Starting phenix.real_space_refine on Fri Mar 6 21:23:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7czz_30522/03_2026/7czz_30522.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czz_30522/03_2026/7czz_30522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7czz_30522/03_2026/7czz_30522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czz_30522/03_2026/7czz_30522.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7czz_30522/03_2026/7czz_30522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czz_30522/03_2026/7czz_30522.map" } resolution = 3.2 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= 0.000 sd= 0.005 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 150 5.16 5 C 22020 2.51 5 N 5682 2.21 5 O 6919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 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: 34771 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "K" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1685 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "M" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1685 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "N" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1685 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.97, per 1000 atoms: 0.23 Number of scatterers: 34771 At special positions: 0 Unit cell: (154.354, 176.094, 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 150 16.00 O 6919 8.00 N 5682 7.00 C 22020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.27 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.15 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.14 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.38 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.15 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.08 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.26 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.15 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.10 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 94 " distance=2.80 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 200 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 149 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=2.80 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 200 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 149 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 94 " distance=2.80 Simple disulfide: pdb=" SG CYS N 140 " - pdb=" SG CYS N 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1409 " - " NAG B1410 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " NAG f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " NAG g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " NAG h 3 " 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 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " 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 B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " 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 C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 331 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 709 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C 343 " " NAG Z 1 " - " ASN C 709 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1074 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " " NAG f 1 " - " ASN H 73 " " NAG g 1 " - " ASN I 73 " " NAG h 1 " - " ASN J 73 " Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.7 seconds 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8120 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 76 sheets defined 17.9% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.626A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.632A 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: 3.771A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.636A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.646A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.575A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.627A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.626A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.012A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.371A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A 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 364 through 370 removed outlier: 4.073A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.626A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.584A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.603A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 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 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (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 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'K' and resid 127 through 134 Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'I' and resid 196 through 198 No H-bonds generated for 'chain 'I' and resid 196 through 198' Processing helix chain 'M' and resid 127 through 134 Processing helix chain 'M' and resid 189 through 193 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'N' and resid 127 through 134 Processing helix chain 'N' and resid 189 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.680A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.336A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.254A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.506A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.610A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.516A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.821A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.654A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.557A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.534A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 132 through 135 removed outlier: 4.138A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 193 through 194 removed outlier: 5.991A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 275 through 279 removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.118A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.605A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.995A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.576A