Starting phenix.real_space_refine on Fri Mar 6 09:03:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq0_32078/03_2026/7vq0_32078.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq0_32078/03_2026/7vq0_32078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vq0_32078/03_2026/7vq0_32078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq0_32078/03_2026/7vq0_32078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vq0_32078/03_2026/7vq0_32078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq0_32078/03_2026/7vq0_32078.map" } resolution = 3.03 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= 0.067 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 128 5.16 5 C 18712 2.51 5 N 4837 2.21 5 O 5840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s 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: 29517 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 8554 Classifications: {'peptide': 1093} Link IDs: {'PTRANS': 54, 'TRANS': 1038} Chain breaks: 6 Chain: "B" Number of atoms: 8524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8524 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 7 Chain: "C" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8540 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 54, 'TRANS': 1037} Chain breaks: 5 Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 885 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.59, per 1000 atoms: 0.26 Number of scatterers: 29517 At special positions: 0 Unit cell: (147.03, 153.12, 225.33, 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 128 16.00 O 5840 8.00 N 4837 7.00 C 18712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 94 " 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=2, symmetry=0 Links applied ALPHA1-4 " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG N 1 " - " FUC N 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1404 " - " ASN A 331 " " NAG A1405 " - " ASN A 343 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1158 " " NAG B1402 " - " ASN B 122 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 657 " " NAG C1410 " - " ASN C 709 " " NAG C1411 " - " ASN C1158 " " NAG H 1 " - " ASN A 122 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 616 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 17 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1074 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 331 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.3 seconds 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6762 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 58 sheets defined 23.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.523A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.536A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.559A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.567A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.740A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.567A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 830 through 835 removed outlier: 3.871A pdb=" N ILE A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 835 " --> pdb=" O ALA A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 835' Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.170A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.931A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.691A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.967A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.911A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.866A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.528A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.048A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.255A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1161 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.779A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 619 through 623 removed outlier: 4.074A pdb=" N ALA C 623 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.069A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.803A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.648A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.017A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.767A pdb=" N THR D 89 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.099A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.611A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.848A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.956A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.630A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.630A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 140 through 143 removed outlier: 4.906A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.174A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.899A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.623A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.693A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 551 through 554 removed outlier: 