb=" O THR A 124 " pdb=" CD1 PHE A 175 " model vdw 1.784 3.340 nonbonded pdb=" ND2 ASN A 122 " pdb=" C1 NAG A1402 " model vdw 1.995 3.550 nonbonded pdb=" NH1 ARG B 21 " pdb=" O PHE B 79 " model vdw 2.059 3.120 nonbonded pdb=" NH1 ARG B1091 " pdb=" O HIS B1118 " model vdw 2.109 3.120 ... (remaining 214687 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 827 or resid 853 through 1408)) selection = (chain 'B' and (resid 14 through 621 or resid 641 through 827 or resid 853 throu \ gh 1408)) selection = (chain 'C' and (resid 14 through 621 or resid 641 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.530 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: 0.670 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.800 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.015 0.565 27678 Z= 0.827 Angle : 1.933 55.720 37827 Z= 1.191 Chirality : 0.133 3.039 4509 Planarity : 0.012 0.095 4713 Dihedral : 14.538 126.271 11362 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.45 % Favored : 93.21 % Rotamer: Outliers : 0.98 % Allowed : 4.19 % Favored : 94.83 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 3240 helix: -1.36 (0.16), residues: 740 sheet: 0.22 (0.19), residues: 647 loop : -1.45 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 355 TYR 0.119 0.021 TYR B 365 PHE 0.118 0.013 PHE A 898 TRP 0.170 0.025 TRP C 104 HIS 0.016 0.004 HIS B1159 Details of bonding type rmsd covalent geometry : bond 0.01373 (27543) covalent geometry : angle 1.77255 (37464) SS BOND : bond 0.01234 ( 42) SS BOND : angle 2.10188 ( 84) hydrogen bonds : bond 0.15619 ( 1119) hydrogen bonds : angle 8.32993 ( 3081) link_ALPHA1-4 : bond 0.02625 ( 6) link_ALPHA1-4 : angle 4.01991 ( 18) link_BETA1-4 : bond 0.02174 ( 29) link_BETA1-4 : angle 3.70957 ( 87) link_BETA1-6 : bond 0.03435 ( 3) link_BETA1-6 : angle 3.82448 ( 9) link_NAG-ASN : bond 0.14415 ( 55) link_NAG-ASN : angle 11.43893 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 791 time to evaluate : 0.996 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 81 ASN cc_start: 0.7418 (m110) cc_final: 0.7063 (m-40) REVERT: A 129 LYS cc_start: 0.8538 (tttt) cc_final: 0.8040 (tttt) REVERT: A 212 LEU cc_start: 0.7705 (tp) cc_final: 0.7303 (tp) REVERT: A 224 GLU cc_start: 0.8061 (mp0) cc_final: 0.7844 (mp0) REVERT: A 298 GLU cc_start: 0.7989 (tt0) cc_final: 0.7780 (tt0) REVERT: A 319 ARG cc_start: 0.7688 (ptp-170) cc_final: 0.7393 (ptp-170) REVERT: A 422 ASN cc_start: 0.5123 (OUTLIER) cc_final: 0.4701 (p0) REVERT: A 493 GLN cc_start: 0.7276 (tm-30) cc_final: 0.7021 (tm-30) REVERT: A 671 CYS cc_start: 0.5722 (m) cc_final: 0.5473 (m) REVERT: A 819 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7874 (mt-10) REVERT: A 823 PHE cc_start: 0.8319 (t80) cc_final: 0.7929 (t80) REVERT: A 936 ASP cc_start: 0.7867 (m-30) cc_final: 0.7474 (m-30) REVERT: A 941 THR cc_start: 0.7497 (t) cc_final: 0.7147 (t) REVERT: A 950 ASP cc_start: 0.8020 (t0) cc_final: 0.7659 (t70) REVERT: A 957 GLN cc_start: 0.8039 (tt0) cc_final: 0.7735 (tp40) REVERT: A 964 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8471 (mttm) REVERT: A 1038 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8592 (mtpp) REVERT: A 1141 LEU cc_start: 0.8924 (tp) cc_final: 0.8711 (tp) REVERT: B 105 ILE cc_start: 0.8987 (mp) cc_final: 0.8783 (mp) REVERT: B 125 ASN cc_start: 0.7644 (p0) cc_final: 0.7281 (p0) REVERT: B 135 PHE cc_start: 0.6734 (m-80) cc_final: 0.6467 (m-80) REVERT: B 224 GLU cc_start: 0.8063 (mp0) cc_final: 0.7723 (mp0) REVERT: B 237 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7641 (ptp90) REVERT: B 417 LYS cc_start: 0.8109 (mmtp) cc_final: 0.7887 (mmmm) REVERT: B 493 GLN cc_start: 0.7430 (tm-30) cc_final: 0.6872 (tm-30) REVERT: B 524 VAL cc_start: 0.7785 (p) cc_final: 0.7571 (p) REVERT: B 564 GLN cc_start: 0.7473 (tp40) cc_final: 0.6874 (tp-100) REVERT: B 580 GLN cc_start: 0.7406 (mt0) cc_final: 0.7135 (mt0) REVERT: B 596 SER cc_start: 0.8991 (m) cc_final: 0.8435 (p) REVERT: B 619 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7109 (mt-10) REVERT: B 737 ASP cc_start: 0.7501 (t0) cc_final: 0.7198 (t0) REVERT: B 740 MET cc_start: 0.8589 (ttt) cc_final: 0.7333 (ttp) REVERT: B 950 ASP cc_start: 0.8029 (m-30) cc_final: 0.7598 (m-30) REVERT: B 964 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8517 (mttp) REVERT: B 984 LEU cc_start: 0.8680 (mm) cc_final: 0.8458 (mt) REVERT: B 986 LYS cc_start: 0.8445 (tttm) cc_final: 0.8111 (tttm) REVERT: B 1141 LEU cc_start: 0.8758 (tt) cc_final: 0.8540 (tt) REVERT: C 45 SER cc_start: 0.8420 (p) cc_final: 0.8111 (t) REVERT: C 52 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 244 LEU cc_start: 0.4911 (tt) cc_final: 0.4686 (tt) REVERT: C 320 VAL cc_start: 0.8770 (t) cc_final: 0.8523 (m) REVERT: C 321 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8394 (mp10) REVERT: C 365 TYR cc_start: 0.8384 (m-80) cc_final: 0.8174 (m-80) REVERT: C 427 ASP cc_start: 0.7590 (m-30) cc_final: 0.7120 (m-30) REVERT: C 487 ASN cc_start: 0.6401 (p0) cc_final: 0.6124 (p0) REVERT: C 508 TYR cc_start: 0.6622 (m-80) cc_final: 0.6188 (m-80) REVERT: C 534 VAL cc_start: 0.8566 (p) cc_final: 0.8273 (m) REVERT: C 540 ASN cc_start: 0.8553 (m-40) cc_final: 0.8269 (m110) REVERT: C 546 LEU cc_start: 0.8482 (mt) cc_final: 0.8158 (mp) REVERT: C 571 ASP cc_start: 0.8245 (t70) cc_final: 0.7918 (t0) REVERT: C 643 PHE cc_start: 0.8327 (t80) cc_final: 0.7960 (t80) REVERT: C 737 ASP cc_start: 0.7393 (t0) cc_final: 0.7107 (t0) REVERT: C 748 GLU cc_start: 0.8015 (pm20) cc_final: 0.7777 (pm20) REVERT: C 752 LEU cc_start: 0.9116 (mt) cc_final: 0.8553 (mm) REVERT: C 808 ASP cc_start: 0.7946 (t0) cc_final: 0.7738 (t70) REVERT: C 886 TRP cc_start: 0.8844 (p90) cc_final: 0.8559 (p90) REVERT: C 933 LYS cc_start: 0.8772 (mmpt) cc_final: 0.8433 (mmmt) REVERT: C 950 ASP cc_start: 0.8067 (t0) cc_final: 0.7653 (t0) REVERT: C 968 SER cc_start: 0.9173 (m) cc_final: 0.8905 (t) REVERT: C 979 ASP cc_start: 0.8025 (m-30) cc_final: 0.7769 (m-30) REVERT: C 987 VAL cc_start: 0.8988 (t) cc_final: 0.8523 (t) REVERT: C 1045 LYS cc_start: 0.8194 (tmtt) cc_final: 0.7890 (tmtt) REVERT: C 1086 LYS cc_start: 0.8990 (ptpp) cc_final: 0.8653 (ptpp) REVERT: C 1118 HIS cc_start: 0.8312 (m-70) cc_final: 0.8112 (m170) REVERT: C 1119 ASN cc_start: 0.8549 (m110) cc_final: 0.8209 (m110) REVERT: C 1141 LEU cc_start: 0.9003 (tt) cc_final: 0.8741 (tt) REVERT: C 1148 PHE cc_start: 0.7280 (t80) cc_final: 0.6813 (t80) outliers start: 28 outliers final: 5 residues processed: 806 average time/residue: 0.1915 time to fit residues: 236.8842 Evaluate side-chains 646 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 640 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain C residue 122 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 872 GLN A1119 ASN B 30 ASN B 149 ASN B 644 GLN B 762 GLN B1119 ASN B1142 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 394 ASN C 675 GLN C 954 GLN C1108 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.102392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.083769 