pdb=" N TYR H 94 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.009A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.009A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 159 through 163 Processing sheet with id=AG1, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.913A pdb=" N THR K 5 " --> pdb=" O LYS K 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS K 24 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS K 23 " --> pdb=" O PHE K 77 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE K 77 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 42 through 44 Processing sheet with id=AG3, first strand: chain 'K' and resid 120 through 124 Processing sheet with id=AG4, first strand: chain 'K' and resid 159 through 160 Processing sheet with id=AG5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.995A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER I 7 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.575A pdb=" N TYR I 94 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA I 146 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL I 193 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 148 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 191 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 150 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 189 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 152 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 187 " --> pdb=" O LYS I 152 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA I 146 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL I 193 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 148 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 191 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 150 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 189 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS I 152 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 187 " --> pdb=" O LYS I 152 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 159 through 163 Processing sheet with id=AH1, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.914A pdb=" N THR M 5 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS M 24 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS M 23 " --> pdb=" O PHE M 77 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE M 77 " --> pdb=" O CYS M 23 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 42 through 44 Processing sheet with id=AH3, first strand: chain 'M' and resid 120 through 124 Processing sheet with id=AH4, first strand: chain 'M' and resid 159 through 160 Processing sheet with id=AH5, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.996A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER J 7 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.575A pdb=" N TYR J 94 " --> pdb=" O THR J 116 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA J 146 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 193 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 148 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 191 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU J 150 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 189 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS J 152 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 187 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA J 146 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 193 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 148 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 191 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU J 150 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 189 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS J 152 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 187 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 159 through 163 Processing sheet with id=AI1, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.914A pdb=" N THR N 5 " --> pdb=" O LYS N 24 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS N 23 " --> pdb=" O PHE N 77 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE N 77 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'N' and resid 42 through 44 Processing sheet with id=AI3, first strand: chain 'N' and resid 120 through 124 Processing sheet with id=AI4, first strand: chain 'N' and resid 159 through 160 1145 hydrogen bonds defined for protein. 3057 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: 9.19 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5784 1.31 - 1.45: 10449 1.45 - 1.58: 19100 1.58 - 1.71: 3 1.71 - 1.85: 192 Bond restraints: 35528 Sorted by residual: bond pdb=" CA GLN C 239 " pdb=" C GLN C 239 " ideal model delta sigma weight residual 1.525 1.420 0.105 1.11e-02 8.12e+03 9.03e+01 bond pdb=" CA HIS B 49 " pdb=" C HIS B 49 " ideal model delta sigma weight residual 1.520 1.405 0.116 1.22e-02 6.72e+03 8.99e+01 bond pdb=" CA ASN C 30 " pdb=" C ASN C 30 " ideal model delta sigma weight residual 1.520 1.416 0.104 1.16e-02 7.43e+03 8.07e+01 bond pdb=" CA ARG C 44 " pdb=" C ARG C 44 " ideal model delta sigma weight residual 1.521 1.415 0.106 1.24e-02 6.50e+03 7.37e+01 bond pdb=" CA TYR B 204 " pdb=" C TYR B 204 " ideal model delta sigma weight residual 1.523 1.422 0.101 1.18e-02 7.18e+03 7.30e+01 ... (remaining 35523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 46089 2.70 - 5.40: 1879 5.40 - 8.09: 291 8.09 - 10.79: 53 10.79 - 13.49: 27 Bond angle restraints: 48339 Sorted by residual: angle pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " pdb=" CG PHE C 32 " ideal model delta sigma weight residual 113.80 103.52 10.28 1.00e+00 1.00e+00 1.06e+02 angle pdb=" CA GLN C 271 " pdb=" C GLN C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 117.82 125.27 -7.45 7.80e-01 1.64e+00 9.11e+01 angle pdb=" CA GLU C 224 " pdb=" C GLU C 224 " pdb=" O GLU C 224 " ideal model delta sigma weight residual 120.19 112.57 7.62 8.40e-01 1.42e+00 8.23e+01 angle pdb=" CA ASN B 188 " pdb=" CB ASN B 188 " pdb=" CG ASN B 188 " ideal model delta sigma weight residual 112.60 103.62 8.98 1.00e+00 1.00e+00 8.06e+01 angle pdb=" CA PHE C 238 " pdb=" CB PHE C 238 " pdb=" CG PHE C 238 " ideal model delta sigma weight