3.519A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.300A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.257A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.784A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.268A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.385A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.566A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.344A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.915A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.997A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.649A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 131 through 140 removed outlier: 6.585A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.220A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.593A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.615A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.270A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.186A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.598A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.693A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.779A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.276A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.097A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.606A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 51 removed outlier: 6.488A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.716A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.209A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.463A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.670A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.647A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.014A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 595 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.525A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.525A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.816A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.277A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.369A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.601A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 18 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET D 81 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 20 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 77 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 36 through 39 removed outlier: 6.409A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AG1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.589A pdb=" N GLN E 5 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR E 67 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.839A pdb=" N VAL E 12 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL E 91 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN E 39 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA E 50 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA E 57 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.752A pdb=" N GLN F 5 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL F 23 " --> pdb=" O GLN F 5 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER F 7 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU F 18 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 20 " --> pdb=" O LEU F 79 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.892A pdb=" N THR F 110 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR F 92 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE F 34 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.37 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9341 1.34 - 1.47: 7674 1.47 - 1.59: 12980 1.59 - 1.71: 0 1.71 - 1.83: 164 Bond restraints: 30159 Sorted by residual: bond pdb=" C5 MAN O 3 " pdb=" O5 MAN O 3 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.64e+00 bond pdb=" C5 MAN P 3 " pdb=" O5 MAN P 3 " ideal model delta sigma weight residual 1.418 1.464 -0.046 2.00e-02 2.50e+03 5.36e+00 bond pdb=" C5 MAN e 3 " pdb=" O5 MAN e 3 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C5 MAN W 3 " pdb=" O5 MAN W 3 " ideal model delta sigma weight residual 1.418 1.462 -0.044 2.00e-02 2.50e+03 4.93e+00 bond pdb=" C5 MAN f 3 " pdb=" O5 MAN f 3 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.91e+00 ... (remaining 30154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 39923 1.66 - 3.32: 945 3.32 - 4.98: 91 4.98 - 6.64: 29 6.64 - 8.30: 10 Bond angle restraints: 40998 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.16 -4.46 1.22e+00 6.72e-01 1.33e+01 angle pdb=" CA PRO A 986 " pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 117.93 121.64 -3.71 1.20e+00 6.94e-01 9.57e+00 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.19 -3.49 1.22e+00 6.72e-01 8.20e+00 angle pdb=" C ASP E 53 " pdb=" CA ASP E 53 " pdb=" CB ASP E 53 " ideal model delta sigma weight residual 110.42 115.98 -5.56 1.99e+00 2.53e-01 7.79e+00 angle pdb=" N VAL C1128 " pdb=" CA VAL C1128 " pdb=" C VAL C1128 " ideal model delta sigma weight residual 113.53 110.86 2.67 9.80e-01 1.04e+00 7.41e+00 ... (remaining 40993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 