restraints weight = 67181.386| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.41 r_work: 0.3148 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27678 Z= 0.165 Angle : 0.820 24.037 37827 Z= 0.398 Chirality : 0.053 1.148 4509 Planarity : 0.005 0.059 4713 Dihedral : 10.495 114.528 5491 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.13 % Allowed : 10.24 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3240 helix: 0.80 (0.19), residues: 747 sheet: 0.01 (0.18), residues: 747 loop : -1.14 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 403 TYR 0.041 0.002 TYR B 396 PHE 0.030 0.002 PHE B1148 TRP 0.026 0.002 TRP A 353 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00364 (27543) covalent geometry : angle 0.75023 (37464) SS BOND : bond 0.00494 ( 42) SS BOND : angle 2.08443 ( 84) hydrogen bonds : bond 0.04783 ( 1119) hydrogen bonds : angle 6.33600 ( 3081) link_ALPHA1-4 : bond 0.01482 ( 6) link_ALPHA1-4 : angle 2.93928 ( 18) link_BETA1-4 : bond 0.00466 ( 29) link_BETA1-4 : angle 1.91293 ( 87) link_BETA1-6 : bond 0.01443 ( 3) link_BETA1-6 : angle 1.89645 ( 9) link_NAG-ASN : bond 0.00661 ( 55) link_NAG-ASN : angle 4.58365 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 650 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8827 (tttt) cc_final: 0.8212 (tptt) REVERT: A 153 MET cc_start: 0.6981 (tmm) cc_final: 0.6652 (ppp) REVERT: A 174 PRO cc_start: 0.8419 (Cg_exo) cc_final: 0.8184 (Cg_endo) REVERT: A 212 LEU cc_start: 0.7600 (tp) cc_final: 0.7094 (tt) REVERT: A 287 ASP cc_start: 0.8216 (t70) cc_final: 0.7971 (t0) REVERT: A 298 GLU cc_start: 0.8432 (tt0) cc_final: 0.8200 (tt0) REVERT: A 495 TYR cc_start: 0.6714 (m-80) cc_final: 0.6234 (m-80) REVERT: A 516 GLU cc_start: 0.7627 (tt0) cc_final: 0.7243 (tt0) REVERT: A 571 ASP cc_start: 0.8029 (t70) cc_final: 0.7628 (t0) REVERT: A 583 GLU cc_start: 0.8187 (pm20) cc_final: 0.7985 (pm20) REVERT: A 646 ARG cc_start: 0.8892 (mmm160) cc_final: 0.8623 (mmm-85) REVERT: A 759 PHE cc_start: 0.8232 (m-80) cc_final: 0.7960 (m-80) REVERT: A 796 ASP cc_start: 0.8036 (t70) cc_final: 0.7828 (t70) REVERT: A 936 ASP cc_start: 0.8148 (m-30) cc_final: 0.7769 (m-30) REVERT: A 941 THR cc_start: 0.7626 (t) cc_final: 0.7373 (t) REVERT: A 949 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8394 (mm-40) REVERT: A 950 ASP cc_start: 0.8279 (t0) cc_final: 0.7989 (t70) REVERT: A 957 GLN cc_start: 0.8658 (tt0) cc_final: 0.8412 (tt0) REVERT: A 964 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8765 (mttm) REVERT: B 125 ASN cc_start: 0.7565 (p0) cc_final: 0.7340 (p0) REVERT: B 237 ARG cc_start: 0.8409 (mtm110) cc_final: 0.7973 (ptp90) REVERT: B 281 GLU cc_start: 0.9099 (tt0) cc_final: 0.8840 (pt0) REVERT: B 346 ARG cc_start: 0.7740 (mmm160) cc_final: 0.7378 (tpt-90) REVERT: B 436 TRP cc_start: 0.7963 (p90) cc_final: 0.7302 (p90) REVERT: B 564 GLN cc_start: 0.7688 (tp40) cc_final: 0.7047 (tp-100) REVERT: B 577 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7857 (ttm-80) REVERT: B 580 GLN cc_start: 0.8065 (mt0) cc_final: 0.7852 (mt0) REVERT: B 950 ASP cc_start: 0.8432 (m-30) cc_final: 0.8042 (m-30) REVERT: B 986 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8405 (tttm) REVERT: B 1148 PHE cc_start: 0.7079 (t80) cc_final: 0.6554 (t80) REVERT: C 52 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8681 (tm-30) REVERT: C 180 GLU cc_start: 0.4059 (OUTLIER) cc_final: 0.3603 (pm20) REVERT: C 190 ARG cc_start: 0.8193 (mmt180) cc_final: 0.7589 (mmt180) REVERT: C 319 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8087 (ttm-80) REVERT: C 321 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8595 (mp10) REVERT: C 365 TYR cc_start: 0.8524 (m-80) cc_final: 0.8206 (m-80) REVERT: C 386 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8898 (mmtm) REVERT: C 400 PHE cc_start: 0.8240 (p90) cc_final: 0.8001 (p90) REVERT: C 427 ASP cc_start: 0.7964 (m-30) cc_final: 0.7621 (m-30) REVERT: C 437 ASN cc_start: 0.7320 (t0) cc_final: 0.6922 (t0) REVERT: C 455 LEU cc_start: 0.8714 (mt) cc_final: 0.8498 (mt) REVERT: C 508 TYR cc_start: 0.6729 (m-80) cc_final: 0.6269 (m-80) REVERT: C 534 VAL cc_start: 0.8757 (p) cc_final: 0.8522 (m) REVERT: C 568 ASP cc_start: 0.8532 (t0) cc_final: 0.8222 (t0) REVERT: C 571 ASP cc_start: 0.8594 (t70) cc_final: 0.8369 (t70) REVERT: C 574 ASP cc_start: 0.8664 (p0) cc_final: 0.8422 (p0) REVERT: C 751 ASN cc_start: 0.9038 (m-40) cc_final: 0.8713 (m-40) REVERT: C 808 ASP cc_start: 0.8327 (t0) cc_final: 0.8095 (t70) REVERT: C 816 SER cc_start: 0.8781 (p) cc_final: 0.8556 (p) REVERT: C 950 ASP cc_start: 0.8502 (t0) cc_final: 0.8158 (t0) REVERT: C 968 SER cc_start: 0.9358 (m) cc_final: 0.9113 (t) REVERT: C 1086 LYS cc_start: 0.9091 (ptpp) cc_final: 0.8854 (ptpp) REVERT: C 1106 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8518 (pt0) REVERT: C 1119 ASN cc_start: 0.8850 (m110) cc_final: 0.8497 (m-40) REVERT: C 1141 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8877 (tp) outliers start: 61 outliers final: 28 residues processed: 680 average time/residue: 0.1966 time to fit residues: 207.9707 Evaluate side-chains 610 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 578 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 986 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 199 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 274 optimal weight: 0.0980 chunk 251 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 283 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 540 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1101 HIS A1142 GLN B 218 GLN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 481 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082189 restraints weight = 66642.929| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.36 r_work: 0.3121 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27678 Z= 0.181 Angle : 0.748 20.186 37827 Z= 0.361 Chirality : 0.050 0.853 4509 Planarity : 0.004 0.058 4713 Dihedral : 9.713 111.389 5487 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.66 % Allowed : 13.24 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3240 helix: 1.35 (0.19), residues: 742 sheet: -0.17 (0.18), residues: 767 loop : -1.06 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 237 TYR 0.030 0.002 TYR B 396 PHE 0.023 0.002 PHE C 342 TRP 0.027 0.002 TRP A 353 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00411 (27543) covalent geometry : angle 0.69508 (37464) SS BOND : bond 0.00508 ( 42) SS BOND : angle 1.78640 ( 84) hydrogen bonds : bond 0.04434 ( 1119) hydrogen bonds : angle 5.91328 ( 3081) link_ALPHA1-4 : bond 0.01725 ( 6) link_ALPHA1-4 : angle 3.14253 ( 18) link_BETA1-4 : bond 0.00368 ( 29) link_BETA1-4 : angle 1.67496 ( 87) link_BETA1-6 : bond 0.01564 ( 3) link_BETA1-6 : angle 2.19297 ( 9) link_NAG-ASN : bond 0.00528 ( 55) link_NAG-ASN : angle 3.75092 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 609 time to evaluate : 1.039 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: A 21 ARG