Starting phenix.real_space_refine on Fri Mar 6 20:18:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xid_33203/03_2026/7xid_33203.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xid_33203/03_2026/7xid_33203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xid_33203/03_2026/7xid_33203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xid_33203/03_2026/7xid_33203.map" model { file = "/net/cci-nas-00/data/ceres_data/7xid_33203/03_2026/7xid_33203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xid_33203/03_2026/7xid_33203.cif" } resolution = 3.3 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= 0.008 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 21850 2.51 5 N 5566 2.21 5 O 6676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34256 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7558 Classifications: {'peptide': 963} Link IDs: {'PTRANS': 52, 'TRANS': 910} Chain breaks: 10 Chain: "B" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7842 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7842 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.11, per 1000 atoms: 0.21 Number of scatterers: 34256 At special positions: 0 Unit cell: (135.875, 196.747, 246.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 164 16.00 O 6676 8.00 N 5566 7.00 C 21850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.19 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.97 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.39 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.15 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.15 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.18 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.07 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.14 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.09 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.20 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.17 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.09 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.18 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.09 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.06 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.08 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.20 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.15 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.19 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.14 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.19 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A1406 " - " NAG A1407 " " NAG B1410 " - " NAG B1411 " " NAG D 905 " - " NAG D 906 " " NAG D 906 " - " NAG D 907 " " NAG E 905 " - " NAG E 906 " " NAG E 906 " - " NAG E 907 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " NAG B1406 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " NAG C1406 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " ASN C 657 " " NAG D 901 " - " ASN D 90 " " NAG D 902 " - " ASN D 103 " " NAG D 903 " - " ASN D 322 " " NAG D 904 " - " ASN D 432 " " NAG D 905 " - " ASN D 546 " " NAG E 901 " - " ASN E 90 " " NAG E 902 " - " ASN E 103 " " NAG E 903 " - " ASN E 322 " " NAG E 904 " - " ASN E 432 " " NAG E 905 " - " ASN E 546 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 331 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 709 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 343 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " " NAG a 1 " - " ASN D 53 " " NAG b 1 " - " ASN E 53 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.4 seconds 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7824 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 47 sheets defined 37.2% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.491A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.529A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.791A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.703A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.758A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.982A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.801A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.158A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.515A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.802A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.158A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 933 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.322A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.810A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 21 through 53 removed outlier: 4.081A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.694A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 4.522A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.585A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.562A pdb=" N SER D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 154 removed outlier: 3.932A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 193 removed outlier: 3.935A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.598A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.641A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 221 through 231 removed outlier: 4.100A pdb=" N ASP D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.550A pdb=" N TYR D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR D 243 " --> pdb=" O HIS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.732A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.527A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.809A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.592A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.555A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 466 removed outlier: 3.608A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 472 through 482 removed outlier: 4.546A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.769A pdb=" N ALA D 501 " --> pdb=" O CYS D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 529 removed outlier: 4.750A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU D 527 " --> pdb=" O PHE