17988 24.39 - 48.77: 925 48.77 - 73.16: 119 73.16 - 97.54: 64 97.54 - 121.93: 20 Dihedral angle restraints: 19116 sinusoidal: 8598 harmonic: 10518 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.03 76.03 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -12.41 -73.59 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.01 71.01 1 1.00e+01 1.00e-02 6.48e+01 ... (remaining 19113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4248 0.070 - 0.141: 608 0.141 - 0.211: 7 0.211 - 0.281: 2 0.281 - 0.352: 3 Chirality restraints: 4868 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4865 not shown) Planarity restraints: 5224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO A 527 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.001 2.00e-02 2.50e+03 2.28e-02 6.52e+00 pdb=" CG ASN A 616 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.33e+00 pdb=" N PRO A 561 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.025 5.00e-02 4.00e+02 ... (remaining 5221 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 636 2.68 - 3.23: 27914 3.23 - 3.79: 45765 3.79 - 4.34: 61508 4.34 - 4.90: 101858 Nonbonded interactions: 237681 Sorted by model distance: nonbonded pdb=" OG SER A 884 " pdb=" OG1 THR A 887 " model vdw 2.124 3.040 nonbonded pdb=" NH2 ARG A 34 " pdb=" OE2 GLU A 191 " model vdw 2.183 3.120 nonbonded pdb=" OG SER B 469 " pdb=" OE1 GLU B 471 " model vdw 2.192 3.040 nonbonded pdb=" OG1 THR C 470 " pdb=" O TYR F 58 " model vdw 2.200 3.040 nonbonded pdb=" O SER A 937 " pdb=" OG1 THR A 941 " model vdw 2.204 3.040 ... (remaining 237676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 145 or resid 152 through 623 or resid 636 throu \ gh 836 or resid 854 through 1409)) selection = (chain 'B' and (resid 14 through 68 or resid 77 through 836 or resid 854 through \ 1409)) selection = (chain 'C' and (resid 14 through 68 or resid 77 through 145 or resid 152 through \ 177 or resid 185 through 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'N' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.170 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.004 0.047 30279 Z= 0.181 Angle : 0.614 9.932 41308 Z= 0.289 Chirality : 0.045 0.352 4868 Planarity : 0.003 0.068 5185 Dihedral : 15.233 121.930 12222 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % Favored : 99.75 % 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: -0.40 (0.14), residues: 3576 helix: 1.91 (0.20), residues: 741 sheet: -0.18 (0.19), residues: 752 loop : -1.14 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.019 0.001 TYR A 170 PHE 0.025 0.001 PHE A 168 TRP 0.016 0.001 TRP A 64 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00382 (30159) covalent geometry : angle 0.59385 (40998) SS BOND : bond 0.00298 ( 44) SS BOND : angle 1.33541 ( 88) hydrogen bonds : bond 0.19194 ( 1067) hydrogen bonds : angle 8.35111 ( 2976) Misc. bond : bond 0.00148 ( 2) link_ALPHA1-4 : bond 0.00704 ( 6) link_ALPHA1-4 : angle 2.28604 ( 18) link_BETA1-4 : bond 0.00542 ( 26) link_BETA1-4 : angle 1.31046 ( 78) link_BETA1-6 : bond 0.00716 ( 3) link_BETA1-6 : angle 1.43163 ( 9) link_NAG-ASN : bond 0.00345 ( 39) link_NAG-ASN : angle 2.47592 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 1.046 Fit side-chains REVERT: B 237 ARG cc_start: 0.7453 (mtp-110) cc_final: 0.7121 (ttp-110) REVERT: B 568 ASP cc_start: 0.7065 (t0) cc_final: 0.6782 (t0) REVERT: B 904 TYR cc_start: 0.7881 (m-10) cc_final: 0.7542 (m-10) REVERT: C 52 GLN cc_start: 0.7740 (pp30) cc_final: 0.7534 (pp30) REVERT: C 586 ASP cc_start: 0.8041 (m-30) cc_final: 0.7775 (m-30) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.1790 time to fit residues: 82.2882 Evaluate side-chains 196 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 1.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 613 GLN A 907 ASN A1010 GLN B 607 GLN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 914 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN D 39 GLN D 55 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.206974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136966 restraints weight = 41735.619| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.15 r_work: 0.3404 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30279 Z= 0.130 Angle : 0.584 10.953 41308 Z= 0.290 Chirality : 0.044 0.274 4868 Planarity : 0.004 0.049 5185 Dihedral : 10.348 111.314 5771 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.42 % Favored : 95.50 % Rotamer: Outliers : 0.35 % Allowed : 6.15 % Favored : 93.50 % 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: -0.29 (0.14), residues: 3576 helix: 2.05 (0.20), residues: 743 sheet: -0.01 (0.19), residues: 747 loop : -1.14 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.024 0.001 TYR A 453 PHE 0.015 0.001 PHE A 168 TRP 0.016 0.001 TRP C 64 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00291 (30159) covalent geometry : angle 0.56747 (40998) SS BOND : bond 0.00285 ( 44) SS BOND : angle 1.15933 ( 88) hydrogen bonds : bond 0.04495 ( 1067) hydrogen bonds : angle 6.47885 ( 