cc_start: 0.3938 (OUTLIER) cc_final: 0.3072 (ppt-90) REVERT: A 129 LYS cc_start: 0.8811 (tttt) cc_final: 0.8246 (tttt) REVERT: A 153 MET cc_start: 0.6913 (tmm) cc_final: 0.6680 (ppp) REVERT: A 174 PRO cc_start: 0.8477 (Cg_exo) cc_final: 0.8239 (Cg_endo) REVERT: A 287 ASP cc_start: 0.8253 (t70) cc_final: 0.7973 (t0) REVERT: A 298 GLU cc_start: 0.8474 (tt0) cc_final: 0.8191 (tt0) REVERT: A 418 ILE cc_start: 0.8400 (mt) cc_final: 0.8199 (mm) REVERT: A 516 GLU cc_start: 0.7790 (tt0) cc_final: 0.7533 (tt0) REVERT: A 568 ASP cc_start: 0.8486 (t0) cc_final: 0.8185 (p0) REVERT: A 583 GLU cc_start: 0.8299 (pm20) cc_final: 0.8078 (pm20) REVERT: A 586 ASP cc_start: 0.8361 (m-30) cc_final: 0.8127 (m-30) REVERT: A 646 ARG cc_start: 0.8952 (mmm160) cc_final: 0.8621 (mmm-85) REVERT: A 796 ASP cc_start: 0.8147 (t70) cc_final: 0.7892 (t70) REVERT: A 901 GLN cc_start: 0.8815 (tt0) cc_final: 0.8560 (tt0) REVERT: A 936 ASP cc_start: 0.8280 (m-30) cc_final: 0.7927 (m-30) REVERT: A 941 THR cc_start: 0.7675 (t) cc_final: 0.7398 (t) REVERT: A 949 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8355 (mm-40) REVERT: A 957 GLN cc_start: 0.8562 (tt0) cc_final: 0.8359 (tt0) REVERT: A 960 ASN cc_start: 0.8600 (t0) cc_final: 0.8394 (t0) REVERT: A 964 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8660 (mmmt) REVERT: A 1123 SER cc_start: 0.8909 (m) cc_final: 0.8691 (m) REVERT: B 125 ASN cc_start: 0.7707 (p0) cc_final: 0.7429 (p0) REVERT: B 237 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8089 (ptp90) REVERT: B 281 GLU cc_start: 0.9115 (tt0) cc_final: 0.8864 (pt0) REVERT: B 436 TRP cc_start: 0.7930 (p90) cc_final: 0.7440 (p90) REVERT: B 456 PHE cc_start: 0.7817 (m-80) cc_final: 0.7436 (m-80) REVERT: B 564 GLN cc_start: 0.7851 (tp40) cc_final: 0.7227 (tp-100) REVERT: B 577 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7819 (ttm-80) REVERT: B 580 GLN cc_start: 0.8037 (mt0) cc_final: 0.7805 (mt0) REVERT: B 737 ASP cc_start: 0.8148 (p0) cc_final: 0.7494 (p0) REVERT: B 740 MET cc_start: 0.8701 (ttt) cc_final: 0.8186 (ttm) REVERT: B 750 SER cc_start: 0.8954 (m) cc_final: 0.8658 (p) REVERT: B 950 ASP cc_start: 0.8389 (m-30) cc_final: 0.7998 (m-30) REVERT: C 52 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8709 (tm-30) REVERT: C 180 GLU cc_start: 0.4113 (OUTLIER) cc_final: 0.3650 (pm20) REVERT: C 321 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8711 (mm-40) REVERT: C 368 LEU cc_start: 0.9075 (mt) cc_final: 0.8865 (mp) REVERT: C 386 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8878 (mmtm) REVERT: C 455 LEU cc_start: 0.8666 (mt) cc_final: 0.8462 (mt) REVERT: C 508 TYR cc_start: 0.6835 (m-80) cc_final: 0.6446 (m-80) REVERT: C 523 THR cc_start: 0.8670 (p) cc_final: 0.8204 (t) REVERT: C 619 GLU cc_start: 0.7322 (mp0) cc_final: 0.7023 (mp0) REVERT: C 748 GLU cc_start: 0.8276 (pm20) cc_final: 0.8060 (pm20) REVERT: C 765 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8078 (ttp80) REVERT: C 808 ASP cc_start: 0.8291 (t0) cc_final: 0.8026 (t70) REVERT: C 933 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8673 (mmmt) REVERT: C 945 LEU cc_start: 0.8858 (mt) cc_final: 0.8635 (mp) REVERT: C 950 ASP cc_start: 0.8415 (t0) cc_final: 0.8026 (t0) REVERT: C 985 ASP cc_start: 0.8021 (p0) cc_final: 0.7451 (p0) REVERT: C 1045 LYS cc_start: 0.8704 (tmtt) cc_final: 0.8477 (tmtt) REVERT: C 1086 LYS cc_start: 0.9052 (ptpp) cc_final: 0.8815 (ptpp) REVERT: C 1106 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8530 (pt0) REVERT: C 1119 ASN cc_start: 0.8849 (m110) cc_final: 0.8499 (m-40) outliers start: 76 outliers final: 48 residues processed: 651 average time/residue: 0.1931 time to fit residues: 195.3944 Evaluate side-chains 627 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 575 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 34 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 138 optimal weight: 0.0470 chunk 192 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 165 optimal weight: 0.7980 chunk 279 optimal weight: 0.7980 chunk 247 optimal weight: 0.0010 chunk 60 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 764 ASN A 935 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 271 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 955 ASN ** 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 = 0.3659 r_free = 0.3659 target = 0.101380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.083319 restraints weight = 65737.333| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.34 r_work: 0.3164 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27678 Z= 0.132 Angle : 0.699 17.851 37827 Z= 0.335 Chirality : 0.048 0.778 4509 Planarity : 0.004 0.052 4713 Dihedral : 8.939 109.814 5487 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.94 % Allowed : 14.54 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3240 helix: 1.59 (0.19), residues: 750 sheet: -0.15 (0.18), residues: 729 loop : -1.01 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.035 0.001 TYR C 904 PHE 0.033 0.001 PHE B1148 TRP 0.032 0.001 TRP A 353 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00286 (27543) covalent geometry : angle 0.65372 (37464) SS BOND : bond 0.00450 ( 42) SS BOND : angle 1.60961 ( 84) hydrogen bonds : bond 0.03896 ( 1119) hydrogen bonds : angle 5.69299 ( 3081) link_ALPHA1-4 : bond 0.01757 ( 6) link_ALPHA1-4 : angle 3.02487 ( 18) link_BETA1-4 : bond 0.00361 ( 29) link_BETA1-4 : angle 1.52004 ( 87) link_BETA1-6 : bond 0.01801 ( 3) link_BETA1-6 : angle 2.32483 ( 9) link_NAG-ASN : bond 0.00454 ( 55) link_NAG-ASN : angle 3.31594 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 609 time to evaluate : 1.092 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 21 ARG cc_start: 0.3980 (OUTLIER) cc_final: 0.3114 (ppt-90) REVERT: A 129 LYS cc_start: 0.8792 (tttt) cc_final: 0.8221 (tttt) REVERT: A 174 PRO cc_start: 0.8469 (Cg_exo) cc_final: 0.8236 (Cg_endo) REVERT: A 191 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7929 (mt-10) REVERT: A 287 ASP cc_start: 0.8273 (t70) cc_final: 0.7979 (t0) REVERT: A 583 GLU cc_start: 0.8325 (pm20) cc_final: 0.8082 (pm20) REVERT: A 586 ASP cc_start: 0.8361 (m-30) cc_final: 0.8100 (m-30) REVERT: A 646 ARG cc_start: 0.8940 (mmm160) cc_final: 0.8608 (mmm-85) REVERT: A 796 ASP cc_start: 0.8155 (t70) cc_final: 0.7906 (t70) REVERT: A 901 GLN cc_start: 0.8756 (tt0) cc_final: 0.8502 (tt0) REVERT: A 936 ASP cc_start: 0.8213 (m-30) cc_final: 0.7879 (m-30) REVERT: A 941 THR cc_start: 0.7542 (t) cc_final: 0.7242 (t) REVERT: A 949 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8343 (mm-40) REVERT: A 957 GLN cc_start: 0.8561 (tt0) cc_final: 0.8337 (tt0) REVERT: A 1055 SER cc_start: 0.9129 (t) cc_final: 0.8778 (m) REVERT: A 1123 SER cc_start: 0.8797 (m) cc_final: 0.8546 (m) REVERT: B 125 ASN cc_start: 0.7603 (p0) cc_final: 0.7343 (p0) REVERT: B 177 MET cc_start: 0.6085 (ppp) cc_final: 0.4868 (ppp) REVERT: B 237 ARG cc_start: 0.8434 (mtm110) cc_final: 0.8051 (ptp90) REVERT: B 281 GLU cc_start: 0.9054 (tt0) cc_final: 0.8830 (pt0) REVERT: B 346 ARG cc_start: 0.7723 (mmm160) cc_final: 0.7337 (tpt90) REVERT: B 436 TRP cc_start: 0.7992 (p90) cc_final: 0.7695 (p90) REVERT: B 456 PHE cc_start: 0.7807 (m-80) cc_final: 0.7406 (m-80) REVERT: B 564 GLN cc_start: 0.7828 (tp40) cc_final: 0.7244 (tp-100) REVERT: B 577 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7855 (ttm-80) REVERT: B 580 GLN cc_start: 0.8054 (mt0) cc_final: 0.7832 (mt0) REVERT: B 750 SER cc_start: 0.8924 (m) cc_final: 0.8667 (p) REVERT: B 814 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8089 (mmmt) REVERT: B 950 ASP cc_start: 0.8390 (m-30) cc_final: 0.7997 (m-30) REVERT: B 986 LYS cc_start: 0.8516 (tmtt) cc_final: 0.8249 (ttpp) REVERT: C 40 ASP cc_start: 0.8504 (m-30) cc_final: 0.8258 (p0) REVERT: C 52 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8659 (tm-30) REVERT: C 130 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7734 (p) REVERT: C 190 ARG cc_start: 0.8263 (mmt180) cc_final: 0.7950 (mmt180) REVERT: C 319 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.8321 (ttm-80) REVERT: C 321 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8700 (mm-40) REVERT: C 386 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8847 (mmtm) REVERT: C 437 ASN cc_start: 0.7349 (t0) cc_final: 0.6834 (t0) REVERT: C 508 TYR cc_start: 0.6723 (m-80) cc_final: 0.6205 (m-80) REVERT: C 523 THR cc_start: 0.8625 (p) cc_final: 0.8173 (t) REVERT: C 568 ASP cc_start: 0.8552 (t0) cc_final: 0.8277 (t0) REVERT: C 619 GLU cc_start: 0.7429 (mp0) cc_final: 0.7227 (mp0) REVERT: C 765 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8050 (ttp80) REVERT: C 950 ASP cc_start: 0.8354 (t0) cc_final: 0.7958 (t0) REVERT: C 1086 LYS cc_start: 0.9030 (ptpp) cc_final: 0.8788 (ptpp) REVERT: C 1106 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8475 (pt0) REVERT: C 1119 ASN cc_start: 0.8830 (m110) cc_final: 0.8470 (m-40) REVERT: C 1141 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8835 (tp) REVERT: C 1148 PHE cc_start: 0.6045 (t80) cc_final: 0.5836 (t80) outliers start: 84 outliers final: 52 residues processed: 655 average time/residue: 0.1902 time to fit residues: 194.4974 Evaluate side-chains 636 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 579 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 96 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 242 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 247 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 658 ASN A 764 ASN B 658 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.082037 restraints weight = 66679.154| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.34 r_work: 0.3139 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27678 Z= 0.168 Angle : 0.709 16.798 37827 Z= 0.337 Chirality : 0.048 0.748 4509 Planarity : 0.004 0.057 4713 Dihedral : 8.601 107.793 5487 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.39 % Allowed : 14.99 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3240 helix: 1.71 (0.19), residues: 751 sheet: -0.18 (0.18), residues: 730 loop : -1.01 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 408 TYR 0.032 0.002 TYR C 904 PHE 0.035 0.002 PHE B 133 TRP 0.021 0.002 TRP A 353 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00377 (27543) covalent geometry : angle 0.66436 (37464) SS BOND : bond 0.00479 ( 42) SS BOND : angle 1.67248 ( 84) hydrogen bonds : bond 0.03946 ( 1119) hydrogen bonds : angle 5.60451 ( 3081) link_ALPHA1-4 : bond 0.01870 ( 6) link_ALPHA1-4 : angle 3.13951 ( 18) link_BETA1-4 : bond 0.00303 ( 29) link_BETA1-4 : angle 1.52391 ( 87) link_BETA1-6 : bond 0.01858 ( 3) link_BETA1-6 : angle 2.23580 ( 9) link_NAG-ASN : bond 0.00461 ( 55) link_NAG-ASN : angle 3.30421 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 594 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.3950 (OUTLIER) cc_final: 0.2960 (ppt-90) REVERT: A 129 LYS cc_start: 0.8764 (tttt) cc_final: 0.8208 (tttt) REVERT: A 153 MET cc_start: 0.6801 (ppp) cc_final: 0.6473 (ppp) REVERT: A 174 PRO cc_start: 0.8458 (Cg_exo) cc_final: 0.8209 (Cg_endo) REVERT: A 188 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7467 (p0) REVERT: A 191 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7879 (mt-10) REVERT: A 287 ASP cc_start: 0.8211 (t70) cc_final: 0.7940 (t0) REVERT: A 304 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8682 (mmtt) REVERT: A 495 TYR cc_start: 0.6496 (m-80) cc_final: 0.6162 (m-80) REVERT: A 586 ASP cc_start: 0.8322 (m-30) cc_final: 0.8038 (m-30) REVERT: A 646 ARG cc_start: 0.8887 (mmm160) cc_final: 0.8630 (mmm-85) REVERT: A 796 ASP cc_start: 0.8108 (t70) cc_final: 0.7865 (t70) REVERT: A 901 GLN cc_start: 0.8765 (tt0) cc_final: 0.8536 (tt0) REVERT: A 936 ASP cc_start: 0.8197 (m-30) cc_final: 0.7868 (m-30) REVERT: A 941 THR cc_start: 0.7546 (t) cc_final: 0.7244 (t) REVERT: A 949 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8390 (mm-40) REVERT: A 1123 SER cc_start: 0.8764 (m) cc_final: 0.8527 (m) REVERT: B 125 ASN cc_start: 0.7585 (p0) cc_final: 0.7331 (p0) REVERT: B 177 MET cc_start: 0.6277 (ppp) cc_final: 0.5187 (ppp) REVERT: B 202 LYS cc_start: 0.8872 (mttm) cc_final: 0.8662 (mttp) REVERT: B 237 ARG cc_start: 0.8397 (mtm110) cc_final: 0.8050 (ptp90) REVERT: B 239 GLN cc_start: 0.8369 (tt0) cc_final: 0.8160 (mm-40) REVERT: B 319 ARG cc_start: 0.8884 (ttm110) cc_final: 0.8614 (ttm170) REVERT: B 346 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7245 (tpt90) REVERT: B 456 PHE cc_start: 0.7746 (m-80) cc_final: 0.7485 (m-80) REVERT: B 564 GLN cc_start: 0.7910 (tp40) cc_final: 0.7386 (tp-100) REVERT: B 740 MET cc_start: 0.8878 (ttm) cc_final: 0.8550 (ttm) REVERT: B 750 SER cc_start: 0.8973 (m) cc_final: 0.8711 (p) REVERT: B 762 GLN cc_start: 0.8240 (tt0) cc_final: 0.8018 (tt0) REVERT: B 764 ASN cc_start: 0.8608 (m-40) cc_final: 0.8197 (m110) REVERT: B 814 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8082 (mmmt) REVERT: B 950 ASP cc_start: 0.8384 (m-30) cc_final: 0.8001 (m-30) REVERT: B 986 LYS cc_start: 0.8491 (tmtt) cc_final: 0.8278 (ttpp) REVERT: C 52 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8673 (tm-30) REVERT: C 180 GLU cc_start: 0.4242 (OUTLIER) cc_final: 0.3907 (pm20) REVERT: C 321 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8822 (mm-40) REVERT: C 386 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8867 (mmtm) REVERT: C 437 ASN cc_start: 0.7325 (t0) cc_final: 0.6846 (t0) REVERT: C 508 TYR cc_start: 0.6758 (m-80) cc_final: 0.6093 (m-80) REVERT: C 523 THR cc_start: 0.8656 (p) cc_final: 0.8217 (t) REVERT: C 568 ASP cc_start: 0.8577 (t0) cc_final: 0.8324 (t0) REVERT: C 574 ASP cc_start: 0.8573 (p0) cc_final: 0.8264 (p0) REVERT: C 750 SER cc_start: 0.9066 (m) cc_final: 0.8845 (p) REVERT: C 765 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8100 (ttp80) REVERT: C 808 ASP cc_start: 0.8160 (t0) cc_final: 0.7906 (t70) REVERT: C 868 GLU cc_start: 0.8119 (mp0) cc_final: 0.7872 (mp0) REVERT: C 950 ASP cc_start: 0.8343 (t0) cc_final: 0.7948 (t0) REVERT: C 1086 LYS