D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.628A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.753A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 4.382A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'E' and resid 21 through 53 removed outlier: 4.081A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.694A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.585A pdb=" N LYS E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.562A pdb=" N SER E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 154 removed outlier: 3.932A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 193 removed outlier: 3.935A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.597A pdb=" N GLU E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.641A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 221 through 231 removed outlier: 4.100A pdb=" N ASP E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 247 removed outlier: 3.551A pdb=" N TYR E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR E 243 " --> pdb=" O HIS E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.732A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.527A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN E 330 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.810A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.592A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.555A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 466 removed outlier: 3.608A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR E 449 " --> pdb=" O THR E 445 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU E 450 " --> pdb=" O ILE E 446 " (cutoff:3.500A) Proline residue: E 451 - end of helix Processing helix chain 'E' and resid 472 through 482 removed outlier: 4.547A pdb=" N TRP E 478 " --> pdb=" O MET E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 removed outlier: 3.768A pdb=" N ALA E 501 " --> pdb=" O CYS E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 529 removed outlier: 4.751A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU E 527 " --> pdb=" O PHE E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.628A pdb=" N LYS E 541 " --> pdb=" O PRO E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.752A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 removed outlier: 4.383A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 602 No H-bonds generated for 'chain 'E' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.515A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.395A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.326A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.306A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.468A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 328 removed outlier: 5.675A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.777A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.174A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.292A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.769A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.850A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.590A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 7.471A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.512A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.696A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.857A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.550A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.577A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.546A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.944A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.686A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.739A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.478A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 323 through 328 removed outlier: 5.456A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.551A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.307A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.301A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AE7, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.367A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.174A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AF1, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.368A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.175A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1382 hydrogen bonds defined for protein. 3867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.05 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7165 1.33 - 1.45: 9149 1.45 - 1.58: 18523 1.58 - 1.70: 0 1.70 - 1.83: 233 Bond restraints: 35070 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.080 1.20e-02 6.94e+03 4.40e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.386 -0.058 1.20e-02 6.94e+03 2.31e+01 bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.08e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.08e+01 bond pdb=" N PRO A1143 " pdb=" CD PRO A1143 " ideal model delta sigma weight residual 1.473 1.412 0.061 1.40e-02 5.10e+03 1.90e+01 ... (remaining 35065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 46538 2.78 - 5.56: 1002 5.56 - 8.33: 99 8.33 - 11.11: 22 11.11 - 13.89: 10 Bond angle restraints: 47671 Sorted by residual: angle pdb=" N ASN D 432 " pdb=" CA ASN D 432 " pdb=" C ASN D 432 " ideal model delta sigma weight residual 111.82 120.40 -8.58 1.16e+00 7.43e-01 5.47e+01 angle pdb=" N ASN E 432 " pdb=" CA ASN E 432 " pdb=" C ASN E 432 " ideal model delta sigma weight residual 111.82 120.39 -8.57 1.16e+00 7.43e-01 5.45e+01 angle pdb=" N ILE A 794 " pdb=" CA ILE A 794 " pdb=" C ILE A 794 " ideal model delta sigma weight residual 110.05 103.19 6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" C THR C 208 " pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 120.31 114.37 5.94 9.80e-01 1.04e+00 3.68e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 122.44 115.30 7.14 1.19e+00 7.06e-01 3.60e+01 ... (remaining 47666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 20417 17.73 - 35.46: 1243 35.46 - 53.18: 252 53.18 - 70.91: 103 70.91 - 88.64: 37 Dihedral angle restraints: 22052 sinusoidal: 9916 