2976) Misc. bond : bond 0.00129 ( 2) link_ALPHA1-4 : bond 0.01552 ( 6) link_ALPHA1-4 : angle 2.58980 ( 18) link_BETA1-4 : bond 0.00415 ( 26) link_BETA1-4 : angle 1.15292 ( 78) link_BETA1-6 : bond 0.01271 ( 3) link_BETA1-6 : angle 1.80839 ( 9) link_NAG-ASN : bond 0.00364 ( 39) link_NAG-ASN : angle 2.12141 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 224 time to evaluate : 1.039 Fit side-chains REVERT: A 406 GLU cc_start: 0.8462 (mp0) cc_final: 0.8215 (mp0) REVERT: A 935 GLN cc_start: 0.8807 (pp30) cc_final: 0.8567 (tm-30) REVERT: B 675 GLN cc_start: 0.7111 (tm-30) cc_final: 0.6863 (tm-30) REVERT: B 904 TYR cc_start: 0.8585 (m-10) cc_final: 0.8337 (m-10) REVERT: C 52 GLN cc_start: 0.8044 (pp30) cc_final: 0.7726 (pp30) outliers start: 11 outliers final: 5 residues processed: 234 average time/residue: 0.1738 time to fit residues: 67.4585 Evaluate side-chains 202 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 138 optimal weight: 0.0670 chunk 265 optimal weight: 20.0000 chunk 315 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 0.0670 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 607 GLN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.207608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131567 restraints weight = 41935.568| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.54 r_work: 0.3462 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30279 Z= 0.110 Angle : 0.553 9.205 41308 Z= 0.269 Chirality : 0.043 0.271 4868 Planarity : 0.003 0.043 5185 Dihedral : 8.939 110.516 5771 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.17 % Favored : 95.75 % Rotamer: Outliers : 0.67 % Allowed : 8.82 % Favored : 90.51 % 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: -0.25 (0.14), residues: 3576 helix: 2.23 (0.20), residues: 737 sheet: -0.03 (0.18), residues: 757 loop : -1.15 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 983 TYR 0.020 0.001 TYR A 453 PHE 0.016 0.001 PHE A 168 TRP 0.014 0.001 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00246 (30159) covalent geometry : angle 0.53593 (40998) SS BOND : bond 0.00242 ( 44) SS BOND : angle 1.02871 ( 88) hydrogen bonds : bond 0.03845 ( 1067) hydrogen bonds : angle 5.92432 ( 2976) Misc. bond : bond 0.00107 ( 2) link_ALPHA1-4 : bond 0.01533 ( 6) link_ALPHA1-4 : angle 2.83679 ( 18) link_BETA1-4 : bond 0.00407 ( 26) link_BETA1-4 : angle 1.16465 ( 78) link_BETA1-6 : bond 0.01459 ( 3) link_BETA1-6 : angle 2.25322 ( 9) link_NAG-ASN : bond 0.00337 ( 39) link_NAG-ASN : angle 1.95023 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8395 (t-170) cc_final: 0.8190 (t-170) REVERT: A 140 PHE cc_start: 0.6103 (p90) cc_final: 0.5827 (p90) REVERT: A 271 GLN cc_start: 0.8090 (pm20) cc_final: 0.7808 (pm20) REVERT: A 392 PHE cc_start: 0.7393 (m-80) cc_final: 0.7033 (m-80) REVERT: A 935 GLN cc_start: 0.8753 (pp30) cc_final: 0.8526 (tm-30) REVERT: B 237 ARG cc_start: 0.8210 (ttp-170) cc_final: 0.7631 (mtp-110) REVERT: B 904 TYR cc_start: 0.8489 (m-10) cc_final: 0.8267 (m-10) REVERT: C 52 GLN cc_start: 0.7935 (pp30) cc_final: 0.7728 (pp30) REVERT: C 533 LEU cc_start: 0.7469 (tt) cc_final: 0.7258 (tp) REVERT: C 1107 ARG cc_start: 0.8207 (mtt180) cc_final: 0.8005 (mtt180) outliers start: 21 outliers final: 10 residues processed: 238 average time/residue: 0.1800 time to fit residues: 70.8691 Evaluate side-chains 212 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain D residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 208 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 195 optimal weight: 0.8980 chunk 330 optimal weight: 9.9990 chunk 326 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 607 GLN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.206473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136983 restraints weight = 41583.642| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.32 r_work: 0.3368 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30279 Z= 0.139 Angle : 0.568 12.258 41308 Z= 0.275 Chirality : 0.043 0.265 4868 Planarity : 0.003 0.046 5185 Dihedral : 8.174 108.674 5771 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 1.15 % Allowed : 9.90 % Favored : 88.95 % 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: -0.28 (0.14), residues: 3576 helix: 2.11 (0.19), residues: 743 sheet: -0.08 (0.18), residues: 776 loop : -1.14 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.019 0.001 TYR B1067 PHE 0.013 0.001 PHE A 168 TRP 0.019 0.001 TRP A 64 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00324 (30159) covalent geometry : angle 0.55025 (40998) SS BOND : bond 0.00292 ( 44) SS BOND : angle 1.10716 ( 88) hydrogen bonds : bond 0.03855 ( 1067) hydrogen bonds : angle 5.78070 ( 2976) Misc. bond : bond 0.00159 ( 2) link_ALPHA1-4 : bond 0.01615 ( 6) link_ALPHA1-4 : angle 3.10440 ( 18) link_BETA1-4 : bond 0.00376 ( 26) link_BETA1-4 : angle 1.21799 ( 78) link_BETA1-6 : bond 0.01709 ( 3) link_BETA1-6 : angle 2.11889 ( 9) link_NAG-ASN : bond 0.00321 ( 39) link_NAG-ASN : angle 2.01505 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 1.094 Fit side-chains