cc_start: 0.8975 (ptpp) cc_final: 0.8738 (ptpp) REVERT: C 1106 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8540 (pt0) REVERT: C 1119 ASN cc_start: 0.8800 (m110) cc_final: 0.8445 (m-40) REVERT: C 1148 PHE cc_start: 0.6266 (t80) cc_final: 0.5976 (t80) outliers start: 97 outliers final: 69 residues processed: 646 average time/residue: 0.1885 time to fit residues: 189.0980 Evaluate side-chains 636 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 562 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 3 optimal weight: 0.8980 chunk 297 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN A 764 ASN A 853 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 658 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 955 ASN ** 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 = 0.3642 r_free = 0.3642 target = 0.100500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.082186 restraints weight = 66677.924| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.33 r_work: 0.3142 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27678 Z= 0.160 Angle : 0.694 16.225 37827 Z= 0.333 Chirality : 0.048 0.734 4509 Planarity : 0.004 0.060 4713 Dihedral : 8.196 106.551 5487 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.42 % Allowed : 16.04 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3240 helix: 1.75 (0.19), residues: 751 sheet: -0.13 (0.18), residues: 714 loop : -1.02 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 408 TYR 0.027 0.002 TYR C 904 PHE 0.034 0.002 PHE B1148 TRP 0.033 0.002 TRP A 353 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00361 (27543) covalent geometry : angle 0.65536 (37464) SS BOND : bond 0.00523 ( 42) SS BOND : angle 1.54589 ( 84) hydrogen bonds : bond 0.03860 ( 1119) hydrogen bonds : angle 5.55730 ( 3081) link_ALPHA1-4 : bond 0.01846 ( 6) link_ALPHA1-4 : angle 3.19040 ( 18) link_BETA1-4 : bond 0.00322 ( 29) link_BETA1-4 : angle 1.51393 ( 87) link_BETA1-6 : bond 0.01915 ( 3) link_BETA1-6 : angle 2.19884 ( 9) link_NAG-ASN : bond 0.00488 ( 55) link_NAG-ASN : angle 3.02359 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 586 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.3969 (OUTLIER) cc_final: 0.2979 (ppt-90) REVERT: A 45 SER cc_start: 0.9273 (p) cc_final: 0.9066 (t) REVERT: A 129 LYS cc_start: 0.8730 (tttt) cc_final: 0.8188 (tttt) REVERT: A 174 PRO cc_start: 0.8461 (Cg_exo) cc_final: 0.8211 (Cg_endo) REVERT: A 188 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7562 (p0) REVERT: A 190 ARG cc_start: 0.8015 (tpt170) cc_final: 0.7716 (mmt180) REVERT: A 287 ASP cc_start: 0.8202 (t70) cc_final: 0.7925 (t0) REVERT: A 304 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8678 (mmtt) REVERT: A 493 GLN cc_start: 0.6985 (tm-30) cc_final: 0.6769 (tm-30) REVERT: A 495 TYR cc_start: 0.6438 (m-80) cc_final: 0.6221 (m-80) REVERT: A 586 ASP cc_start: 0.8316 (m-30) cc_final: 0.8011 (m-30) REVERT: A 646 ARG cc_start: 0.8917 (mmm160) cc_final: 0.8634 (mmm-85) REVERT: A 796 ASP cc_start: 0.8104 (t70) cc_final: 0.7861 (t70) REVERT: A 901 GLN cc_start: 0.8752 (tt0) cc_final: 0.8507 (tt0) REVERT: A 941 THR cc_start: 0.7486 (t) cc_final: 0.7163 (t) REVERT: A 949 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8374 (mm-40) REVERT: A 1123 SER cc_start: 0.8736 (m) cc_final: 0.8494 (m) REVERT: A 1148 PHE cc_start: 0.5149 (OUTLIER) cc_final: 0.4882 (m-10) REVERT: B 177 MET cc_start: 0.6252 (ppp) cc_final: 0.5194 (ppp) REVERT: B 223 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8876 (mt) REVERT: B 237 ARG cc_start: 0.8395 (mtm110) cc_final: 0.8073 (mtm110) REVERT: B 281 GLU cc_start: 0.9012 (tt0) cc_final: 0.8809 (pt0) REVERT: B 319 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8633 (ttm170) REVERT: B 346 ARG cc_start: 0.7613 (mmm160) cc_final: 0.7186 (tpt90) REVERT: B 421 TYR cc_start: 0.4509 (OUTLIER) cc_final: 0.4107 (p90) REVERT: B 452 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7212 (mp) REVERT: B 456 PHE cc_start: 0.7716 (m-80) cc_final: 0.7509 (m-80) REVERT: B 564 GLN cc_start: 0.7930 (tp40) cc_final: 0.7692 (tp40) REVERT: B 633 TRP cc_start: 0.7162 (OUTLIER) cc_final: 0.6773 (p-90) REVERT: B 740 MET cc_start: 0.8832 (ttm) cc_final: 0.8589 (ttm) REVERT: B 750 SER cc_start: 0.8977 (m) cc_final: 0.8709 (p) REVERT: B 764 ASN cc_start: 0.8591 (m-40) cc_final: 0.8228 (m110) REVERT: B 814 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8057 (mmmt) REVERT: B 950 ASP cc_start: 0.8392 (m-30) cc_final: 0.8012 (m-30) REVERT: B 979 ASP cc_start: 0.8519 (t0) cc_final: 0.8221 (t70) REVERT: B 986 LYS cc_start: 0.8525 (tmtt) cc_final: 0.8205 (tttm) REVERT: C 52 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8683 (tm-30) REVERT: C 152 TRP cc_start: 0.4927 (m-90) cc_final: 0.4509 (m-90) REVERT: C 189 LEU cc_start: 0.8678 (tt) cc_final: 0.8383 (tp) REVERT: C 190 ARG cc_start: 0.8258 (mmt180) cc_final: 0.7599 (ttt90) REVERT: C 237 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7991 (mtp-110) REVERT: C 321 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8845 (mm-40) REVERT: C 437 ASN cc_start: 0.7341 (t0) cc_final: 0.6880 (t0) REVERT: C 508 TYR cc_start: 0.6750 (m-80) cc_final: 0.6118 (m-80) REVERT: C 568 ASP cc_start: 0.8567 (t0) cc_final: 0.8338 (t0) REVERT: C 574 ASP cc_start: 0.8549 (p0) cc_final: 0.8238 (p0) REVERT: C 750 SER cc_start: 0.9052 (m) cc_final: 0.8841 (p) REVERT: C 765 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8058 (ttp80) REVERT: C 808 ASP cc_start: 0.8149 (t0) cc_final: 0.7880 (t70) REVERT: C 950 ASP cc_start: 0.8329 (t0) cc_final: 0.7916 (t0) REVERT: C 1086 LYS cc_start: 0.8945 (ptpp) cc_final: 0.8698 (ptpp) REVERT: C 1106 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8495 (pt0) REVERT: C 1119 ASN cc_start: 0.8775 (m110) cc_final: 0.8417 (m-40) REVERT: C 1148 PHE cc_start: 0.6330 (t80) cc_final: 0.5978 (t80) outliers start: 98 outliers final: 74 residues processed: 640 average time/residue: 0.1837 time to fit residues: 183.5935 Evaluate side-chains 645 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 562 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 257 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 205 optimal weight: 0.2980 chunk 321 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN A 853 GLN B 388 ASN B 580 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 271 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** 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 = 0.3628 r_free = 0.3628 target = 0.099677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081557 restraints weight = 66569.465| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.27 r_work: 0.3123 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 27678 Z= 0.210 Angle : 0.723 15.054 37827 Z= 0.349 Chirality : 0.048 0.714 4509 Planarity : 0.004 0.097 4713 Dihedral : 8.218 109.383 5487 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.74 % Allowed : 16.74 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3240 helix: 1.74 (0.19), residues: 744 