harmonic: 12136 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 175.44 -82.44 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 175.40 -82.40 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 22049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 5515 0.335 - 0.669: 14 0.669 - 1.004: 4 1.004 - 1.339: 0 1.339 - 1.673: 6 Chirality restraints: 5539 Sorted by residual: chirality pdb=" C1 NAG B1406 " pdb=" O4 NAG M 2 " pdb=" C2 NAG B1406 " pdb=" O5 NAG B1406 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-02 2.50e+03 5.13e+03 chirality pdb=" C1 NAG C1406 " pdb=" O4 NAG T 2 " pdb=" C2 NAG C1406 " pdb=" O5 NAG C1406 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-02 2.50e+03 5.12e+03 chirality pdb=" C1 NAG A1407 " pdb=" O4 NAG A1406 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.52e+03 ... (remaining 5536 not shown) Planarity restraints: 6091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.193 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" CG ASN A 331 " 0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.505 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.197 2.00e-02 2.50e+03 2.43e-01 7.40e+02 pdb=" CG ASN A 343 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.415 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " -0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 902 " 0.285 2.00e-02 2.50e+03 2.39e-01 7.16e+02 pdb=" C7 NAG D 902 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG D 902 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG D 902 " -0.407 2.00e-02 2.50e+03 pdb=" O7 NAG D 902 " 0.010 2.00e-02 2.50e+03 ... (remaining 6088 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 117 2.44 - 3.05: 21588 3.05 - 3.67: 48690 3.67 - 4.28: 74325 4.28 - 4.90: 120869 Nonbonded interactions: 265589 Sorted by model distance: nonbonded pdb=" O LYS A 528 " pdb=" CG LYS A 529 " model vdw 1.822 3.440 nonbonded pdb=" O PRO A 330 " pdb=" CG ASN A 331 " model vdw 2.040 3.270 nonbonded pdb=" O LEU B 335 " pdb=" O CYS B 336 " model vdw 2.062 3.040 nonbonded pdb=" O PRO B 39 " pdb=" CG ASP B 40 " model vdw 2.088 3.270 nonbonded pdb=" O LYS C 528 " pdb=" O LYS C 529 " model vdw 2.120 3.040 ... (remaining 265584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1409)) selection = (chain 'B' and (resid 27 through 454 or resid 491 through 1409)) selection = (chain 'C' and (resid 27 through 454 or resid 491 through 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.570 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.356 35205 Z= 0.542 Angle : 1.407 48.953 48032 Z= 0.708 Chirality : 0.085 1.673 5539 Planarity : 0.007 0.239 6031 Dihedral : 12.613 88.639 14096 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 1.59 % Allowed : 5.99 % Favored : 92.41 % Rotamer: Outliers : 1.12 % Allowed : 3.88 % Favored : 95.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.95 (0.11), residues: 4087 helix: -1.68 (0.12), residues: 1304 sheet: -0.68 (0.19), residues: 688 loop : -2.63 (0.12), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.027 0.002 TYR D 183 PHE 0.038 0.001 PHE A 377 TRP 0.020 0.002 TRP D 163 HIS 0.007 0.001 HIS D 493 Details of bonding type rmsd covalent geometry : bond 0.00829 (35070) covalent geometry : angle 1.04231 (47671) SS BOND : bond 0.10675 ( 44) SS BOND : angle 7.84796 ( 88) hydrogen bonds : bond 0.21065 ( 1353) hydrogen bonds : angle 8.21693 ( 3867) link_BETA1-4 : bond 0.08535 ( 31) link_BETA1-4 : angle 12.94094 ( 93) link_NAG-ASN : bond 0.07172 ( 60) link_NAG-ASN : angle 11.14573 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 570 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.1325 (OUTLIER) cc_final: 0.0543 (m-10) REVERT: B 153 MET cc_start: 0.1988 (mtp) cc_final: 0.0153 (ppp) REVERT: B 1123 SER cc_start: 0.7587 (t) cc_final: 0.7341 (m) REVERT: D 82 MET cc_start: 0.0480 (mmt) cc_final: 0.0209 (tmm) REVERT: D 376 MET cc_start: 0.2872 (ttm) cc_final: 0.2264 (ptt) REVERT: D 594 TRP cc_start: 0.0336 (t60) cc_final: -0.0987 (t-100) REVERT: D 596 LYS cc_start: 0.2288 (mttt) cc_final: 0.1748 (tttm) REVERT: E 114 LYS cc_start: 0.4617 (mmtm) cc_final: 0.3609 (mmmm) REVERT: E 127 TYR cc_start: -0.0004 (t80) cc_final: -0.2135 (t80) REVERT: E 480 MET cc_start: 0.0395 (mtp) cc_final: -0.0036 (ttt) outliers start: 41 outliers final: 7 residues processed: 611 average time/residue: 0.2186 time to fit residues: 211.2200 Evaluate side-chains 277 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 269 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain D residue 610 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 121 ASN A 519 HIS A 953 ASN A1010 GLN A1058 HIS B 49 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 354 ASN B 360 ASN B 388 ASN B 448 ASN B 487 ASN B 556 ASN B 613 GLN B 965 GLN C 354 ASN C 360 ASN C 448 ASN C 487 ASN C 607 GLN D 96 GLN D 98 GLN D 241 HIS E 42 GLN E 96 GLN E 241 HIS E 378 HIS E 417 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.228826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.167319 restraints weight = 71016.526| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 4.57 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35205 Z= 0.159 Angle : 0.831 19.823 48032 Z= 0.396 Chirality : 0.052 0.679 5539 Planarity : 0.005 0.051 6031 Dihedral : 6.981 59.841 6377 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.77 % Favored : 93.83 % Rotamer: Outliers : 2.05 % Allowed : 8.88 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.73 (0.12), residues: 4087 helix: -0.04 (0.14), residues: 1315 sheet: -0.37 (0.19), residues: 675 loop : -2.22 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 983 TYR 0.032 0.002 TYR E 41 PHE 0.025 0.002 PHE C 970 TRP 0.043 0.002 TRP D 271 HIS 0.010 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00340 (35070) covalent geometry : angle 0.74963 (47671) SS BOND : bond 0.00495 ( 44) SS BOND : angle 2.34492 ( 88) hydrogen bonds : bond 0.05318 ( 1353) hydrogen bonds : angle 5.88797 ( 3867) link_BETA1-4 : bond 0.00690 ( 31) link_BETA1-4 : angle 2.87506 ( 93) link_NAG-ASN : bond 0.00748 ( 60) link_NAG-ASN : angle 5.33796 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 287 time to