REVERT: A 49 HIS cc_start: 0.8362 (t-170) cc_final: 0.8129 (t-170) REVERT: A 140 PHE cc_start: 0.6065 (p90) cc_final: 0.5807 (p90) REVERT: A 271 GLN cc_start: 0.8063 (pm20) cc_final: 0.7727 (pm20) REVERT: A 392 PHE cc_start: 0.7431 (m-80) cc_final: 0.6879 (m-80) REVERT: A 406 GLU cc_start: 0.8575 (mp0) cc_final: 0.8367 (mp0) REVERT: A 935 GLN cc_start: 0.8712 (pp30) cc_final: 0.8467 (tm-30) REVERT: B 235 ILE cc_start: 0.5866 (OUTLIER) cc_final: 0.5646 (tp) REVERT: B 237 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7555 (mtp85) REVERT: B 239 GLN cc_start: 0.7861 (tt0) cc_final: 0.7366 (tt0) REVERT: B 568 ASP cc_start: 0.7506 (t0) cc_final: 0.7125 (t0) REVERT: B 675 GLN cc_start: 0.6926 (tm-30) cc_final: 0.6723 (tm-30) REVERT: B 904 TYR cc_start: 0.8383 (m-10) cc_final: 0.8169 (m-10) REVERT: C 118 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7489 (tp) REVERT: C 1107 ARG cc_start: 0.8245 (mtt180) cc_final: 0.8036 (mtt90) outliers start: 36 outliers final: 19 residues processed: 237 average time/residue: 0.1688 time to fit residues: 66.9496 Evaluate side-chains 217 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 144 optimal weight: 7.9990 chunk 340 optimal weight: 0.8980 chunk 249 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 175 optimal weight: 0.0370 chunk 233 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.205295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131393 restraints weight = 41728.178| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.03 r_work: 0.3353 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30279 Z= 0.171 Angle : 0.584 12.314 41308 Z= 0.284 Chirality : 0.044 0.258 4868 Planarity : 0.004 0.050 5185 Dihedral : 7.784 108.270 5771 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 1.21 % Allowed : 11.21 % Favored : 87.58 % 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: -0.33 (0.14), residues: 3576 helix: 2.02 (0.19), residues: 744 sheet: -0.08 (0.18), residues: 762 loop : -1.16 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 509 TYR 0.021 0.001 TYR B1138 PHE 0.013 0.001 PHE B 565 TRP 0.020 0.001 TRP A 64 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00407 (30159) covalent geometry : angle 0.56512 (40998) SS BOND : bond 0.00304 ( 44) SS BOND : angle 1.21342 ( 88) hydrogen bonds : bond 0.04041 ( 1067) hydrogen bonds : angle 5.70815 ( 2976) Misc. bond : bond 0.00153 ( 2) link_ALPHA1-4 : bond 0.01681 ( 6) link_ALPHA1-4 : angle 3.38895 ( 18) link_BETA1-4 : bond 0.00354 ( 26) link_BETA1-4 : angle 1.27212 ( 78) link_BETA1-6 : bond 0.01629 ( 3) link_BETA1-6 : angle 1.75029 ( 9) link_NAG-ASN : bond 0.00321 ( 39) link_NAG-ASN : angle 2.04503 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8664 (mt) REVERT: A 49 HIS cc_start: 0.8516 (t-170) cc_final: 0.8263 (t-170) REVERT: A 140 PHE cc_start: 0.6073 (p90) cc_final: 0.5787 (p90) REVERT: A 271 GLN cc_start: 0.8142 (pm20) cc_final: 0.7805 (pm20) REVERT: A 392 PHE cc_start: 0.7535 (m-80) cc_final: 0.7055 (m-80) REVERT: A 509 ARG cc_start: 0.6892 (mtt90) cc_final: 0.6630 (mtt-85) REVERT: A 935 GLN cc_start: 0.8781 (pp30) cc_final: 0.8523 (tm-30) REVERT: B 237 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7576 (mtp85) REVERT: B 568 ASP cc_start: 0.7745 (t0) cc_final: 0.7327 (t0) REVERT: B 990 GLU cc_start: 0.8357 (tt0) cc_final: 0.8023 (mm-30) REVERT: C 118 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7511 (tp) REVERT: C 537 LYS cc_start: 0.8628 (mmpt) cc_final: 0.8273 (mtmm) REVERT: D 66 PHE cc_start: 0.3992 (m-10) cc_final: 0.3338 (m-80) REVERT: D 74 LYS cc_start: 0.5012 (ptmm) cc_final: 0.4279 (tttm) outliers start: 38 outliers final: 27 residues processed: 244 average time/residue: 0.1728 time to fit residues: 71.0546 Evaluate side-chains 228 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain D residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 34 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 321 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1010 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 501 ASN C1010 GLN C1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.203964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131212 restraints weight = 41424.469| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.19 r_work: 0.3328 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 30279 Z= 0.196 Angle : 0.597 9.171 41308 Z= 0.292 Chirality : 0.045 0.258 4868 Planarity : 0.004 0.047 5185 Dihedral : 7.674 107.810 5771 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.71 % Rotamer: Outliers : 1.62 % Allowed : 12.32 % Favored : 86.05 % 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: -0.42 (0.14), residues: 3576 helix: 1.89 (0.19), residues: 741 sheet: -0.13 (0.18), residues: 765 loop : -1.20 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 509 TYR 0.019 0.001 TYR B1067 PHE 0.017 0.001 PHE C 194 TRP 0.024 0.001 TRP A 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00468 (30159) covalent geometry : angle 0.57816 (40998) SS BOND : bond 0.00345 ( 44) SS BOND : angle 1.22473 ( 88) hydrogen