residual 113.80 122.42 -8.62 1.00e+00 1.00e+00 7.43e+01 ... (remaining 48334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 19170 17.92 - 35.83: 2118 35.83 - 53.75: 687 53.75 - 71.67: 209 71.67 - 89.59: 62 Dihedral angle restraints: 22246 sinusoidal: 9612 harmonic: 12634 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.05 71.95 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 35.72 57.28 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CA ASP B 198 " pdb=" CB ASP B 198 " ideal model delta harmonic sigma weight residual 122.80 138.69 -15.89 0 2.50e+00 1.60e-01 4.04e+01 ... (remaining 22243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5684 0.328 - 0.657: 30 0.657 - 0.985: 6 0.985 - 1.313: 1 1.313 - 1.642: 3 Chirality restraints: 5724 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-02 2.50e+03 6.61e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.56e+02 ... (remaining 5721 not shown) Planarity restraints: 6179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 282 " 0.243 2.00e-02 2.50e+03 3.37e-01 1.42e+03 pdb=" CG ASN B 282 " -0.115 2.00e-02 2.50e+03 pdb=" OD1 ASN B 282 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 282 " -0.561 2.00e-02 2.50e+03 pdb=" C1 NAG B1405 " 0.424 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 2 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG Q 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG Q 2 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG Q 2 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG Q 2 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 2 " -0.295 2.00e-02 2.50e+03 2.48e-01 7.68e+02 pdb=" C7 NAG f 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG f 2 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG f 2 " 0.423 2.00e-02 2.50e+03 pdb=" O7 NAG f 2 " -0.017 2.00e-02 2.50e+03 ... (remaining 6176 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 391 2.47 - 3.08: 24676 3.08 - 3.69: 50073 3.69 - 4.29: 76148 4.29 - 4.90: 125450 Nonbonded interactions: 276738 Sorted by model distance: nonbonded pdb=" O ALA K 86 " pdb=" OE1 GLU K 87 " model vdw 1.865 3.040 nonbonded pdb=" O ALA M 86 " pdb=" OE1 GLU M 87 " model vdw 1.865 3.040 nonbonded pdb=" O ALA N 86 " pdb=" OE1 GLU N 87 " model vdw 1.865 3.040 nonbonded pdb=" O ARG C 273 " pdb=" OG1 THR C 274 " model vdw 1.914 3.040 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.980 3.120 ... (remaining 276733 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 620 or resid 641 through 939 or resid 944 throu \ gh 1408)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1408)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' 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' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'f' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.960 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.170 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.771 35659 Z= 0.781 Angle : 1.636 56.794 48681 Z= 0.860 Chirality : 0.088 1.642 5724 Planarity : 0.012 0.302 6128 Dihedral : 17.639 89.587 13973 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 40.68 Ramachandran Plot: Outliers : 4.97 % Allowed : 11.72 % Favored : 83.31 % Rotamer: Outliers : 12.78 % Allowed : 17.52 % Favored : 69.69 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.11), residues: 4283 helix: -2.26 (0.16), residues: 683 sheet: -1.54 (0.14), residues: 1149 loop : -3.48 (0.10), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 98 TYR 0.091 0.003 TYR C 38 PHE 0.119 0.005 PHE C 220 TRP 0.166 0.004 TRP C 64 HIS 0.009 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.01244 (35528) covalent geometry : angle 1.28337 (48339) SS BOND : bond 0.20302 ( 51) SS BOND : angle 11.00427 ( 102) hydrogen bonds : bond 0.21024 ( 1085) hydrogen bonds : angle 8.22858 ( 3057) link_BETA1-4 : bond 0.05848 ( 29) link_BETA1-4 : angle 14.35602 ( 87) link_NAG-ASN : bond 0.03990 ( 51) link_NAG-ASN : angle 11.53478 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 483 poor density : 484 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.5167 (OUTLIER) cc_final: 0.4743 (mt) REVERT: A 459 SER cc_start: 0.4454 (OUTLIER) cc_final: 0.4036 (m) REVERT: A 486 PHE cc_start: 0.1855 (OUTLIER) cc_final: 0.1309 (p90) REVERT: A 746 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8502 (p) REVERT: A 878 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8979 (tt) REVERT: A 998 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8607 (m) REVERT: B 34 ARG cc_start: 0.5764 (OUTLIER) cc_final: 0.5500 (mtp85) REVERT: B 157 PHE cc_start: 0.4068 (OUTLIER) cc_final: 0.3743 (t80) REVERT: B 190 ARG cc_start: 0.5893 (OUTLIER) cc_final: 0.4901 (ptp90) REVERT: B 640 SER cc_start: 0.5078 (OUTLIER) cc_final: 0.4048 (m) REVERT: B 787 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: C 878 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8738 (tt) REVERT: H 31 SER cc_start: 0.1001 (p) cc_final: 0.0729 (t) REVERT: H 165 SER cc_start: 0.3475 (OUTLIER) cc_final: 0.2717 (t) REVERT: H 174 THR cc_start: 0.3878 (t) cc_final: 0.3568 (m) REVERT: H 204 ILE cc_start: 0.0989 (OUTLIER) cc_final: 0.0785 (pt) REVERT: K 59 THR cc_start: 0.4175 (OUTLIER) cc_final: 0.3958 (p) REVERT: I 30 THR cc_start: 0.3042 (OUTLIER) cc_final: 0.2806 (p) REVERT: I 48 MET cc_start: -0.0612 (OUTLIER) cc_final: -0.0889 (ptm) REVERT: I 165 SER cc_start: 0.0512 (OUTLIER) cc_final: 0.0141 (p) REVERT: M 97 TYR cc_start: 0.2509 (OUTLIER) cc_final: 0.1973 (m-10) REVERT: J 33 ASP cc_start: 0.1145 (OUTLIER) cc_final: 0.0553 (p0) REVERT: J 103 VAL cc_start: 0.0870 (OUTLIER) cc_final: 0.0518 (t) REVERT: N 4 MET cc_start: 0.1177 (mmm) cc_final: 0.0912 (ttt) REVERT: N 6 GLN cc_start: 0.1742 (OUTLIER) cc_final: 0.1172 (mm110) outliers start: 483 outliers final: 125 residues processed: 891 average time/residue: 0.1939 time to fit residues: 287.3527 Evaluate side-chains 378 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 231 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain H residue 212 SER Chi-restraints excluded: chain K residue 31 TYR Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain M residue 38 TYR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 97 