sheet: -0.14 (0.18), residues: 704 loop : -1.10 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1107 TYR 0.036 0.002 TYR C 904 PHE 0.038 0.002 PHE B1148 TRP 0.032 0.002 TRP A 353 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00477 (27543) covalent geometry : angle 0.68352 (37464) SS BOND : bond 0.00557 ( 42) SS BOND : angle 1.82041 ( 84) hydrogen bonds : bond 0.04062 ( 1119) hydrogen bonds : angle 5.62738 ( 3081) link_ALPHA1-4 : bond 0.01755 ( 6) link_ALPHA1-4 : angle 3.37384 ( 18) link_BETA1-4 : bond 0.00311 ( 29) link_BETA1-4 : angle 1.61064 ( 87) link_BETA1-6 : bond 0.01663 ( 3) link_BETA1-6 : angle 2.03418 ( 9) link_NAG-ASN : bond 0.00435 ( 55) link_NAG-ASN : angle 3.05472 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 573 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.4021 (OUTLIER) cc_final: 0.3088 (ppt-90) REVERT: A 45 SER cc_start: 0.9293 (p) cc_final: 0.9085 (t) REVERT: A 129 LYS cc_start: 0.8712 (tttt) cc_final: 0.8189 (tttt) REVERT: A 174 PRO cc_start: 0.8488 (Cg_exo) cc_final: 0.8224 (Cg_endo) REVERT: A 188 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7543 (p0) REVERT: A 190 ARG cc_start: 0.8054 (tpt170) cc_final: 0.7722 (mmt180) REVERT: A 287 ASP cc_start: 0.8215 (t70) cc_final: 0.7930 (t0) REVERT: A 493 GLN cc_start: 0.7148 (tm-30) cc_final: 0.6892 (tm-30) REVERT: A 586 ASP cc_start: 0.8286 (m-30) cc_final: 0.7971 (m-30) REVERT: A 646 ARG cc_start: 0.8922 (mmm160) cc_final: 0.8643 (mmm-85) REVERT: A 796 ASP cc_start: 0.8093 (t70) cc_final: 0.7837 (t70) REVERT: A 901 GLN cc_start: 0.8781 (tt0) cc_final: 0.8542 (tt0) REVERT: A 936 ASP cc_start: 0.8207 (m-30) cc_final: 0.7912 (m-30) REVERT: A 949 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8372 (mm-40) REVERT: A 1123 SER cc_start: 0.8777 (m) cc_final: 0.8522 (m) REVERT: A 1148 PHE cc_start: 0.5238 (OUTLIER) cc_final: 0.4855 (m-10) REVERT: B 223 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8885 (mt) REVERT: B 237 ARG cc_start: 0.8373 (mtm110) cc_final: 0.8043 (ptp90) REVERT: B 319 ARG cc_start: 0.8924 (ttm110) cc_final: 0.8656 (ttm170) REVERT: B 346 ARG cc_start: 0.7623 (mmm160) cc_final: 0.7170 (tpt90) REVERT: B 421 TYR cc_start: 0.4557 (OUTLIER) cc_final: 0.4248 (p90) REVERT: B 587 ILE cc_start: 0.8995 (mt) cc_final: 0.8714 (mp) REVERT: B 633 TRP cc_start: 0.7204 (OUTLIER) cc_final: 0.6809 (p-90) REVERT: B 737 ASP cc_start: 0.7995 (p0) cc_final: 0.7595 (p0) REVERT: B 740 MET cc_start: 0.8879 (ttm) cc_final: 0.8577 (ttm) REVERT: B 750 SER cc_start: 0.8985 (m) cc_final: 0.8719 (p) REVERT: B 814 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8077 (mmmt) REVERT: B 950 ASP cc_start: 0.8430 (m-30) cc_final: 0.8027 (m-30) REVERT: B 979 ASP cc_start: 0.8545 (t0) cc_final: 0.8246 (t70) REVERT: B 986 LYS cc_start: 0.8590 (tmtt) cc_final: 0.8270 (tttm) REVERT: C 52 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8673 (tm-30) REVERT: C 86 PHE cc_start: 0.7938 (t80) cc_final: 0.7696 (t80) REVERT: C 189 LEU cc_start: 0.8664 (tt) cc_final: 0.8410 (tp) REVERT: C 190 ARG cc_start: 0.8260 (mmt180) cc_final: 0.8001 (mmt180) REVERT: C 347 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: C 508 TYR cc_start: 0.6758 (m-80) cc_final: 0.6434 (m-80) REVERT: C 546 LEU cc_start: 0.8603 (mp) cc_final: 0.8263 (mp) REVERT: C 568 ASP cc_start: 0.8602 (t0) cc_final: 0.8373 (t0) REVERT: C 574 ASP cc_start: 0.8592 (p0) cc_final: 0.8172 (p0) REVERT: C 750 SER cc_start: 0.9064 (m) cc_final: 0.8848 (p) REVERT: C 765 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8065 (ttp80) REVERT: C 808 ASP cc_start: 0.8189 (t0) cc_final: 0.7923 (t70) REVERT: C 945 LEU cc_start: 0.8889 (mt) cc_final: 0.8668 (mp) REVERT: C 950 ASP cc_start: 0.8302 (t0) cc_final: 0.7901 (t0) REVERT: C 986 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8145 (tmmt) REVERT: C 1086 LYS cc_start: 0.8945 (ptpp) cc_final: 0.8699 (ptpp) REVERT: C 1106 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8547 (pt0) REVERT: C 1119 ASN cc_start: 0.8769 (m110) cc_final: 0.8400 (m-40) REVERT: C 1148 PHE cc_start: 0.6617 (t80) cc_final: 0.6269 (t80) outliers start: 107 outliers final: 79 residues processed: 632 average time/residue: 0.1841 time to fit residues: 182.4257 Evaluate side-chains 649 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 561 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 63 optimal weight: 0.8980 chunk 215 optimal weight: 0.4980 chunk 290 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 853 GLN B 540 ASN B 580 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 703 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C 955 ASN ** 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 = 0.3640 r_free = 0.3640 target = 0.100349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082251 restraints weight = 67205.187| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.30 r_work: 0.3135 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27678 Z= 0.167 Angle : 0.709 14.680 37827 Z= 0.342 Chirality : 0.047 0.687 4509 Planarity : 0.004 0.072 4713 Dihedral : 8.053 109.068 5487 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.49 % Allowed : 17.47 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3240 helix: 1.84 (0.19), residues: 743 sheet: -0.10 (0.19), residues: 698 loop : -1.10 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 408 TYR 0.037 0.002 TYR C 904 PHE 0.036 0.002 PHE B1148 TRP 0.032 0.002 TRP A 353 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00378 (27543) covalent geometry : angle 0.67264 (37464) SS BOND : bond 0.00554 ( 42) SS BOND : angle 1.67372 ( 84) hydrogen bonds : bond 0.03872 ( 1119) hydrogen bonds : angle 5.60527 ( 3081) link_ALPHA1-4 : bond 0.01672 ( 6) link_ALPHA1-4 : angle 3.39240 ( 18) link_BETA1-4 : bond 0.00322 ( 29) link_BETA1-4 : angle 1.54408 ( 87) link_BETA1-6 : bond 0.01600 ( 3) link_BETA1-6 : angle 1.94819 ( 9) link_NAG-ASN : bond 0.00408 ( 55) link_NAG-ASN : angle 2.90759 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 581 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.4037 (OUTLIER) cc_final: 0.3123 (ppt-90) REVERT: A 129 LYS cc_start: 0.8722 (tttt) cc_final: 0.8191 (tttt) REVERT: A 174 PRO cc_start: 0.8503 (Cg_exo) cc_final: 0.8243 (Cg_endo) REVERT: A 188 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7496 (p0) REVERT: A 190 ARG cc_start: 0.7930 (tpt170) cc_final: 0.7643 (mmt180) REVERT: A 287 ASP cc_start: 0.8231 (t70) cc_final: 0.7946 (t0) REVERT: A 493 GLN cc_start: 0.7047 (tm-30) cc_final: 0.6405 (tm-30) REVERT: A 586 ASP cc_start: 0.8294 (m-30) cc_final: 0.7962 (m-30) REVERT: A 794 ILE cc_start: 0.8716 (mt) cc_final: 0.8509 (mm) REVERT: A 796 ASP cc_start: 0.8088 (t70) cc_final: 0.7812 (t70) REVERT: A 821 LEU cc_start: 0.8787 (mm) cc_final: 0.8413 (mp) REVERT: A 853 GLN cc_start: 0.8133 (tt0) cc_final: 0.7888 (tt0) REVERT: A 901 GLN cc_start: 0.8758 (tt0) cc_final: 0.8509 (tt0) REVERT: A 936 ASP cc_start: 0.8194 (m-30) cc_final: 0.7903 (m-30) REVERT: A 949 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8343 (mm-40) REVERT: A 1123 SER cc_start: 0.8770 (m) cc_final: 0.8511 (m) REVERT: B 223 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8849 (mt) REVERT: B 237 ARG cc_start: 0.8355 (mtm110) cc_final: 0.8053 (ptp90) REVERT: B 319 ARG cc_start: 0.8937 (ttm110) cc_final: 0.8634 (ttm170) REVERT: B 346 ARG cc_start: 0.7609 (mmm160) cc_final: 0.7173 (tpt90) REVERT: B 421 TYR cc_start: 0.4729 (OUTLIER) cc_final: 0.4194 (p90) REVERT: B 456 PHE cc_start: 0.7800 (m-80) cc_final: 0.7527 (m-80) REVERT: B 564 GLN cc_start: 0.8049 (tp40) cc_final: 0.7727 (tp40) REVERT: B 587 ILE cc_start: 0.9006 (mt) cc_final: 0.8698 (mp) REVERT: B 633 TRP cc_start: 0.7224 (OUTLIER) cc_final: 0.6819 (p-90) REVERT: B 737 ASP cc_start: 0.8000 (p0) cc_final: 0.7611 (p0) REVERT: B 740 MET cc_start: 0.8859 (ttm) cc_final: 0.8508 (ttm) REVERT: B 750 SER cc_start: 0.8972 (m) cc_final: 0.8714 (p) REVERT: B 764 ASN cc_start: 0.8536 (m-40) cc_final: 0.8026 (m-40) REVERT: B 814 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8106 (mmmt) REVERT: B 950 ASP cc_start: 0.8428 (m-30) cc_final: 0.8030 (m-30) REVERT: B 979 ASP cc_start: 0.8517 (t0) cc_final: 0.8224 (t70) REVERT: B 986 LYS cc_start: 0.8545 (tmtt) cc_final: 0.8317 (tttm) REVERT: C 52 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8689 (tm-30) REVERT: C 86 PHE cc_start: 0.7916 (t80) cc_final: 0.7665 (t80) REVERT: C 100 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8081 (mp) REVERT: C 164 ASN cc_start: 0.6032 (OUTLIER) cc_final: 0.5061 (p0) REVERT: C 189 LEU cc_start: 0.8697 (tt) cc_final: 0.8447 (tp) REVERT: C 190 ARG cc_start: 0.8276 (mmt180) cc_final: 0.8004 (mmt180) REVERT: C 329 PHE cc_start: 0.8218 (m-80) cc_final: 0.8002 (m-80) REVERT: C 508 TYR cc_start: 0.6721 (m-80) cc_final: 0.6492 (m-80) REVERT: C 568 ASP cc_start: 0.8582 (t0) cc_final: 0.8368 (t0) REVERT: C 574 ASP cc_start: 0.8612 (p0) cc_final: 0.8307 (p0) REVERT: C 750 SER cc_start: 0.9061 (m) cc_final: 0.8849 (p) REVERT: C 765 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8043 (ttp80) REVERT: C 790 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8440 (mtmt) REVERT: C 945 LEU cc_start: 0.8866 (mt) cc_final: 0.8645 (mp) REVERT: C 950 ASP cc_start: 0.8299 (t0) cc_final: 0.7895 (t0) REVERT: C 986 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8152 (tmmt) REVERT: C 1086 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8630 (ptpp) REVERT: C 1119 ASN cc_start: 0.8762 (m110) cc_final: 0.8414 (m-40) outliers start: 100 outliers final: 81 residues processed: 638 average time/residue: 0.1865 time to fit residues: 186.7654 Evaluate side-chains 652 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 563 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 901 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 33 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 227 optimal weight: 0.2980 chunk 289 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 316 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 321 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081642 restraints weight = 66864.574| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.28 r_work: 0.3126 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27678 Z= 0.189 Angle : 0.724 14.120 37827 Z= 0.349 Chirality : 0.047 0.689 4509 Planarity : 0.004 0.062 4713 Dihedral : 7.950 109.407 5487 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.25 % Allowed : 18.10 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3240 helix: 1.82 (0.19), residues: 742 sheet: -0.09 (0.19), residues: 680 loop : -1.09 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 408 TYR 0.040 0.002 TYR C 904 PHE 0.042 0.002 PHE B1148 TRP 0.038 0.002 TRP A 353 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00427 (27543) covalent geometry : angle 0.68730 (37464) SS BOND : bond 0.00528 ( 42) SS BOND : angle 1.73659 ( 84) hydrogen bonds : bond 0.03940 ( 1119) hydrogen bonds : angle 5.63331 ( 3081) link_ALPHA1-4 : bond 0.01690 ( 6) link_ALPHA1-4 : angle 3.61749 ( 18) link_BETA1-4 : bond 0.00300 ( 29) link_BETA1-4 : angle 1.55973 ( 87) link_BETA1-6 : bond 0.01591 ( 3) link_BETA1-6 : angle 1.94425 ( 9) link_NAG-ASN : bond 0.00407 ( 55) link_NAG-ASN : angle 2.91841 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 562 time to evaluate : 0.940 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: A 21 ARG cc_start: 0.4124 (OUTLIER) cc_final: 0.3158 (ppt-90) REVERT: A 129 LYS cc_start: 0.8686 (tttt) cc_final: 0.8148 (tttt) REVERT: A 174 PRO cc_start: 0.8520 (Cg_exo) cc_final: 0.8270 (Cg_endo) REVERT: A 188 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7531 (p0) REVERT: A 190 ARG cc_start: 0.7949 (tpt170) cc_final: 0.7682 (mmt180) REVERT: A 287 ASP cc_start: 0.8239 (t70) cc_final: 0.7938 (t0) REVERT: A 369 TYR cc_start: 0.7746 (t80) cc_final: 0.7486 (t80) REVERT: A 493 GLN cc_start: 0.7083 (tm-30) cc_final: 0.6787 (tm-30) REVERT: A 586 ASP cc_start: 0.8284 (m-30) cc_final: 0.7927 (m-30) REVERT: A 796 ASP cc_start: 0.8068 (t70) cc_final: 0.7805 (t70) REVERT: A 821 LEU cc_start: 0.8790 (mm) cc_final: 0.8483 (mp) REVERT: A 901 GLN cc_start: 0.8760 (tt0) cc_final: 0.8512 (tt0) REVERT: A 936 ASP cc_start: 0.8196 (m-30) cc_final: 0.7907 (m-30) REVERT: A 949 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8348 (mm-40) REVERT: B 173 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8565 (pp30) REVERT: B 223 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8855 (mt) REVERT: B 237 ARG cc_start: 0.8355 (mtm110) cc_final: 0.8040 (ptp90) REVERT: B 319 ARG cc_start: 0.8940 (ttm110) cc_final: 0.8664 (ttm170) REVERT: B 421 TYR cc_start: 0.4570 (OUTLIER) cc_final: 0.4230 (p90) REVERT: B 456 PHE cc_start: 0.7837 (m-80) cc_final: 0.7544 (m-80) REVERT: B 564 GLN cc_start: 0.8063 (tp40) cc_final: 0.7752 (tp40) REVERT: B 587 ILE cc_start: 0.9051 (mt) cc_final: 0.8793 (mp) REVERT: B 633 TRP cc_start: 0.7224 (OUTLIER) cc_final: 0.6882 (p-90) REVERT: B 737 ASP cc_start: 0.7995 (p0) cc_final: 0.7572 (p0) REVERT: B 740 MET cc_start: 0.8835 (ttm) cc_final: 0.8539 (ttm) REVERT: B 750 SER cc_start: 0.8969 (m) cc_final: 0.8708 (p) REVERT: B 814 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8087 (mmmt) REVERT: B 950 ASP cc_start: 0.8429 (m-30) cc_final: 0.8024 (m-30) REVERT: B 979 ASP cc_start: 0.8516 (t0) cc_final: 0.8219 (t70) REVERT: C 52 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8675 (tm-30) REVERT: C 86 PHE cc_start: 0.7881 (t80) cc_final: 0.7614 (t80) REVERT: C 100 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8175 (mp) REVERT: C 164 ASN cc_start: 0.6118 (OUTLIER) cc_final: 0.5132 (p0) REVERT: C 189 LEU cc_start: 0.8682 (tt) cc_final: 0.8440 (tp) REVERT: C 508 TYR cc_start: 0.6764 (m-80) cc_final: 0.6494 (m-80) REVERT: C 568 ASP cc_start: 0.8619 (t0) cc_final: 0.8402 (t0) REVERT: C 574 ASP cc_start: 0.8593 (p0) cc_final: 0.8305 (p0) REVERT: C 750 SER cc_start: 0.9043 (m) cc_final: 0.8841 (p) REVERT: C 765 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8096 (ttp80) REVERT: C 945 