bonds : bond 0.04190 ( 1067) hydrogen bonds : angle 5.72002 ( 2976) Misc. bond : bond 0.00206 ( 2) link_ALPHA1-4 : bond 0.01649 ( 6) link_ALPHA1-4 : angle 3.51283 ( 18) link_BETA1-4 : bond 0.00341 ( 26) link_BETA1-4 : angle 1.31482 ( 78) link_BETA1-6 : bond 0.01442 ( 3) link_BETA1-6 : angle 1.60662 ( 9) link_NAG-ASN : bond 0.00350 ( 39) link_NAG-ASN : angle 2.11148 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 49 HIS cc_start: 0.8566 (t-170) cc_final: 0.8321 (t-170) REVERT: A 140 PHE cc_start: 0.6076 (p90) cc_final: 0.5788 (p90) REVERT: A 271 GLN cc_start: 0.8153 (pm20) cc_final: 0.7804 (pm20) REVERT: A 392 PHE cc_start: 0.7638 (m-80) cc_final: 0.7214 (m-80) REVERT: A 509 ARG cc_start: 0.6907 (mtt90) cc_final: 0.6552 (mtt-85) REVERT: A 515 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.6417 (p90) REVERT: A 935 GLN cc_start: 0.8771 (pp30) cc_final: 0.8515 (tm-30) REVERT: B 237 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7657 (mtp85) REVERT: B 568 ASP cc_start: 0.7820 (t0) cc_final: 0.7379 (t0) REVERT: B 726 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8784 (mp) REVERT: B 990 GLU cc_start: 0.8427 (tt0) cc_final: 0.8074 (mm-30) REVERT: C 118 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7508 (tp) REVERT: C 537 LYS cc_start: 0.8595 (mmpt) cc_final: 0.8260 (mtmm) REVERT: D 74 LYS cc_start: 0.4984 (ptmm) cc_final: 0.4158 (tttm) outliers start: 51 outliers final: 33 residues processed: 257 average time/residue: 0.1698 time to fit residues: 73.8588 Evaluate side-chains 238 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 17 optimal weight: 10.0000 chunk 219 optimal weight: 0.0060 chunk 74 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 229 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 chunk 170 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1002 GLN B 607 GLN B1054 GLN C 360 ASN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.205632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.133324 restraints weight = 41491.659| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.23 r_work: 0.3363 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30279 Z= 0.108 Angle : 0.551 12.408 41308 Z= 0.267 Chirality : 0.043 0.273 4868 Planarity : 0.003 0.048 5185 Dihedral : 7.267 107.145 5771 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 1.08 % Allowed : 13.54 % Favored : 85.38 % 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: -0.28 (0.14), residues: 3576 helix: 2.11 (0.19), residues: 743 sheet: -0.09 (0.18), residues: 749 loop : -1.12 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 214 TYR 0.017 0.001 TYR A1067 PHE 0.015 0.001 PHE B 565 TRP 0.024 0.001 TRP A 64 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00242 (30159) covalent geometry : angle 0.53279 (40998) SS BOND : bond 0.00242 ( 44) SS BOND : angle 1.08191 ( 88) hydrogen bonds : bond 0.03600 ( 1067) hydrogen bonds : angle 5.50421 ( 2976) Misc. bond : bond 0.00072 ( 2) link_ALPHA1-4 : bond 0.01670 ( 6) link_ALPHA1-4 : angle 3.40127 ( 18) link_BETA1-4 : bond 0.00412 ( 26) link_BETA1-4 : angle 1.16959 ( 78) link_BETA1-6 : bond 0.01382 ( 3) link_BETA1-6 : angle 1.67298 ( 9) link_NAG-ASN : bond 0.00318 ( 39) link_NAG-ASN : angle 1.97362 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8570 (mt) REVERT: A 49 HIS cc_start: 0.8399 (t-170) cc_final: 0.8163 (t-170) REVERT: A 140 PHE cc_start: 0.6091 (p90) cc_final: 0.5794 (p90) REVERT: A 271 GLN cc_start: 0.8055 (pm20) cc_final: 0.7696 (pm20) REVERT: A 338 PHE cc_start: 0.8440 (m-10) cc_final: 0.8103 (m-80) REVERT: A 392 PHE cc_start: 0.7546 (m-80) cc_final: 0.7084 (m-80) REVERT: A 509 ARG cc_start: 0.6932 (mtt90) cc_final: 0.6670 (mtt-85) REVERT: A 515 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.6352 (p90) REVERT: A 935 GLN cc_start: 0.8699 (pp30) cc_final: 0.8436 (tm-30) REVERT: B 237 ARG cc_start: 0.8014 (ttp-170) cc_final: 0.7539 (mtp85) REVERT: B 568 ASP cc_start: 0.7575 (t0) cc_final: 0.7197 (t0) REVERT: B 990 GLU cc_start: 0.8180 (tt0) cc_final: 0.7964 (mm-30) REVERT: C 118 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7442 (tp) REVERT: C 195 LYS cc_start: 0.6975 (mtmt) cc_final: 0.6479 (mtpp) REVERT: C 537 LYS cc_start: 0.8513 (mmpt) cc_final: 0.8215 (mtmm) REVERT: D 74 LYS cc_start: 0.4911 (ptmm) cc_final: 0.4216 (ttpp) outliers start: 34 outliers final: 25 residues processed: 248 average time/residue: 0.1743 time to fit residues: 72.3495 Evaluate side-chains 240 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 129 optimal weight: 7.9990 chunk 271 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 302 optimal weight: 0.9990 chunk 279 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 357 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN A1010 GLN B 607 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 774 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.203428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130537 restraints weight = 41738.390| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.25 r_work: 0.3290 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 