TYR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 177 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 134 GLN A 137 ASN A 188 ASN A 239 GLN A 314 GLN A 394 ASN A 422 ASN A 440 ASN A 481 ASN A 498 GLN A 540 ASN A 613 GLN A 644 GLN A 690 GLN A 703 ASN A 787 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 935 GLN A 955 ASN A 969 ASN A 992 GLN A1002 GLN B 81 ASN B 87 ASN B 115 GLN B 125 ASN B 239 GLN B 394 ASN B 422 ASN B 440 ASN B 481 ASN B 498 GLN B 580 GLN B 804 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1054 GLN C 30 ASN C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 207 HIS C 321 GLN C 394 ASN C 422 ASN C 440 ASN C 481 ASN C 498 GLN C 641 ASN C 655 HIS C 703 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1005 GLN C1010 GLN C1071 GLN C1101 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN I 6 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN J 6 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN N 6 GLN N 43 GLN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.221741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.186092 restraints weight = 57778.805| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.51 r_work: 0.3621 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 35659 Z= 0.222 Angle : 0.932 17.745 48681 Z= 0.450 Chirality : 0.055 0.615 5724 Planarity : 0.006 0.071 6128 Dihedral : 10.283 69.563 6561 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.57 % Favored : 89.47 % Rotamer: Outliers : 6.06 % Allowed : 18.77 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -2.69 (0.12), residues: 4283 helix: -0.27 (0.19), residues: 689 sheet: -0.82 (0.14), residues: 1207 loop : -2.92 (0.11), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 273 TYR 0.029 0.002 TYR B 28 PHE 0.027 0.002 PHE C 65 TRP 0.033 0.003 TRP H 36 HIS 0.011 0.002 HIS I 173 Details of bonding type rmsd covalent geometry : bond 0.00511 (35528) covalent geometry : angle 0.87151 (48339) SS BOND : bond 0.00839 ( 51) SS BOND : angle 2.26465 ( 102) hydrogen bonds : bond 0.05125 ( 1085) hydrogen bonds : angle 5.92296 ( 3057) link_BETA1-4 : bond 0.01064 ( 29) link_BETA1-4 : angle 3.67923 ( 87) link_NAG-ASN : bond 0.00864 ( 51) link_NAG-ASN : angle 5.04689 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 276 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8477 (t) cc_final: 0.8173 (m) REVERT: A 646 ARG cc_start: 0.8211 (tpm170) cc_final: 0.7472 (tpt90) REVERT: A 856 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8197 (p0) REVERT: B 34 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7164 (ptp-110) REVERT: B 153 MET cc_start: 0.0562 (tpp) cc_final: 0.0346 (tmm) REVERT: B 157 PHE cc_start: 0.5835 (OUTLIER) cc_final: 0.5302 (t80) REVERT: B 223 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7916 (mt) REVERT: B 586 ASP cc_start: 0.8520 (m-30) cc_final: 0.8238 (m-30) REVERT: B 740 MET cc_start: 0.8664 (ttt) cc_final: 0.8369 (ttt) REVERT: C 239 GLN cc_start: 0.8365 (tt0) cc_final: 0.8142 (tm-30) REVERT: C 361 CYS cc_start: 0.3213 (p) cc_final: 0.3006 (p) REVERT: C 770 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8572 (pt) REVERT: I 48 MET cc_start: -0.0369 (tpt) cc_final: -0.0760 (ptm) REVERT: I 70 MET cc_start: 0.1355 (tmm) cc_final: 0.0499 (tmm) REVERT: I 81 MET cc_start: 0.2760 (mmm) cc_final: 0.0701 (ttp) REVERT: I 118 VAL cc_start: -0.0511 (OUTLIER) cc_final: -0.0767 (t) REVERT: M 4 MET cc_start: -0.0787 (mmt) cc_final: -0.1389 (mmm) REVERT: N 179 TYR cc_start: 0.2726 (OUTLIER) cc_final: 0.2242 (m-80) outliers start: 229 outliers final: 110 residues processed: 477 average time/residue: 0.1814 time to fit residues: 148.9953 Evaluate side-chains 314 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 197 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 122 PHE Chi-restraints excluded: chain N residue 179 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 151 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 chunk 378 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 856 ASN A 935 GLN A 955 ASN B 30 ASN B 690 GLN B1005 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 134 GLN C 207 HIS C 394 ASN C 450 ASN C 606 ASN C 804 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 GLN K 95 GLN K 166 GLN I 39 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.216717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.180467 restraints weight = 56829.816| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.64 r_work: 0.3767 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35659 Z= 0.217 Angle : 0.830 15.411 48681 Z= 0.401 Chirality : 0.051 0.417 5724 Planarity : 0.005 0.055 6128 Dihedral : 8.844 59.955 6407 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.65 % Allowed : 9.27 % Favored : 90.08 % Rotamer: Outliers : 5.98 % Allowed : 19.48 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.09 (0.12), residues: 4283 helix: 0.40 (0.20), residues: 688 sheet: -0.45 (0.14), residues: 1224 loop : -2.58 (0.11), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 34 TYR 0.036 0.002 TYR M 38 PHE 0.027 0.002 PHE M 122 TRP 0.027 0.002 TRP M 56 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00520 (35528) covalent geometry : angle 0.78341 (48339) SS BOND : bond 0.00542 ( 51) SS BOND : angle 2.00114 ( 102) hydrogen bonds : bond 0.04959 ( 1085) hydrogen bonds : angle 5.62564 ( 3057) link_BETA1-4 : bond 0.00624 ( 29) link_BETA1-4 : angle 3.14792 ( 87) link_NAG-ASN : bond 0.00619 ( 51) link_NAG-ASN : angle 4.09030 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 228 time to evaluate : 1.151 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 169 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6608 (tt0) REVERT: A 347 PHE cc_start: 0.5161 (OUTLIER) cc_final: 0.4829 (m-10) REVERT: A 509 ARG cc_start: 0.3923 (OUTLIER) cc_final: 0.2974 (mtm-85) REVERT: A 525 CYS cc_start: 0.5350 (OUTLIER) cc_final: 0.5023 (m) REVERT: A 646 ARG cc_start: 0.8138 (tpm170) cc_final: 0.7549 (tpt90) REVERT: A 787 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: B 153 MET cc_start: 0.0931 (tpp) cc_final: 0.0602 (tmm) REVERT: B 469 SER cc_start: 0.1654 (OUTLIER) cc_final: 0.1160 (t) REVERT: B 740 MET cc_start: 0.8722 (ttt) cc_final: 0.8407 (ttt) REVERT: C 361 CYS cc_start: 