evaluate : 1.279 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: A 192 PHE cc_start: 0.7793 (m-80) cc_final: 0.7536 (m-10) REVERT: A 374 PHE cc_start: 0.2660 (OUTLIER) cc_final: 0.1958 (m-10) REVERT: A 562 PHE cc_start: 0.7133 (p90) cc_final: 0.6800 (p90) REVERT: A 902 MET cc_start: 0.7987 (mmm) cc_final: 0.7751 (tpt) REVERT: A 995 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7705 (mmp80) REVERT: B 122 ASN cc_start: 0.4965 (OUTLIER) cc_final: 0.4167 (m110) REVERT: B 153 MET cc_start: 0.2096 (mtp) cc_final: 0.0916 (ppp) REVERT: B 762 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: C 287 ASP cc_start: 0.7459 (t0) cc_final: 0.7247 (t0) REVERT: C 660 TYR cc_start: 0.8041 (m-80) cc_final: 0.7809 (m-10) REVERT: C 763 LEU cc_start: 0.8482 (mt) cc_final: 0.8277 (mt) REVERT: C 867 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6438 (m-30) REVERT: D 297 MET cc_start: 0.0769 (mtm) cc_final: 0.0542 (ptp) REVERT: D 323 MET cc_start: 0.1070 (OUTLIER) cc_final: 0.0751 (tpp) REVERT: D 433 GLU cc_start: 0.2131 (mp0) cc_final: 0.1783 (pt0) REVERT: D 474 MET cc_start: 0.1220 (OUTLIER) cc_final: 0.0708 (mtm) REVERT: D 596 LYS cc_start: 0.1504 (mttt) cc_final: 0.1102 (tmtt) REVERT: E 82 MET cc_start: 0.0687 (tpp) cc_final: 0.0215 (mmt) REVERT: E 90 ASN cc_start: 0.3135 (OUTLIER) cc_final: 0.2880 (p0) REVERT: E 127 TYR cc_start: 0.0326 (t80) cc_final: -0.1624 (t80) REVERT: E 323 MET cc_start: 0.0238 (mpp) cc_final: -0.2880 (mmm) REVERT: E 444 LEU cc_start: 0.3343 (OUTLIER) cc_final: 0.1638 (mt) REVERT: E 480 MET cc_start: -0.0381 (mtp) cc_final: -0.0598 (ttt) REVERT: E 514 ARG cc_start: 0.3408 (ptt180) cc_final: 0.3005 (ptt-90) outliers start: 75 outliers final: 33 residues processed: 347 average time/residue: 0.2029 time to fit residues: 116.4138 Evaluate side-chains 261 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 16 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 295 optimal weight: 20.0000 chunk 363 optimal weight: 50.0000 chunk 282 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 391 optimal weight: 30.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A1010 GLN B 207 HIS B 218 GLN B 544 ASN B 556 ASN B 564 GLN B 955 ASN B1088 HIS C 762 GLN C 901 GLN D 51 ASN E 58 ASN E 194 ASN E 442 GLN E 522 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.219708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.150667 restraints weight = 70735.918| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.96 r_work: 0.3621 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 35205 Z= 0.262 Angle : 0.842 23.779 48032 Z= 0.403 Chirality : 0.052 0.537 5539 Planarity : 0.005 0.054 6031 Dihedral : 6.886 57.593 6368 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.58 % Favored : 93.17 % Rotamer: Outliers : 2.32 % Allowed : 11.10 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.51 (0.12), residues: 4087 helix: 0.32 (0.14), residues: 1329 sheet: -0.48 (0.20), residues: 609 loop : -2.10 (0.12), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 815 TYR 0.026 0.002 TYR A1067 PHE 0.029 0.002 PHE A1103 TRP 0.033 0.002 TRP D 473 HIS 0.012 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00627 (35070) covalent geometry : angle 0.77722 (47671) SS BOND : bond 0.00741 ( 44) SS BOND : angle 2.36016 ( 88) hydrogen bonds : bond 0.05377 ( 1353) hydrogen bonds : angle 5.63709 ( 3867) link_BETA1-4 : bond 0.00597 ( 31) link_BETA1-4 : angle 2.73008 ( 93) link_NAG-ASN : bond 0.00615 ( 60) link_NAG-ASN : angle 4.75411 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 239 time to evaluate : 1.220 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: A 374 PHE cc_start: 0.2230 (OUTLIER) cc_final: 0.2018 (p90) REVERT: A 557 LYS cc_start: 0.4835 (mttt) cc_final: 0.4362 (mmmm) REVERT: A 762 GLN cc_start: 0.8135 (mp10) cc_final: 0.7859 (mp10) REVERT: A 995 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7816 (mmm-85) REVERT: A 1017 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8409 (tm-30) REVERT: B 122 ASN cc_start: 0.5419 (OUTLIER) cc_final: 0.4311 (m110) REVERT: B 153 MET cc_start: 0.2467 (mtp) cc_final: 0.1024 (ppp) REVERT: B 402 ILE cc_start: 0.0760 (OUTLIER) cc_final: 0.0546 (pt) REVERT: B 762 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: C 237 ARG cc_start: 0.7090 (mtm110) cc_final: 0.6879 (mtp-110) REVERT: C 287 ASP cc_start: 0.7857 (t0) cc_final: 0.7573 (t0) REVERT: C 661 GLU cc_start: 0.7999 (tp30) cc_final: 0.7777 (pm20) REVERT: C 918 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: C 993 ILE cc_start: 0.8620 (mm) cc_final: 0.8304 (pt) REVERT: D 82 MET cc_start: 0.1377 (tmm) cc_final: 0.1041 (ppp) REVERT: D 83 TYR cc_start: -0.0493 (p90) cc_final: -0.0779 (p90) REVERT: D 594 TRP cc_start: 0.1345 (p-90) cc_final: 0.0762 (t60) REVERT: D 596 LYS cc_start: 0.1419 (mttt) cc_final: 0.1086 (tmtt) REVERT: E 82 MET cc_start: 0.0437 (tpp) cc_final: 0.0184 (mmt) REVERT: E 90 ASN cc_start: 0.3927 (OUTLIER) cc_final: 0.3545 (p0) REVERT: E 127 TYR cc_start: 0.1078 (t80) cc_final: -0.0282 (t80) REVERT: E 323 MET cc_start: 0.1435 (mpp) cc_final: -0.1660 (mmm) REVERT: E 332 MET cc_start: 0.1220 (tmm) cc_final: 0.0789 (tmm) REVERT: E 444 LEU cc_start: 0.3301 (OUTLIER) cc_final: 0.2178 (mt) outliers start: 85 outliers final: 45 residues processed: 308 average time/residue: 0.1988 time to fit residues: 102.9589 Evaluate side-chains 251 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 170 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 333 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 164 optimal weight: 0.3980 chunk 299 optimal weight: 10.0000 chunk 405 optimal weight: 0.0980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS C 544 ASN C 675 GLN C 762 GLN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.221741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.153021 restraints weight = 69181.794| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.85 r_work: 0.3682 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35205 Z= 0.142 Angle : 0.702 18.004 48032 Z= 0.334 Chirality : 0.048 0.558 5539 Planarity : 0.004 0.046 6031 Dihedral : 6.470 59.985 6368 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.36 % Favored : 94.37 % Rotamer: Outliers : 2.05 % Allowed : 11.67 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.14 (0.13), residues: 4087 helix: 0.81 (0.14), residues: 1326 sheet: -0.46 (0.20), residues: 670 loop : -1.97 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.020 0.001 TYR C1067 PHE 0.028 0.002 PHE A 855 TRP 0.030 0.001 TRP D 473 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00319 (35070) covalent geometry : angle 0.64393 (47671) SS BOND : bond 0.00393 ( 44) SS BOND : angle 1.77664 ( 88) hydrogen bonds : bond 0.04329 ( 1353) hydrogen bonds : angle 5.28350 ( 3867) link_BETA1-4 : bond 0.00695 ( 31) link_BETA1-4 : angle 2.65106 ( 93) link_NAG-ASN : bond 0.00669 ( 60) link_NAG-ASN : angle 4.08485 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 218 time to evaluate : 1.474 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 226 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7480 (mp) REVERT: A 374 PHE cc_start: 0.2353 (OUTLIER) cc_final: 0.2044 (p90) REVERT: A 557 LYS cc_start: 0.4708 (mttt) cc_final: 0.4288 (mmmm) REVERT: A 740 MET cc_start: 0.7290 (tpp) cc_final: 0.7069 (tpp) REVERT: A 756 TYR cc_start: 0.7448 (m-80) cc_final: 0.7143 (m-80) REVERT: A 761 THR cc_start: 0.9142 (m) cc_final: 0.8892 (p) REVERT: A 762 GLN cc_start: 0.8177 (mp10) cc_final: 0.7884 (mp10) REVERT: A 1017 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8428 (tm-30) REVERT: B 153 MET cc_start: 0.2962 (mtp) cc_final: 0.1152 (ppp) REVERT: B 402 ILE cc_start: 0.0682 (OUTLIER) cc_final: 0.0430 (pt) REVERT: B 762 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: C 133 PHE cc_start: 0.5103 (m-80) cc_final: 0.4709 (m-80) REVERT: C 287 ASP cc_start: 0.7746 (t0) cc_final: 0.7541 (t0) REVERT: C 918 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: C 993 ILE cc_start: 0.8617 (mm) cc_final: 0.8276 (pt) REVERT: D 82 MET cc_start: 0.1654 (OUTLIER) cc_final: 0.1337 (ppp) REVERT: D 83 TYR cc_start: 0.0027 (p90) cc_final: -0.0552 (p90) REVERT: D 323 MET cc_start: 0.3128 (tpp) cc_final: 0.2643 (tpp) REVERT: D 433 GLU cc_start: 0.1869 (mp0) cc_final: 0.1636 (tm-30) REVERT: D 594 TRP cc_start: 0.1112 (p-90) cc_final: 0.0596 (t60) REVERT: E 82 MET cc_start: 0.0404 (tpp) cc_final: 0.0174 (mmt) REVERT: E 90 ASN cc_start: 0.3725 (OUTLIER) cc_final: 0.3485 (p0) REVERT: E 127 TYR cc_start: 0.0847 (t80) cc_final: -0.0545 (t80) REVERT: E 323 MET cc_start: 0.1323 (mpp) cc_final: -0.1716 (mmm) REVERT: E 332 MET cc_start: 0.1051 (tmm) cc_final: 0.0674 (tmm) REVERT: E 444 LEU cc_start: 0.3105 (OUTLIER) cc_final: 0.2155 (mm) REVERT: E 474 MET cc_start: 0.0644 (mmp) cc_final: -0.0253 (mtp) outliers start: 75 outliers final: 41 residues processed: 278 average time/residue: 0.1851 time to fit residues: 87.3028 Evaluate side-chains 250 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 513 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 104 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 377 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 chunk 328 optimal weight: 30.0000 chunk 236 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 340 optimal weight: 50.0000 chunk 255 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 375 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1088 HIS B 207 HIS B 437 ASN B 556 ASN B 675 GLN D 442 GLN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.220655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.149597 restraints weight = 69798.669| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.46 r_work: 0.3650 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35205 Z= 0.186 Angle : 0.701 17.490 48032 Z= 0.337 Chirality : 0.049 0.527 5539 Planarity : 0.004 0.045 6031 Dihedral : 6.290 59.977 6368 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.99 % Favored : 93.79 % Rotamer: Outliers : 2.41 % Allowed : 12.11 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.01 (0.13), residues: 4087 helix: 1.00 (0.14), residues: 1321 sheet: -0.47 (0.20), residues: 680 loop : -1.92 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.029 0.001 TYR D 199 PHE 0.020 0.002 PHE B 92 TRP 0.017 0.001 TRP E 69 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00439 (35070) covalent geometry : angle 0.64996 (47671) SS BOND : bond 0.00405 ( 44) SS BOND : angle 2.00382 ( 88) hydrogen bonds : bond 0.04436 ( 1353) hydrogen bonds : angle 5.22125 ( 3867) link_BETA1-4 : bond 0.00593 ( 31) link_BETA1-4 : angle 2.34858 ( 93) link_NAG-ASN : bond 0.00610 ( 60) link_NAG-ASN : angle 3.79940 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 205 time to evaluate : 1.219 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 153 MET cc_start: 0.2349 (pmm) cc_final: 0.0583 (ptp) REVERT: A 226 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7551 (mp) REVERT: A 557 LYS cc_start: 0.4768 (mttt) cc_final: 0.4100 (mmmm) REVERT: A 740 MET cc_start: 0.7175 (tpp) cc_final: 0.6753 (tpp) REVERT: A 761 THR cc_start: 0.9111 (m) cc_final: 0.8730 (p) REVERT: A 762 GLN cc_start: 0.8109 (mp10) cc_final: 0.7759 (mp10) REVERT: B 153 MET cc_start: 0.3112 (mtp) cc_final: 0.1069 (ppp) REVERT: B 402 ILE cc_start: 0.0485 (OUTLIER) cc_final: 0.0222 (pt) REVERT: B 762 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: B 765 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8171 (ttm170) REVERT: C 135 PHE cc_start: 0.4918 (p90) cc_final: 0.4681 (p90) REVERT: C 287 ASP cc_start: 0.7827 (t0) cc_final: 0.7618 (t0) REVERT: C 918 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: C 1111 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: D 433 GLU cc_start: 0.1823 (mp0) cc_final: 0.1456 (pt0) REVERT: D 594 TRP cc_start: 0.1135 (p-90) cc_final: 0.0552 (t60) REVERT: E 41 TYR cc_start: 0.3850 (t80) cc_final: 0.3539 (t80) REVERT: E 90 ASN cc_start: 0.3772 (OUTLIER) cc_final: 0.3424 (p0) REVERT: E 127 TYR cc_start: 0.0882 (t80) cc_final: -0.0708 (t80) REVERT: E 323 MET cc_start: 0.0961 (mpp) cc_final: -0.2402 (mmm) REVERT: E 444 LEU cc_start: 0.3292 (OUTLIER) cc_final: 0.2221 (mm) REVERT: E 474 MET cc_start: 0.0407 (mmp) cc_final: -0.0477 (mmm) outliers start: 88 outliers final: 52 residues processed: 274 average time/residue: 0.1884 time to fit residues: 86.5142 Evaluate side-chains 258 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 160 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 0.1980 chunk 409 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 360 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 332 optimal weight: 50.