30279 Z= 0.223 Angle : 0.620 11.595 41308 Z= 0.302 Chirality : 0.045 0.265 4868 Planarity : 0.004 0.047 5185 Dihedral : 7.452 107.309 5771 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.69 % Rotamer: Outliers : 1.34 % Allowed : 14.01 % Favored : 84.65 % 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: -0.45 (0.14), residues: 3576 helix: 1.82 (0.19), residues: 742 sheet: -0.12 (0.18), residues: 778 loop : -1.21 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.019 0.001 TYR B1067 PHE 0.016 0.002 PHE C1148 TRP 0.019 0.001 TRP A 64 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00537 (30159) covalent geometry : angle 0.60002 (40998) SS BOND : bond 0.00387 ( 44) SS BOND : angle 1.33371 ( 88) hydrogen bonds : bond 0.04297 ( 1067) hydrogen bonds : angle 5.66718 ( 2976) Misc. bond : bond 0.00185 ( 2) link_ALPHA1-4 : bond 0.01579 ( 6) link_ALPHA1-4 : angle 3.56910 ( 18) link_BETA1-4 : bond 0.00319 ( 26) link_BETA1-4 : angle 1.34619 ( 78) link_BETA1-6 : bond 0.01286 ( 3) link_BETA1-6 : angle 1.67975 ( 9) link_NAG-ASN : bond 0.00380 ( 39) link_NAG-ASN : angle 2.16414 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8630 (mt) REVERT: A 140 PHE cc_start: 0.6044 (p90) cc_final: 0.5771 (p90) REVERT: A 271 GLN cc_start: 0.8061 (pm20) cc_final: 0.7696 (pm20) REVERT: A 392 PHE cc_start: 0.7661 (m-80) cc_final: 0.7182 (m-80) REVERT: A 509 ARG cc_start: 0.6905 (mtt90) cc_final: 0.6528 (mtt-85) REVERT: A 515 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.6419 (p90) REVERT: A 935 GLN cc_start: 0.8724 (pp30) cc_final: 0.8455 (tm-30) REVERT: B 237 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7466 (mtp85) REVERT: B 568 ASP cc_start: 0.7721 (t0) cc_final: 0.7321 (t0) REVERT: B 990 GLU cc_start: 0.8245 (tt0) cc_final: 0.8016 (mm-30) REVERT: C 118 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7481 (tp) REVERT: C 537 LYS cc_start: 0.8538 (mmpt) cc_final: 0.8220 (mtmm) REVERT: D 74 LYS cc_start: 0.4918 (ptmm) cc_final: 0.4161 (ttpp) outliers start: 42 outliers final: 32 residues processed: 245 average time/residue: 0.1701 time to fit residues: 69.9085 Evaluate side-chains 240 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 233 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 295 optimal weight: 6.9990 chunk 350 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 259 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.203566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132948 restraints weight = 41456.996| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.16 r_work: 0.3334 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 30279 Z= 0.203 Angle : 0.609 11.180 41308 Z= 0.297 Chirality : 0.045 0.262 4868 Planarity : 0.004 0.049 5185 Dihedral : 7.444 107.122 5771 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 1.53 % Allowed : 14.20 % Favored : 84.27 % 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: -0.49 (0.14), residues: 3576 helix: 1.81 (0.19), residues: 742 sheet: -0.16 (0.18), residues: 776 loop : -1.24 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.018 0.001 TYR B1067 PHE 0.015 0.001 PHE B 565 TRP 0.014 0.001 TRP A 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00487 (30159) covalent geometry : angle 0.58842 (40998) SS BOND : bond 0.00399 ( 44) SS BOND : angle 1.62094 ( 88) hydrogen bonds : bond 0.04174 ( 1067) hydrogen bonds : angle 5.64215 ( 2976) Misc. bond : bond 0.00164 ( 2) link_ALPHA1-4 : bond 0.01547 ( 6) link_ALPHA1-4 : angle 3.50528 ( 18) link_BETA1-4 : bond 0.00340 ( 26) link_BETA1-4 : angle 1.31011 ( 78) link_BETA1-6 : bond 0.01265 ( 3) link_BETA1-6 : angle 1.71706 ( 9) link_NAG-ASN : bond 0.00350 ( 39) link_NAG-ASN : angle 2.13474 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8672 (mt) REVERT: A 140 PHE cc_start: 0.6011 (p90) cc_final: 0.5730 (p90) REVERT: A 271 GLN cc_start: 0.8130 (pm20) cc_final: 0.7780 (pm20) REVERT: A 324 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: A 338 PHE cc_start: 0.8476 (m-10) cc_final: 0.8176 (m-80) REVERT: A 392 PHE cc_start: 0.7688 (m-80) cc_final: 0.7225 (m-80) REVERT: A 509 ARG cc_start: 0.6933 (mtt90) cc_final: 0.6556 (mtt-85) REVERT: A 515 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.6369 (p90) REVERT: A 935 GLN cc_start: 0.8772 (pp30) cc_final: 0.8510 (tm-30) REVERT: B 237 ARG cc_start: 0.8194 (ttp-170) cc_final: 0.7641 (mtp85) REVERT: B 568 ASP cc_start: 0.7829 (t0) cc_final: 0.7444 (t0) REVERT: B 726 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8799 (mp) REVERT: B 990 GLU cc_start: 0.8417 (tt0) cc_final: 0.8092 (mm-30) REVERT: C 118 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7532 (tp) REVERT: C 537 LYS cc_start: 0.8587 (mmpt) cc_final: 0.8297 (mtmm) REVERT: C 1010 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: D 74 LYS cc_start: 0.4915 (ptmm) cc_final: 0.4136 (ttpp) outliers start: 48 outliers final: 35 residues processed: 248 average time/residue: 0.1697 time to fit residues: 71.1837 Evaluate side-chains 243 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 45 optimal weight: 0.0370 