0.4824 (p) cc_final: 0.4508 (p) REVERT: H 70 MET cc_start: 0.0808 (tpt) cc_final: -0.1237 (ttm) REVERT: I 23 LYS cc_start: 0.3720 (tptt) cc_final: 0.3324 (mttp) REVERT: I 48 MET cc_start: 0.0591 (OUTLIER) cc_final: -0.0088 (ptm) REVERT: I 70 MET cc_start: 0.1683 (tmm) cc_final: 0.1367 (tmm) REVERT: I 81 MET cc_start: 0.3293 (mmm) cc_final: 0.2902 (mmt) REVERT: I 187 LEU cc_start: 0.2039 (OUTLIER) cc_final: 0.1539 (tp) REVERT: I 215 LYS cc_start: 0.3602 (tppt) cc_final: 0.2764 (tptm) REVERT: M 4 MET cc_start: -0.0659 (mmt) cc_final: -0.1057 (mmm) REVERT: J 81 MET cc_start: 0.4385 (mmm) cc_final: 0.4132 (mmm) REVERT: N 31 TYR cc_start: 0.0646 (OUTLIER) cc_final: 0.0401 (t80) REVERT: N 179 TYR cc_start: 0.2866 (OUTLIER) cc_final: 0.2171 (m-80) outliers start: 226 outliers final: 131 residues processed: 426 average time/residue: 0.1752 time to fit residues: 128.4423 Evaluate side-chains 336 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 195 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 31 TYR Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 179 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 38 optimal weight: 20.0000 chunk 192 optimal weight: 2.9990 chunk 420 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 387 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 chunk 321 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN A 824 ASN A 935 GLN A 955 ASN B 450 ASN B 957 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 394 ASN C 935 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 166 GLN J 180 GLN J 206 ASN N 37 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.219589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.183980 restraints weight = 56651.085| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.47 r_work: 0.3844 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 35659 Z= 0.161 Angle : 0.756 14.871 48681 Z= 0.362 Chirality : 0.049 0.561 5724 Planarity : 0.005 0.054 6128 Dihedral : 8.221 59.437 6393 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.24 % Favored : 91.20 % Rotamer: Outliers : 5.48 % Allowed : 20.20 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.02 % 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: -1.69 (0.12), residues: 4283 helix: 0.76 (0.20), residues: 692 sheet: -0.17 (0.15), residues: 1211 loop : -2.34 (0.11), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.019 0.001 TYR M 38 PHE 0.020 0.002 PHE C 342 TRP 0.021 0.001 TRP M 56 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00377 (35528) covalent geometry : angle 0.71315 (48339) SS BOND : bond 0.00425 ( 51) SS BOND : angle 1.63713 ( 102) hydrogen bonds : bond 0.04172 ( 1085) hydrogen bonds : angle 5.35422 ( 3057) link_BETA1-4 : bond 0.00748 ( 29) link_BETA1-4 : angle 2.80017 ( 87) link_NAG-ASN : bond 0.00480 ( 51) link_NAG-ASN : angle 3.88459 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 235 time to evaluate : 1.171 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 110 LEU cc_start: 0.6884 (mm) cc_final: 0.6670 (mp) REVERT: A 169 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6632 (tt0) REVERT: A 347 PHE cc_start: 0.5159 (OUTLIER) cc_final: 0.4851 (m-10) REVERT: A 509 ARG cc_start: 0.3998 (OUTLIER) cc_final: 0.2948 (mtm-85) REVERT: A 525 CYS cc_start: 0.5537 (OUTLIER) cc_final: 0.5164 (m) REVERT: A 646 ARG cc_start: 0.8164 (tpm170) cc_final: 0.7627 (tpt90) REVERT: A 787 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: A 882 ILE cc_start: 0.9155 (mt) cc_final: 0.8836 (mm) REVERT: A 983 ARG cc_start: 0.7535 (ptm-80) cc_final: 0.7235 (ptp90) REVERT: B 329 PHE cc_start: 0.8096 (m-80) cc_final: 0.7723 (m-80) REVERT: B 469 SER cc_start: 0.1905 (OUTLIER) cc_final: 0.1357 (t) REVERT: B 569 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7407 (mp) REVERT: B 740 MET cc_start: 0.8836 (ttt) cc_final: 0.8554 (ttt) REVERT: B 861 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9056 (mp) REVERT: C 239 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 361 CYS cc_start: 0.5278 (p) cc_final: 0.4974 (p) REVERT: C 770 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8596 (pt) REVERT: I 23 LYS cc_start: 0.3921 (tptt) cc_final: 0.3453 (mttp) REVERT: I 48 MET cc_start: 0.0726 (OUTLIER) cc_final: 0.0083 (ptm) REVERT: I 70 MET cc_start: 0.1136 (tmm) cc_final: 0.0687 (tmm) REVERT: I 81 MET cc_start: 0.3493 (mmm) cc_final: 0.3061 (mmt) REVERT: I 187 LEU cc_start: 0.1853 (OUTLIER) cc_final: 0.1383 (tp) REVERT: I 215 LYS cc_start: 0.3603 (tppt) cc_final: 0.2743 (tptm) REVERT: M 4 MET cc_start: -0.0831 (mmt) cc_final: -0.1755 (ttm) REVERT: M 169 VAL cc_start: 0.1964 (t) cc_final: 0.1346 (m) REVERT: N 111 GLU cc_start: 0.1872 (OUTLIER) cc_final: 0.1459 (tm-30) REVERT: N 179 TYR cc_start: 0.2780 (OUTLIER) cc_final: 0.2102 (m-80) outliers start: 207 outliers final: 124 residues processed: 415 average time/residue: 0.1817 time to fit residues: 128.8001 Evaluate side-chains 334 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 197 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 122 PHE Chi-restraints excluded: chain N residue 148 ARG Chi-restraints excluded: chain N residue 179 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 287 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 333 optimal weight: 30.0000 chunk 17 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 388 optimal weight: 30.0000 chunk 228 optimal weight: 0.3980 chunk 168 optimal weight: 0.7980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 115 GLN A 188 ASN A 955 ASN B 422 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.217770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.182096 restraints weight = 56593.473| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.43 r_work: 0.3835 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35659 Z= 0.184 Angle : 0.759 16.540 48681 Z= 0.364 Chirality : 0.049 0.589 5724 Planarity : 0.005 0.053 6128 Dihedral : 8.030 59.983 6391 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.90 % Favored : 90.59 % Rotamer: Outliers : 5.13 % Allowed : 20.65 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4283 helix: 0.93 (0.20), residues: 686 sheet: -0.06 (0.15), residues: 1207 loop : -2.21 