LEU cc_start: 0.8867 (mt) cc_final: 0.8647 (mp) REVERT: C 950 ASP cc_start: 0.8287 (t0) cc_final: 0.7892 (t0) REVERT: C 1086 LYS cc_start: 0.8849 (ptpp) cc_final: 0.8578 (ptpp) REVERT: C 1119 ASN cc_start: 0.8766 (m110) cc_final: 0.8412 (m-40) outliers start: 93 outliers final: 79 residues processed: 613 average time/residue: 0.1747 time to fit residues: 168.9103 Evaluate side-chains 633 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 546 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 901 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 92 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 279 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 853 GLN A 919 ASN B 580 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 978 ASN B1005 GLN B1119 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.081938 restraints weight = 66644.060| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.29 r_work: 0.3136 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27678 Z= 0.177 Angle : 0.719 13.949 37827 Z= 0.346 Chirality : 0.047 0.677 4509 Planarity : 0.004 0.054 4713 Dihedral : 7.752 110.185 5487 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.28 % Allowed : 18.62 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3240 helix: 1.85 (0.19), residues: 744 sheet: -0.11 (0.19), residues: 680 loop : -1.07 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.033 0.002 TYR C 904 PHE 0.034 0.002 PHE B1148 TRP 0.036 0.002 TRP A 353 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00402 (27543) covalent geometry : angle 0.68270 (37464) SS BOND : bond 0.00509 ( 42) SS BOND : angle 1.74481 ( 84) hydrogen bonds : bond 0.03864 ( 1119) hydrogen bonds : angle 5.64166 ( 3081) link_ALPHA1-4 : bond 0.01648 ( 6) link_ALPHA1-4 : angle 3.99073 ( 18) link_BETA1-4 : bond 0.00307 ( 29) link_BETA1-4 : angle 1.52779 ( 87) link_BETA1-6 : bond 0.01466 ( 3) link_BETA1-6 : angle 1.92902 ( 9) link_NAG-ASN : bond 0.00385 ( 55) link_NAG-ASN : angle 2.84300 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 557 time to evaluate : 1.085 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: A 21 ARG cc_start: 0.4031 (OUTLIER) cc_final: 0.3048 (ppt-90) REVERT: A 129 LYS cc_start: 0.8681 (tttt) cc_final: 0.8145 (tttt) REVERT: A 174 PRO cc_start: 0.8506 (Cg_exo) cc_final: 0.8249 (Cg_endo) REVERT: A 188 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7619 (p0) REVERT: A 190 ARG cc_start: 0.7920 (tpt170) cc_final: 0.7669 (mmt180) REVERT: A 287 ASP cc_start: 0.8247 (t70) cc_final: 0.7945 (t0) REVERT: A 369 TYR cc_start: 0.7707 (t80) cc_final: 0.7477 (t80) REVERT: A 493 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6734 (tm-30) REVERT: A 586 ASP cc_start: 0.8290 (m-30) cc_final: 0.7937 (m-30) REVERT: A 796 ASP cc_start: 0.8072 (t70) cc_final: 0.7814 (t70) REVERT: A 821 LEU cc_start: 0.8779 (mm) cc_final: 0.8411 (mp) REVERT: A 853 GLN cc_start: 0.8154 (tt0) cc_final: 0.7913 (tt0) REVERT: A 901 GLN cc_start: 0.8753 (tt0) cc_final: 0.8497 (tt0) REVERT: A 936 ASP cc_start: 0.8170 (m-30) cc_final: 0.7880 (m-30) REVERT: A 949 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8273 (mm-40) REVERT: B 173 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8565 (pp30) REVERT: B 223 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8839 (mt) REVERT: B 237 ARG cc_start: 0.8351 (mtm110) cc_final: 0.8047 (ptp90) REVERT: B 421 TYR cc_start: 0.4601 (OUTLIER) cc_final: 0.4032 (p90) REVERT: B 456 PHE cc_start: 0.7806 (m-80) cc_final: 0.7577 (m-80) REVERT: B 587 ILE cc_start: 0.9036 (mt) cc_final: 0.8777 (mp) REVERT: B 633 TRP cc_start: 0.7194 (OUTLIER) cc_final: 0.6905 (p-90) REVERT: B 737 ASP cc_start: 0.8026 (p0) cc_final: 0.7681 (p0) REVERT: B 740 MET cc_start: 0.8829 (ttm) cc_final: 0.8520 (ttm) REVERT: B 750 SER cc_start: 0.8981 (m) cc_final: 0.8713 (p) REVERT: B 814 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8084 (mmmt) REVERT: B 900 MET cc_start: 0.8935 (mtm) cc_final: 0.8583 (mtm) REVERT: B 950 ASP cc_start: 0.8432 (m-30) cc_final: 0.8031 (m-30) REVERT: B 979 ASP cc_start: 0.8521 (t0) cc_final: 0.8222 (t70) REVERT: C 22 THR cc_start: 0.6629 (OUTLIER) cc_final: 0.6310 (m) REVERT: C 52 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8681 (tm-30) REVERT: C 86 PHE cc_start: 0.7911 (t80) cc_final: 0.7643 (t80) REVERT: C 164 ASN cc_start: 0.6171 (OUTLIER) cc_final: 0.5192 (p0) REVERT: C 189 LEU cc_start: 0.8696 (tt) cc_final: 0.8464 (tp) REVERT: C 508 TYR cc_start: 0.6775 (m-80) cc_final: 0.6548 (m-80) REVERT: C 568 ASP cc_start: 0.8576 (t0) cc_final: 0.8342 (t0) REVERT: C 574 ASP cc_start: 0.8598 (p0) cc_final: 0.8183 (p0) REVERT: C 750 SER cc_start: 0.9042 (m) cc_final: 0.8837 (p) REVERT: C 765 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8078 (ttp80) REVERT: C 790 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8535 (mtmt) REVERT: C 945 LEU cc_start: 0.8857 (mt) cc_final: 0.8638 (mp) REVERT: C 950 ASP cc_start: 0.8277 (t0) cc_final: 0.7891 (t0) REVERT: C 1017 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8249 (tt0) REVERT: C 1086 LYS cc_start: 0.8836 (ptpp) cc_final: 0.8636 (ptpp) REVERT: C 1119 ASN cc_start: 0.8759 (m110) cc_final: 0.8403 (m-40) outliers start: 94 outliers final: 80 residues processed: 611 average time/residue: 0.1777 time to fit residues: 171.9199 Evaluate side-chains 637 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 549 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 901 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 235 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 314 optimal weight: 0.6980 chunk 260 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.100110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082080 restraints weight = 66736.124| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.30 r_work: 0.3141 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 27678 Z= 0.159 Angle : 0.722 13.784 37827 Z= 0.347 Chirality : 0.047 0.659 4509 Planarity : 0.004 0.054 4713 Dihedral : 7.561 110.008 5487 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.14 % Allowed : 19.15 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3240 helix: 1.91 (0.19), residues: 738 sheet: -0.12 (0.19), residues: 664 loop : -1.02 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.028 0.001 TYR C 904 PHE 0.037 0.002 PHE B1148 TRP 0.032 0.002 TRP C 152 HIS 0.006 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00363 (27543) covalent geometry : angle 0.68490 (37464) SS BOND : bond 0.00490 ( 42) SS BOND : angle 1.98440 ( 84) hydrogen bonds : bond 0.03837 ( 1119) hydrogen bonds : angle 5.62790 ( 3081) link_ALPHA1-4 : bond 0.01574 ( 6) link_ALPHA1-4 : angle 4.20155 ( 18) link_BETA1-4 : bond 0.00319 ( 29) link_BETA1-4 : angle 1.50758 ( 87) link_BETA1-6 : bond 0.01500 ( 3) link_BETA1-6 : angle 1.94193 ( 9) link_NAG-ASN : bond 0.00373 ( 55) link_NAG-ASN : angle 2.77601 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6800.71 seconds wall clock time: 117 minutes 35.95 seconds (7055.95 seconds total)