chunk 201 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 181 optimal weight: 0.1980 chunk 168 optimal weight: 0.5980 chunk 195 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 337 optimal weight: 20.0000 chunk 304 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 914 ASN C 360 ASN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.206447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136201 restraints weight = 41300.152| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.15 r_work: 0.3384 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30279 Z= 0.105 Angle : 0.558 11.224 41308 Z= 0.270 Chirality : 0.043 0.274 4868 Planarity : 0.003 0.050 5185 Dihedral : 7.019 106.375 5771 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 1.08 % Allowed : 14.62 % Favored : 84.30 % 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: -0.32 (0.14), residues: 3576 helix: 2.08 (0.19), residues: 743 sheet: -0.19 (0.18), residues: 766 loop : -1.12 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.017 0.001 TYR A1067 PHE 0.021 0.001 PHE B 643 TRP 0.013 0.001 TRP A 436 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00230 (30159) covalent geometry : angle 0.53921 (40998) SS BOND : bond 0.00264 ( 44) SS BOND : angle 1.23980 ( 88) hydrogen bonds : bond 0.03532 ( 1067) hydrogen bonds : angle 5.41741 ( 2976) Misc. bond : bond 0.00193 ( 2) link_ALPHA1-4 : bond 0.01651 ( 6) link_ALPHA1-4 : angle 3.34607 ( 18) link_BETA1-4 : bond 0.00450 ( 26) link_BETA1-4 : angle 1.17725 ( 78) link_BETA1-6 : bond 0.01338 ( 3) link_BETA1-6 : angle 1.76695 ( 9) link_NAG-ASN : bond 0.00320 ( 39) link_NAG-ASN : angle 1.96417 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7152 Ramachandran restraints generated. 3576 Oldfield, 0 Emsley, 3576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8631 (mt) REVERT: A 49 HIS cc_start: 0.8485 (t-170) cc_final: 0.8240 (t-170) REVERT: A 140 PHE cc_start: 0.5953 (p90) cc_final: 0.5663 (p90) REVERT: A 271 GLN cc_start: 0.8113 (pm20) cc_final: 0.7763 (pm20) REVERT: A 338 PHE cc_start: 0.8458 (m-10) cc_final: 0.8147 (m-80) REVERT: A 392 PHE cc_start: 0.7626 (m-80) cc_final: 0.7155 (m-80) REVERT: A 509 ARG cc_start: 0.6962 (mtt90) cc_final: 0.6724 (mtt-85) REVERT: A 515 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.6323 (p90) REVERT: A 935 GLN cc_start: 0.8766 (pp30) cc_final: 0.8514 (tm-30) REVERT: B 237 ARG cc_start: 0.8159 (ttp-170) cc_final: 0.7695 (mtp85) REVERT: B 239 GLN cc_start: 0.7954 (tt0) cc_final: 0.7570 (mt0) REVERT: B 568 ASP cc_start: 0.7701 (t0) cc_final: 0.7334 (t0) REVERT: B 675 GLN cc_start: 0.6968 (tm-30) cc_final: 0.6730 (tm-30) REVERT: B 990 GLU cc_start: 0.8348 (tt0) cc_final: 0.8038 (mm-30) REVERT: C 118 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7472 (tp) REVERT: C 195 LYS cc_start: 0.7239 (mtmt) cc_final: 0.6779 (mtmt) REVERT: C 269 TYR cc_start: 0.7318 (m-80) cc_final: 0.6655 (m-80) REVERT: C 537 LYS cc_start: 0.8580 (mmpt) cc_final: 0.8303 (mtmm) REVERT: D 74 LYS cc_start: 0.4899 (ptmm) cc_final: 0.4191 (ttpp) outliers start: 34 outliers final: 28 residues processed: 247 average time/residue: 0.1775 time to fit residues: 73.9066 Evaluate side-chains 244 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain F residue 95 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 80 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 210 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 chunk 341 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 239 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN C 360 ASN C1010 GLN E 95 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.205919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135236 restraints weight = 41641.716| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.11 r_work: 0.3379 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30279 Z= 0.124 Angle : 0.558 10.835 41308 Z= 0.270 Chirality : 0.043 0.267 4868 Planarity : 0.003 0.049 5185 Dihedral : 6.839 106.190 5771 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 1.31 % Allowed : 14.87 % Favored : 83.82 % 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: -0.31 (0.14), residues: 3576 helix: 2.10 (0.19), residues: 744 sheet: -0.20 (0.18), residues: 780 loop : -1.12 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.017 0.001 TYR B1067 PHE 0.015 0.001 PHE C 106 TRP 0.014 0.001 TRP B 104 HIS 0.003 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00288 (30159) covalent geometry : angle 0.53935 (40998) SS BOND : bond 0.00298 ( 44) SS BOND : angle 1.27814 ( 88) hydrogen bonds : bond 0.03613 ( 1067) hydrogen bonds : angle 5.36970 ( 2976) Misc. bond : bond 0.00282 ( 2) link_ALPHA1-4 : bond 0.01633 ( 6) link_ALPHA1-4 : angle 3.42590 ( 18) link_BETA1-4 : bond 0.00378 ( 26) link_BETA1-4 : angle 1.15655 ( 78) link_BETA1-6 : bond 0.01351 ( 3) link_BETA1-6 : angle 1.78870 ( 9) link_NAG-ASN : bond 0.00297 ( 39) link_NAG-ASN : angle 1.98030 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11088.82 seconds wall clock time: 189 minutes 21.65 seconds (11361.65 seconds total)