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.019 0.001 TYR A1067 PHE 0.017 0.002 PHE A 86 TRP 0.016 0.002 TRP K 56 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00441 (35528) covalent geometry : angle 0.71648 (48339) SS BOND : bond 0.00496 ( 51) SS BOND : angle 1.72186 ( 102) hydrogen bonds : bond 0.04431 ( 1085) hydrogen bonds : angle 5.36077 ( 3057) link_BETA1-4 : bond 0.00513 ( 29) link_BETA1-4 : angle 2.69233 ( 87) link_NAG-ASN : bond 0.00466 ( 51) link_NAG-ASN : angle 3.85975 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 207 time to evaluate : 1.142 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 315 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8907 (m) REVERT: A 509 ARG cc_start: 0.4065 (OUTLIER) cc_final: 0.2626 (mtm-85) REVERT: B 274 THR cc_start: 0.7566 (OUTLIER) cc_final: 0.7328 (m) REVERT: B 329 PHE cc_start: 0.7998 (m-80) cc_final: 0.7660 (m-80) REVERT: B 469 SER cc_start: 0.2367 (OUTLIER) cc_final: 0.1846 (t) REVERT: B 569 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7290 (mp) REVERT: B 740 MET cc_start: 0.8670 (ttt) cc_final: 0.8372 (ttt) REVERT: C 361 CYS cc_start: 0.4639 (p) cc_final: 0.4379 (p) REVERT: C 388 ASN cc_start: 0.5818 (t0) cc_final: 0.4978 (t0) REVERT: C 770 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8583 (pt) REVERT: I 48 MET cc_start: 0.0948 (tpt) cc_final: 0.0387 (ptm) REVERT: I 187 LEU cc_start: 0.1688 (OUTLIER) cc_final: 0.1330 (tp) REVERT: M 4 MET cc_start: -0.0742 (mmt) cc_final: -0.1609 (ttm) REVERT: N 111 GLU cc_start: 0.2094 (OUTLIER) cc_final: 0.1632 (tm-30) REVERT: N 179 TYR cc_start: 0.2920 (OUTLIER) cc_final: 0.2247 (m-80) outliers start: 194 outliers final: 148 residues processed: 378 average time/residue: 0.1704 time to fit residues: 112.1061 Evaluate side-chains 347 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 190 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 179 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 185 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 348 optimal weight: 20.0000 chunk 302 optimal weight: 0.0040 chunk 414 optimal weight: 1.9990 chunk 383 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 134 GLN C 207 HIS C 935 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.218734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.182657 restraints weight = 56425.037| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.50 r_work: 0.3813 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35659 Z= 0.154 Angle : 0.717 15.276 48681 Z= 0.343 Chirality : 0.047 0.495 5724 Planarity : 0.004 0.056 6128 Dihedral : 7.663 59.679 6386 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.92 % Favored : 91.59 % Rotamer: Outliers : 4.74 % Allowed : 20.91 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 4283 helix: 1.03 (0.20), residues: 694 sheet: 0.08 (0.15), residues: 1193 loop : -2.11 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.029 0.001 TYR N 38 PHE 0.024 0.001 PHE B 133 TRP 0.018 0.001 TRP M 56 HIS 0.003 0.001 HIS I 173 Details of bonding type rmsd covalent geometry : bond 0.00365 (35528) covalent geometry : angle 0.68064 (48339) SS BOND : bond 0.00391 ( 51) SS BOND : angle 1.48662 ( 102) hydrogen bonds : bond 0.04036 ( 1085) hydrogen bonds : angle 5.24571 ( 3057) link_BETA1-4 : bond 0.00559 ( 29) link_BETA1-4 : angle 2.44362 ( 87) link_NAG-ASN : bond 0.00395 ( 51) link_NAG-ASN : angle 3.49067 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 204 time to evaluate : 1.145 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: A 787 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8177 (mt0) REVERT: B 274 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7155 (m) REVERT: B 329 PHE cc_start: 0.7947 (m-80) cc_final: 0.7627 (m-10) REVERT: B 569 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7157 (mp) REVERT: B 740 MET cc_start: 0.8627 (ttt) cc_final: 0.8340 (ttt) REVERT: C 239 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7304 (tm-30) REVERT: C 388 ASN cc_start: 0.5985 (t0) cc_final: 0.5109 (t0) REVERT: C 770 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8564 (pt) REVERT: I 48 MET cc_start: 0.0859 (tpt) cc_final: 0.0336 (ptm) REVERT: I 187 LEU cc_start: 0.1657 (OUTLIER) cc_final: 0.1304 (tp) REVERT: M 4 MET cc_start: -0.0974 (mmt) cc_final: -0.1784 (ttm) REVERT: N 111 GLU cc_start: 0.1726 (OUTLIER) cc_final: 0.1221 (tm-30) outliers start: 179 outliers final: 134 residues processed: 361 average time/residue: 0.1784 time to fit residues: 111.3993 Evaluate side-chains 327 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 187 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 201 GLN Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 365 optimal weight: 7.9990 chunk 104 optimal weight: 0.0000 chunk 208 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 199 optimal weight: 0.0370 chunk 258 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 362 optimal weight: 30.0000 chunk 165 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 327 optimal weight: 8.9990 overall best weight: 0.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A 957 GLN B 607 GLN B1005 GLN C 81 ASN C 207 HIS C 542 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 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 = 0.4589 r_free = 0.4589 target = 0.220259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.184894 restraints weight = 56823.079| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.48 r_work: 0.3845 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35659 Z= 0.116 Angle : 0.677 14.420 48681 Z= 0.325 Chirality : 0.047 0.757 5724 Planarity : 0.004 0.058 6128 Dihedral : 7.179 58.721 6379 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.77 % Favored : 91.78 % Rotamer: Outliers : 3.76 % Allowed : 22.13 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 4283 helix: 1.33 (0.20), residues: 692 sheet: 0.26 (0.15), residues: 1196 loop : -1.99 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 98 TYR 0.040 0.001 TYR N 38 PHE 0.019 0.001 PHE K 77 TRP 0.016 0.001 TRP M 56 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00255 (35528) covalent geometry : angle 0.64610 (48339) SS BOND : bond 0.00391 ( 51) SS BOND : angle 1.20029 ( 102) hydrogen bonds : bond 0.03471 ( 1085) hydrogen bonds : angle 5.04793 ( 3057) link_BETA1-4 : bond 0.00560 ( 29) link_BETA1-4 : angle 2.26342 ( 87) link_NAG-ASN : bond 0.00451 ( 51) link_NAG-ASN : angle 3.18363 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 210 time to evaluate : 1.065 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 787 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: B 274 THR cc_start: 0.7040 (OUTLIER) cc_final: 0.6819 (m) REVERT: B 329 PHE cc_start: 0.7821 (m-80) cc_final: 0.7552 (m-10) REVERT: B 574 ASP cc_start: 0.7193 (t70) cc_final: 0.6925 (t70) REVERT: B 740 MET cc_start: 0.8595 (ttt) cc_final: 0.8305 (ttt) REVERT: C 239 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7309 (tm-30) REVERT: C 388 ASN cc_start: 0.5694 (t0) cc_final: 0.5158 (t0) REVERT: I 23 LYS cc_start: 0.3977 (tptt) cc_final: 0.3558 (mttp) REVERT: I 48 MET cc_start: 0.0769 (tpt) cc_final: 0.0265 (ptm) REVERT: I 107 LYS cc_start: 0.1463 (mmmm) cc_final: 0.1168 (pttp) REVERT: I 187 LEU cc_start: 0.1571 (OUTLIER) cc_final: 0.1250 (tp) REVERT: I 215 LYS cc_start: 0.3842 (tppt) cc_final: 0.2790 (tptm) REVERT: M 4 MET cc_start: -0.1159 (mmt) cc_final: -0.1872 (ttm) REVERT: M 169 VAL cc_start: 0.1496 (t) cc_final: 0.0941 (m) REVERT: J 216 VAL cc_start: 0.0563 (t) cc_final: 0.0361 (p) REVERT: N 111 GLU cc_start: 0.1364 (OUTLIER) cc_final: 0.0913 (tm-30) outliers start: 142 outliers final: 104 residues processed: 334 average time/residue: 0.1747 time to fit residues: 101.3310 Evaluate side-chains 306 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 198 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 111 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 207 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 355 optimal weight: 50.0000 chunk 426 optimal weight: 8.9990 chunk 347 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 384 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 957 GLN A1101 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 GLN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** N 95 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 = 0.4534 r_free = 0.4534 target = 0.215280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.175223 restraints weight = 56218.523| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.65 r_work: 0.3693 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 35659 Z= 0.340 Angle : 0.850 14.216 48681 Z= 0.411 Chirality : 0.054 0.707 5724 Planarity : 0.005 0.062 6128 Dihedral : 8.168 59.949 6371 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.32 % Favored : 90.19 % Rotamer: Outliers : 4.66 % Allowed : 21.31 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.53 (0.12), residues: 4283 helix: 0.64 (0.20), residues: 693 sheet: -0.04 (0.15), residues: 1205 loop : -2.15 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 403 TYR 0.029 0.002 TYR A 451 PHE 0.020 0.003 PHE A 92 TRP 0.020 0.002 TRP C 64 HIS 0.008 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00846 (35528) covalent geometry : angle 0.81365 (48339) SS BOND : bond 0.00500 ( 51) SS BOND : angle 1.84274 ( 102) hydrogen bonds : bond 0.05535 ( 1085) hydrogen bonds : angle 5.60760 ( 3057) link_BETA1-4 : bond 0.00454 ( 29) link_BETA1-4 : angle 2.70319 ( 87) link_NAG-ASN : bond 0.00544 ( 51) link_NAG-ASN : angle 3.80239 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 214 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 PRO cc_start: 0.8491 (Cg_endo) cc_final: 0.8248 (Cg_exo) REVERT: A 347 PHE cc_start: 0.5226 (OUTLIER) cc_final: 0.4869 (m-10) REVERT: A 787 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: B 274 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7548 (m) REVERT: B 469 SER cc_start: 0.2290 (OUTLIER) cc_final: 0.1799 (t) REVERT: B 740 MET cc_start: 0.8737 (ttt) cc_final: 0.8479 (ttt) REVERT: C 215 ASP cc_start: 0.0811 (OUTLIER) cc_final: 0.0437 (m-30) REVERT: C 239 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7456 (tm-30) REVERT: C 351 TYR cc_start: 0.3481 (OUTLIER) cc_final: 0.2667 (p90) REVERT: I 48 MET cc_start: 0.0933 (tpt) cc_final: 0.0459 (ptm) REVERT: I 81 MET cc_start: 0.4214 (mmm) cc_final: 0.1846 (ttp) REVERT: I 187 LEU cc_start: 0.1831 (OUTLIER) cc_final: 0.1355 (tp) REVERT: M 4 MET cc_start: -0.0735 (mmt) cc_final: -0.1974 (ttm) REVERT: N 111 GLU cc_start: 0.1016 (OUTLIER) cc_final: 0.0514 (tm-30) outliers start: 176 outliers final: 145 residues processed: 369 average time/residue: 0.1743 time to fit residues: 112.3613 Evaluate side-chains 343 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 190 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 181 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 111 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 317 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 325 optimal weight: 6.9990 chunk 282 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 319 optimal weight: 8.9990 chunk 397 optimal weight: 9.9990 chunk 265 optimal weight: 0.8980 chunk 214 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 208 optimal weight: 0.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A 957 GLN B 762 GLN B1106 GLN C 66 HIS C 207 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 GLN ** 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 = 0.4564 r_free = 0.4564 target = 0.217959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.180545 restraints weight = 56235.663| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.54 r_work: 0.3775 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35659 Z= 0.153 Angle : 0.725 14.365 48681 Z= 0.348 Chirality : 0.048 0.643 5724 Planarity : 0.004 0.063 6128 Dihedral : 7.633 59.602 6371 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.99 % Favored : 91.57 % Rotamer: Outliers : 3.79 % Allowed : 22.79 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.31 (0.13), residues: 4283 helix: 1.03 (0.20), residues: 688 sheet: 0.15 (0.15), residues: 1181 loop : -2.08 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.019 0.001 TYR A1067 PHE 0.022 0.001 PHE A 86 TRP 0.018 0.001 TRP M 56 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00362 (35528) covalent geometry : angle 0.69303 (48339) SS BOND : bond 0.00340 ( 51) SS BOND : angle 1.46895 ( 102) hydrogen bonds : bond 0.04087 ( 1085) hydrogen bonds : angle 5.31644 ( 3057) link_BETA1-4 : bond 0.00516 ( 29) link_BETA1-4 : angle 2.28580 ( 87) link_NAG-ASN : bond 0.00426 ( 51) link_NAG-ASN : angle 3.36065 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 191 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.4868 (OUTLIER) cc_final: 0.4554 (m-10) REVERT: A 787 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: B 101 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7411 (mm) REVERT: B 157 PHE cc_start: 0.5615 (OUTLIER) cc_final: 0.5235 (t80) REVERT: B 274 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.7008 (m) REVERT: B 569 ILE cc_start: 0.7775 (mp) cc_final: 0.7160 (mp) REVERT: B 740 MET cc_start: 0.8632 (ttt) cc_final: 0.8343 (ttt) REVERT: C 239 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7231 (tm-30) REVERT: C 388 ASN cc_start: 0.6194 (t0) cc_final: 0.5356 (t0) REVERT: C 547 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8302 (m) REVERT: I 187 LEU cc_start: 0.1839 (OUTLIER) cc_final: 0.1448 (tp) REVERT: M 4 MET cc_start: -0.0707 (mmt) cc_final: -0.1888 (ttm) REVERT: N 111 GLU cc_start: 0.0723 (OUTLIER) cc_final: 0.0286 (tm-30) outliers start: 143 outliers final: 114 residues processed: 317 average time/residue: 0.1690 time to fit residues: 94.0409 Evaluate side-chains 305 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 183 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 17 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 266 optimal weight: 3.9990 chunk 405 optimal weight: 0.0970 chunk 32 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 347 optimal weight: 8.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A 957 GLN B 394 ASN C 207 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.217345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.182544 restraints weight = 56610.973| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.39 r_work: 0.3816 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35659 Z= 0.163 Angle : 0.723 13.585 48681 Z= 0.346 Chirality : 0.048 0.606 5724 Planarity : 0.005 0.064 6128 Dihedral : 7.497 59.415 6370 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.55 % Favored : 91.06 % Rotamer: Outliers : 3.41 % Allowed : 22.90 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.13), residues: 4283 helix: 1.15 (0.20), residues: 690 sheet: 0.18 (0.15), residues: 1189 loop : -2.05 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 102 TYR 0.022 0.001 TYR K 38 PHE 0.017 0.002 PHE A 86 TRP 0.016 0.001 TRP H 50 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00391 (35528) covalent geometry : angle 0.69300 (48339) SS BOND : bond 0.00356 ( 51) SS BOND : angle 1.42610 ( 102) hydrogen bonds : bond 0.04154 ( 1085) hydrogen bonds : angle 5.28072 ( 3057) link_BETA1-4 : bond 0.00494 ( 29) link_BETA1-4 : angle 2.26574 ( 87) link_NAG-ASN : bond 0.00434 ( 51) link_NAG-ASN : angle 3.23702 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 191 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.4921 (OUTLIER) cc_final: 0.4601 (m-10) REVERT: A 453 TYR cc_start: 0.6019 (p90) cc_final: 0.5738 (p90) REVERT: A 787 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8411 (mt0) REVERT: B 101 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7504 (mm) REVERT: B 274 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7079 (m) REVERT: B 569 ILE cc_start: 0.7959 (mp) cc_final: 0.7309 (mp) REVERT: B 740 MET cc_start: 0.8819 (ttt) cc_final: 0.8550 (ttt) REVERT: C 351 TYR cc_start: 0.3499 (OUTLIER) cc_final: 0.2550 (p90) REVERT: C 388 ASN cc_start: 0.6329 (t0) cc_final: 0.5482 (t0) REVERT: H 81 MET cc_start: 0.3332 (ttt) cc_final: 0.2718 (ttt) REVERT: K 205 GLN cc_start: 0.0810 (tt0) cc_final: -0.0752 (mm-40) REVERT: I 48 MET cc_start: 0.0866 (tpt) cc_final: 0.0587 (ptm) REVERT: I 81 MET cc_start: 0.4116 (mmm) cc_final: 0.1670 (ttp) REVERT: I 187 LEU cc_start: 0.1766 (OUTLIER) cc_final: 0.1372 (tp) REVERT: M 77 PHE cc_start: 0.1605 (OUTLIER) cc_final: 0.1321 (p90) REVERT: N 111 GLU cc_start: 0.0826 (OUTLIER) cc_final: 0.0375 (tm-30) outliers start: 129 outliers final: 110 residues processed: 305 average time/residue: 0.1702 time to fit residues: 91.4164 Evaluate side-chains 301 residues out of total 3787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 183 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 77 PHE Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain M residue 203 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 322 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 316 optimal weight: 30.0000 chunk 233 optimal weight: 0.1980 chunk 326 optimal weight: 4.9990 chunk 374 optimal weight: 30.0000 chunk 385 optimal weight: 0.0980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A 957 GLN B 394 ASN C 207 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 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 = 0.4565 r_free = 0.4565 target = 0.218269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.181196 restraints weight = 56094.498| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.51 r_work: 0.3788 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35659 Z= 0.138 Angle : 0.701 13.672 48681 Z= 0.334 Chirality : 0.047 0.589 5724 Planarity : 0.004 0.064 6128 Dihedral : 7.244 58.970 6363 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.92 % Favored : 91.71 % Rotamer: Outliers : 3.34 % Allowed : 23.16 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 4283 helix: 1.21 (0.20), residues: 698 sheet: 0.23 (0.15), residues: 1170 loop : -2.01 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.021 0.001 TYR K 38 PHE 0.018 0.001 PHE A 86 TRP 0.017 0.001 TRP H 50 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00325 (35528) covalent geometry : angle 0.67231 (48339) SS BOND : bond 0.00293 ( 51) SS BOND : angle 1.34328 ( 102) hydrogen bonds : bond 0.03854 ( 1085) hydrogen bonds : angle 5.17162 ( 3057) link_BETA1-4 : bond 0.00500 ( 29) link_BETA1-4 : angle 2.15758 ( 87) link_NAG-ASN : bond 0.00417 ( 51) link_NAG-ASN : angle 3.11454 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8194.31 seconds wall clock time: 141 minutes 12.32 seconds (8472.32 seconds total)