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 207 HIS B 239 GLN C 762 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.220017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.150951 restraints weight = 68514.992| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 4.18 r_work: 0.3624 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 35205 Z= 0.238 Angle : 0.741 16.924 48032 Z= 0.360 Chirality : 0.050 0.530 5539 Planarity : 0.005 0.059 6031 Dihedral : 6.395 59.371 6366 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.51 % Favored : 93.25 % Rotamer: Outliers : 2.62 % Allowed : 12.82 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.10 (0.13), residues: 4087 helix: 1.00 (0.14), residues: 1319 sheet: -0.66 (0.19), residues: 705 loop : -1.98 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 357 TYR 0.025 0.002 TYR A1067 PHE 0.030 0.002 PHE B 429 TRP 0.025 0.002 TRP E 203 HIS 0.009 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00566 (35070) covalent geometry : angle 0.69705 (47671) SS BOND : bond 0.00421 ( 44) SS BOND : angle 1.93741 ( 88) hydrogen bonds : bond 0.04809 ( 1353) hydrogen bonds : angle 5.33990 ( 3867) link_BETA1-4 : bond 0.00648 ( 31) link_BETA1-4 : angle 2.29873 ( 93) link_NAG-ASN : bond 0.00594 ( 60) link_NAG-ASN : angle 3.66764 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 200 time to evaluate : 0.989 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 102 ARG cc_start: 0.6010 (mmt90) cc_final: 0.4711 (ptp-170) REVERT: A 153 MET cc_start: 0.2543 (pmm) cc_final: 0.1021 (ptp) REVERT: A 226 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7572 (mp) REVERT: A 557 LYS cc_start: 0.5238 (mttt) cc_final: 0.4394 (mmmm) REVERT: A 740 MET cc_start: 0.7233 (tpp) cc_final: 0.6677 (tpp) REVERT: A 761 THR cc_start: 0.9154 (m) cc_final: 0.8925 (p) REVERT: A 762 GLN cc_start: 0.8183 (mp10) cc_final: 0.7965 (mp10) REVERT: B 66 HIS cc_start: 0.4875 (OUTLIER) cc_final: 0.4666 (t-90) REVERT: B 153 MET cc_start: 0.3740 (mtp) cc_final: 0.1115 (ppp) REVERT: B 270 LEU cc_start: 0.8199 (mt) cc_final: 0.7698 (mp) REVERT: B 402 ILE cc_start: 0.0725 (OUTLIER) cc_final: 0.0518 (pt) REVERT: C 135 PHE cc_start: 0.4896 (p90) cc_final: 0.4654 (p90) REVERT: C 287 ASP cc_start: 0.7894 (t0) cc_final: 0.7636 (t0) REVERT: C 1111 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: D 323 MET cc_start: 0.3339 (tpp) cc_final: 0.2470 (tpp) REVERT: D 376 MET cc_start: 0.1013 (ttt) cc_final: 0.0753 (ttp) REVERT: D 433 GLU cc_start: 0.1687 (mp0) cc_final: 0.1296 (pt0) REVERT: D 594 TRP cc_start: 0.0967 (OUTLIER) cc_final: 0.0593 (t60) REVERT: E 33 ASN cc_start: 0.2982 (OUTLIER) cc_final: 0.2364 (m-40) REVERT: E 90 ASN cc_start: 0.3504 (OUTLIER) cc_final: 0.3259 (p0) REVERT: E 127 TYR cc_start: 0.1133 (t80) cc_final: -0.0209 (t80) REVERT: E 323 MET cc_start: 0.0960 (mpp) cc_final: -0.0885 (mmm) REVERT: E 398 GLU cc_start: 0.1524 (pt0) cc_final: 0.1038 (mp0) REVERT: E 444 LEU cc_start: 0.3220 (OUTLIER) cc_final: 0.2265 (mm) REVERT: E 474 MET cc_start: 0.0813 (mmp) cc_final: 0.0150 (mmm) REVERT: E 557 MET cc_start: 0.1032 (tpt) cc_final: -0.0576 (ttp) outliers start: 96 outliers final: 59 residues processed: 277 average time/residue: 0.1855 time to fit residues: 86.5899 Evaluate side-chains 251 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 184 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 304 optimal weight: 30.0000 chunk 196 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 354 optimal weight: 40.0000 chunk 274 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.229702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.155351 restraints weight = 70339.031| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 4.82 r_work: 0.3549 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 35205 Z= 0.185 Angle : 0.686 16.756 48032 Z= 0.332 Chirality : 0.048 0.509 5539 Planarity : 0.004 0.070 6031 Dihedral : 6.206 55.967 6366 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.17 % Favored : 93.56 % Rotamer: Outliers : 2.32 % Allowed : 13.53 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.00 (0.13), residues: 4087 helix: 1.14 (0.14), residues: 1319 sheet: -0.66 (0.19), residues: 701 loop : -1.94 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.025 0.001 TYR D 510 PHE 0.025 0.002 PHE E 356 TRP 0.022 0.001 TRP E 203 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00439 (35070) covalent geometry : angle 0.64158 (47671) SS BOND : bond 0.00358 ( 44) SS BOND : angle 1.80035 ( 88) hydrogen bonds : bond 0.04351 ( 1353) hydrogen bonds : angle 5.21758 ( 3867) link_BETA1-4 : bond 0.00551 ( 31) link_BETA1-4 : angle 2.22978 ( 93) link_NAG-ASN : bond 0.00574 ( 60) link_NAG-ASN : angle 3.53095 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 196 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6046 (mmt90) cc_final: 0.4688 (ptp-170) REVERT: A 153 MET cc_start: 0.2302 (pmm) cc_final: 0.0840 (ptp) REVERT: A 557 LYS cc_start: 0.5214 (mttt) cc_final: 0.4290 (mmmm) REVERT: A 740 MET cc_start: 0.7410 (tpp) cc_final: 0.6936 (tpp) REVERT: B 66 HIS cc_start: 0.4914 (OUTLIER) cc_final: 0.4660 (t-90) REVERT: B 153 MET cc_start: 0.3371 (mtp) cc_final: 0.1127 (ppp) REVERT: B 270 LEU cc_start: 0.8218 (mt) cc_final: 0.7698 (mp) REVERT: B 402 ILE cc_start: 0.0739 (OUTLIER) cc_final: 0.0526 (pt) REVERT: B 765 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8252 (ttm170) REVERT: C 287 ASP cc_start: 0.7889 (t0) cc_final: 0.7645 (t0) REVERT: C 649 CYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7709 (p) REVERT: C 1111 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: D 433 GLU cc_start: 0.1776 (mp0) cc_final: 0.1394 (pt0) REVERT: D 594 TRP cc_start: 0.0921 (OUTLIER) cc_final: 0.0570 (t60) REVERT: E 90 ASN cc_start: 0.3504 (OUTLIER) cc_final: 0.3219 (p0) REVERT: E 127 TYR cc_start: 0.1329 (t80) cc_final: -0.0029 (t80) REVERT: E 323 MET cc_start: 0.1007 (mpp) cc_final: -0.1148 (mmm) REVERT: E 398 GLU cc_start: 0.1640 (pt0) cc_final: 0.1176 (mp0) REVERT: E 444 LEU cc_start: 0.3258 (OUTLIER) cc_final: 0.2288 (mm) REVERT: E 474 MET cc_start: 0.0194 (mmp) cc_final: -0.0440 (mmm) REVERT: E 557 MET cc_start: 0.1004 (tpt) cc_final: -0.0771 (ttp) outliers start: 85 outliers final: 49 residues processed: 265 average time/residue: 0.1908 time to fit residues: 84.1821 Evaluate side-chains 241 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 401 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 265 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 36 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 374 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 544 ASN A 690 GLN C 115 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.217918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.147852 restraints weight = 68477.686| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 4.20 r_work: 0.3551 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 35205 Z= 0.304 Angle : 0.802 16.545 48032 Z= 0.392 Chirality : 0.052 0.550 5539 Planarity : 0.005 0.071 6031 Dihedral : 6.693 47.110 6364 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.59 % Favored : 92.15 % Rotamer: Outliers : 2.32 % Allowed : 13.78 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.33 (0.13), residues: 4087 helix: 0.81 (0.14), residues: 1315 sheet: -0.86 (0.19), residues: 710 loop : -2.09 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 646 TYR 0.043 0.002 TYR D 243 PHE 0.034 0.002 PHE B 429 TRP 0.023 0.002 TRP B 886 HIS 0.009 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00735 (35070) covalent geometry : angle 0.75955 (47671) SS BOND : bond 0.00513 ( 44) SS BOND : angle 2.35626 ( 88) hydrogen bonds : bond 0.05231 ( 1353) hydrogen bonds : angle 5.50921 ( 3867) link_BETA1-4 : bond 0.00565 ( 31) link_BETA1-4 : angle 2.30458 ( 93) link_NAG-ASN : bond 0.00610 ( 60) link_NAG-ASN : angle 3.67590 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 197 time to evaluate : 0.891 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 102 ARG cc_start: 0.6464 (mmt90) cc_final: 0.4828 (ptp-170) REVERT: A 169 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7926 (mp0) REVERT: A 557 LYS cc_start: 0.5629 (mttt) cc_final: 0.4557 (mmmm) REVERT: A 740 MET cc_start: 0.7458 (tpp) cc_final: 0.7141 (tpp) REVERT: A 759 PHE cc_start: 0.8243 (m-80) cc_final: 0.7880 (m-80) REVERT: A 1010 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8542 (mp10) REVERT: B 153 MET cc_start: 0.3060 (mtp) cc_final: 0.1039 (ppp) REVERT: B 270 LEU cc_start: 0.8287 (mt) cc_final: 0.7814 (mp) REVERT: B 402 ILE cc_start: 0.0432 (OUTLIER) cc_final: 0.0230 (pt) REVERT: C 153 MET cc_start: 0.4335 (tmm) cc_final: 0.3345 (ttm) REVERT: C 287 ASP cc_start: 0.7833 (t0) cc_final: 0.7595 (t0) REVERT: C 697 MET cc_start: 0.8961 (ptt) cc_final: 0.8746 (ptm) REVERT: C 786 LYS cc_start: 0.9176 (mmtt) cc_final: 0.8731 (pttm) REVERT: C 1111 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: D 237 TYR cc_start: 0.0328 (t80) cc_final: -0.0137 (t80) REVERT: D 376 MET cc_start: 0.1569 (ttt) cc_final: 0.1341 (ttp) REVERT: D 462 MET cc_start: 0.4669 (mmp) cc_final: 0.3406 (mtp) REVERT: D 594 TRP cc_start: 0.0809 (OUTLIER) cc_final: 0.0455 (t60) REVERT: E 90 ASN cc_start: 0.3680 (OUTLIER) cc_final: 0.3262 (p0) REVERT: E 127 TYR cc_start: 0.1146 (t80) cc_final: -0.0036 (p90) REVERT: E 323 MET cc_start: 0.0946 (mpp) cc_final: -0.2137 (mmm) REVERT: E 398 GLU cc_start: 0.1915 (pt0) cc_final: 0.1483 (mp0) REVERT: E 444 LEU cc_start: 0.3235 (OUTLIER) cc_final: 0.2300 (mm) REVERT: E 474 MET cc_start: 0.0131 (mmp) cc_final: -0.0455 (mmm) REVERT: E 557 MET cc_start: 0.0930 (tpt) cc_final: -0.0950 (ttp) outliers start: 85 outliers final: 62 residues processed: 272 average time/residue: 0.1896 time to fit residues: 86.4697 Evaluate side-chains 246 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 178 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 442 GLN Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 122 optimal weight: 0.9980 chunk 285 optimal weight: 0.7980 chunk 344 optimal weight: 50.0000 chunk 246 optimal weight: 4.9990 chunk 400 optimal weight: 7.9990 chunk 408 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 222 optimal weight: 20.0000 chunk 358 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.215638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.147643 restraints weight = 69449.148| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 3.95 r_work: 0.3608 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 35205 Z= 0.214 Angle : 0.728 16.382 48032 Z= 0.353 Chirality : 0.050 0.513 5539 Planarity : 0.004 0.066 6031 Dihedral : 6.426 44.579 6364 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.04 % Favored : 93.69 % Rotamer: Outliers : 2.00 % Allowed : 14.24 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -1.20 (0.13), residues: 4087 helix: 0.96 (0.14), residues: 1317 sheet: -0.89 (0.19), residues: 705 loop : -2.00 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 905 TYR 0.029 0.002 TYR D 243 PHE 0.025 0.002 PHE B 981 TRP 0.015 0.001 TRP B 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00512 (35070) covalent geometry : angle 0.68441 (47671) SS BOND : bond 0.00359 ( 44) SS BOND : angle 2.38283 ( 88) hydrogen bonds : bond 0.04573 ( 1353) hydrogen bonds : angle 5.32486 ( 3867) link_BETA1-4 : bond 0.00584 ( 31) link_BETA1-4 : angle 2.23142 ( 93) link_NAG-ASN : bond 0.00596 ( 60) link_NAG-ASN : angle 3.47685 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6517 (mmt90) cc_final: 0.4672 (ptp-170) REVERT: A 169 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7968 (mp0) REVERT: A 557 LYS cc_start: 0.5418 (mttt) cc_final: 0.4477 (mmmm) REVERT: A 1010 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8463 (mp10) REVERT: B 153 MET cc_start: 0.3576 (mtp) cc_final: 0.1361 (ppp) REVERT: B 765 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8207 (ttm170) REVERT: C 153 MET cc_start: 0.4054 (tmm) cc_final: 0.3444 (ttm) REVERT: C 287 ASP cc_start: 0.7806 (t0) cc_final: 0.7545 (t0) REVERT: C 1111 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: D 237 TYR cc_start: 0.0321 (t80) cc_final: -0.0184 (t80) REVERT: D 376 MET cc_start: 0.1583 (ttt) cc_final: 0.1355 (ttp) REVERT: D 462 MET cc_start: 0.4621 (mmp) cc_final: 0.3590 (mmm) REVERT: D 594 TRP cc_start: 0.0881 (OUTLIER) cc_final: 0.0552 (t60) REVERT: E 33 ASN cc_start: 0.2920 (OUTLIER) cc_final: 0.2346 (m110) REVERT: E 90 ASN cc_start: 0.3341 (OUTLIER) cc_final: 0.3032 (p0) REVERT: E 238 GLU cc_start: -0.1573 (OUTLIER) cc_final: -0.3073 (pt0) REVERT: E 323 MET cc_start: 0.0781 (mpp) cc_final: -0.1459 (mmm) REVERT: E 398 GLU cc_start: 0.2077 (pt0) cc_final: 0.1307 (mp0) REVERT: E 444 LEU cc_start: 0.3562 (OUTLIER) cc_final: 0.2803 (mm) REVERT: E 474 MET cc_start: 0.0002 (mmp) cc_final: -0.0553 (mmm) REVERT: E 557 MET cc_start: 0.1073 (tpt) cc_final: -0.0789 (ttp) outliers start: 73 outliers final: 58 residues processed: 251 average time/residue: 0.1839 time to fit residues: 78.6568 Evaluate side-chains 246 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 442 GLN Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 394 optimal weight: 40.0000 chunk 163 optimal weight: 0.7980 chunk 276 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 373 optimal weight: 20.0000 chunk 270 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 374 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 271 GLN C 437 ASN D 58 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 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 = 0.4921 r_free = 0.4921 target = 0.219032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.150788 restraints weight = 69050.916| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.83 r_work: 0.3704 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 35205 Z= 0.111 Angle : 0.649 16.178 48032 Z= 0.314 Chirality : 0.046 0.476 5539 Planarity : 0.004 0.061 6031 Dihedral : 5.803 42.850 6364 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.14 % Favored : 94.59 % Rotamer: Outliers : 1.12 % Allowed : 15.25 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -0.83 (0.13), residues: 4087 helix: 1.30 (0.15), residues: 1318 sheet: -0.72 (0.19), residues: 710 loop : -1.78 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 983 TYR 0.031 0.001 TYR D 243 PHE 0.030 0.001 PHE C 759 TRP 0.019 0.001 TRP A 104 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00239 (35070) covalent geometry : angle 0.61094 (47671) SS BOND : bond 0.00293 ( 44) SS BOND : angle 1.56795 ( 88) hydrogen bonds : bond 0.03579 ( 1353) hydrogen bonds : angle 5.07805 ( 3867) link_BETA1-4 : bond 0.00579 ( 31) link_BETA1-4 : angle 2.12674 ( 93) link_NAG-ASN : bond 0.00584 ( 60) link_NAG-ASN : angle 3.19015 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8174 Ramachandran restraints generated. 4087 Oldfield, 0 Emsley, 4087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.6215 (mmt90) cc_final: 0.4545 (ptp-170) REVERT: A 169 GLU cc_start: 0.8638 (mt-10) cc_final: 0.7980 (mp0) REVERT: A 557 LYS cc_start: 0.5111 (mttt) cc_final: 0.4243 (mmmm) REVERT: B 153 MET cc_start: 0.3711 (mtp) cc_final: 0.1217 (ppp) REVERT: B 189 LEU cc_start: 0.8340 (tp) cc_final: 0.7717 (pp) REVERT: B 574 ASP cc_start: 0.7609 (p0) cc_final: 0.7228 (p0) REVERT: B 765 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: C 153 MET cc_start: 0.4053 (tmm) cc_final: 0.3503 (ttm) REVERT: C 237 ARG cc_start: 0.6926 (mtm110) cc_final: 0.6649 (mtm110) REVERT: C 287 ASP cc_start: 0.7566 (t0) cc_final: 0.7273 (t0) REVERT: D 237 TYR cc_start: 0.0317 (t80) cc_final: -0.0210 (t80) REVERT: D 323 MET cc_start: 0.3178 (tpp) cc_final: 0.2285 (tpp) REVERT: D 376 MET cc_start: 0.1545 (ttt) cc_final: 0.1207 (ttp) REVERT: D 462 MET cc_start: 0.4607 (mmp) cc_final: 0.3639 (mmm) REVERT: D 594 TRP cc_start: 0.0844 (OUTLIER) cc_final: 0.0510 (t60) REVERT: E 33 ASN cc_start: 0.2930 (OUTLIER) cc_final: 0.2330 (m110) REVERT: E 238 GLU cc_start: -0.1770 (OUTLIER) cc_final: -0.3200 (pt0) REVERT: E 323 MET cc_start: 0.1678 (mpp) cc_final: -0.2104 (mmm) REVERT: E 398 GLU cc_start: 0.1907 (pt0) cc_final: 0.1225 (mp0) REVERT: E 444 LEU cc_start: 0.3581 (OUTLIER) cc_final: 0.2938 (mm) REVERT: E 474 MET cc_start: 0.0056 (mmp) cc_final: -0.0369 (mmm) REVERT: E 557 MET cc_start: 0.0928 (tpt) cc_final: -0.0870 (ttp) outliers start: 41 outliers final: 31 residues processed: 231 average time/residue: 0.1889 time to fit residues: 73.6347 Evaluate side-chains 215 residues out of total 3658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 442 GLN Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain E residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 137 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 348 optimal weight: 30.0000 chunk 129 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS C 437 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.217877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.149469 restraints weight = 68430.292| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.98 r_work: 0.3624 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 35205 Z= 0.226 Angle : 0.718 16.192 48032 Z= 0.350 Chirality : 0.049 0.512 5539 Planarity : 0.004 0.061 6031 Dihedral : 6.036 46.863 6364 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.41 % Favored : 93.32 % Rotamer: Outliers : 1.26 % Allowed : 15.34 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -0.99 (0.13), residues: 4087 helix: 1.16 (0.14), residues: 1317 sheet: -0.84 (0.18), residues: 724 loop : -1.87 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.028 0.002 TYR D 243 PHE 0.025 0.002 PHE B 898 TRP 0.018 0.002 TRP E 48 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00545 (35070) covalent geometry : angle 0.67778 (47671) SS BOND : bond 0.00407 ( 44) SS BOND : angle 2.17347 ( 88) hydrogen bonds : bond 0.04495 ( 1353) hydrogen bonds : angle 5.24398 ( 3867) link_BETA1-4 : bond 0.00542 ( 31) link_BETA1-4 : angle 2.18969 ( 93) link_NAG-ASN : bond 0.00553 ( 60) link_NAG-ASN : angle 3.35922 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12367.24 seconds wall clock time: 210 minutes 47.77 seconds (12647.77 seconds total)