Starting phenix.real_space_refine on Mon Sep 14 00:07:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ybk_33724/09_2026/7ybk_33724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybk_33724/09_2026/7ybk_33724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ybk_33724/09_2026/7ybk_33724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybk_33724/09_2026/7ybk_33724.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ybk_33724/09_2026/7ybk_33724.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ybk_33724/09_2026/7ybk_33724.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ybk_33724/09_2026/7ybk_33724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybk_33724/09_2026/7ybk_33724.map" } resolution = 3.9 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= 0.003 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 114 5.16 5 C 16823 2.51 5 N 4291 2.21 5 O 5263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26491 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8411 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1021} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8431 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 52, 'TRANS': 1024} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8405 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1021} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.98, per 1000 atoms: 0.23 Number of scatterers: 26491 At special positions: 0 Unit cell: (155.15, 153.01, 218.28, 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 114 16.00 O 5263 8.00 N 4291 7.00 C 16823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.04 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=2.03 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=2.03 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 291 " - pdb=" SG CYS B 301 " 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=2.04 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=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 282 " " NAG A1407 " - " ASN A 603 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG A1410 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 911.8 milliseconds 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6040 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 50 sheets defined 26.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.898A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.959A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.022A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.522A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.684A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.527A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.699A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.501A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.604A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.985A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.867A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.648A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.909A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.632A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.510A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.010A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A1160 " --> pdb=" O PHE A1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.462A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.963A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.631A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.557A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.773A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.586A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.833A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.045A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.595A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.633A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (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 982 removed outlier: 3.547A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 3.686A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.917A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 405 through 411 removed outlier: 5.074A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 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 removed outlier: 3.541A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.701A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.556A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.061A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.600A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.524A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.557A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.772A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C1001 " --> pdb=" O ILE C 997 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 4.101A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.234A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.035A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 removed outlier: 3.756A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 removed outlier: 6.891A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.513A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 651 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.662A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.595A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 5.995A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.577A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.351A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.718A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.763A pdb=" N ILE A 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.386A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.801A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.801A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.643A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.546A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 142 through 143 removed outlier: 5.893A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.272A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.826A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.726A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.868A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.755A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.919A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.568A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.568A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 6.018A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.659A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.626A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.713A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 142 through 143 removed outlier: 6.604A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.476A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.451A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.661A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.750A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.516A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 642 through 645 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.624A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 5.289A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.537A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 897 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.76 Time building geometry restraints manager: 3.11 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: 8292 1.34 - 1.46: 6792 1.46 - 1.59: 11842 1.59 - 1.71: 3 1.71 - 1.83: 144 Bond restraints: 27073 Sorted by residual: bond pdb=" C VAL A 991 " pdb=" N GLN A 992 " ideal model delta sigma weight residual 1.334 1.471 -0.136 1.27e-02 6.20e+03 1.15e+02 bond pdb=" CG PRO C 322 " pdb=" CD PRO C 322 " ideal model delta sigma weight residual 1.503 1.256 0.247 3.40e-02 8.65e+02 5.26e+01 bond pdb=" CG PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.56e+01 bond pdb=" C LEU A 977 " pdb=" N ASN A 978 " ideal model delta sigma weight residual 1.334 1.432 -0.098 1.49e-02 4.50e+03 4.35e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.456 1.504 -0.048 1.23e-02 6.61e+03 1.55e+01 ... (remaining 27068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 36545 3.05 - 6.09: 237 6.09 - 9.14: 22 9.14 - 12.19: 6 12.19 - 15.24: 4 Bond angle restraints: 36814 Sorted by residual: angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 96.76 15.24 1.40e+00 5.10e-01 1.18e+02 angle pdb=" CA PRO C 322 " pdb=" N PRO C 322 " pdb=" CD PRO C 322 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.21e+01 angle pdb=" N PRO A 330 " pdb=" CD PRO A 330 " pdb=" CG PRO A 330 " ideal model delta sigma weight residual 103.20 88.83 14.37 1.50e+00 4.44e-01 9.18e+01 angle pdb=" N PRO C 322 " pdb=" CD PRO C 322 " pdb=" CG PRO C 322 " ideal model delta sigma weight residual 103.20 89.55 13.65 1.50e+00 4.44e-01 8.28e+01 angle pdb=" O LEU A 977 " pdb=" C LEU A 977 " pdb=" N ASN A 978 " ideal model delta sigma weight residual 122.39 111.73 10.66 1.30e+00 5.92e-01 6.72e+01 ... (remaining 36809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14080 17.96 - 35.91: 1041 35.91 - 53.87: 208 53.87 - 71.83: 50 71.83 - 89.78: 31 Dihedral angle restraints: 15410 sinusoidal: 6019 harmonic: 9391 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -174.61 88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 -178.40 -88.60 1 1.00e+01 1.00e-02 9.37e+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 93.00 169.40 -76.40 1 1.00e+01 1.00e-02 7.34e+01 ... (remaining 15407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4298 0.112 - 0.224: 104 0.224 - 0.336: 10 0.336 - 0.448: 1 0.448 - 0.560: 3 Chirality restraints: 4416 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 4413 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 801 " -0.001 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" CG ASN B 801 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 801 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN B 801 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 321 " 0.080 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO C 322 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C1078 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO C1079 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C1079 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C1079 " 0.057 5.00e-02 4.00e+02 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 513 2.66 - 3.22: 25266 3.22 - 3.78: 38787 3.78 - 4.34: 51894 4.34 - 4.90: 83903 Nonbonded interactions: 200363 Sorted by model distance: nonbonded pdb=" O ASP C 290 " pdb=" OG SER C 297 " model vdw 2.106 3.040 nonbonded pdb=" OH TYR B 396 " pdb=" OH TYR C 200 " model vdw 2.113 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.181 3.040 nonbonded pdb=" O ASN A 99 " pdb=" NH1 ARG A 102 " model vdw 2.183 3.120 nonbonded pdb=" OG1 THR A 912 " pdb=" OD1 ASN A 914 " model vdw 2.184 3.040 ... (remaining 200358 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 826 or resid 855 through 1407)) selection = (chain 'B' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1407)) selection = (chain 'C' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1407)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 26.120 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 0.005 0.247 27204 Z= 0.244 Angle : 0.816 19.568 37165 Z= 0.427 Chirality : 0.050 0.560 4416 Planarity : 0.005 0.110 4640 Dihedral : 13.620 89.781 9244 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 0.32 % Allowed : 0.53 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3189 helix: -0.10 (0.20), residues: 661 sheet: -0.65 (0.21), residues: 559 loop : -1.49 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 457 TYR 0.017 0.001 TYR A 145 PHE 0.034 0.001 PHE B 135 TRP 0.027 0.002 TRP C 436 HIS 0.011 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.24 (27073) covalent geometry : angle 0.75262 / 0.41 (36814) SS BOND : bond 0.00290 / 0.14 ( 42) SS BOND : angle 1.17799 / 0.80 ( 84) hydrogen bonds : bond 0.30171 / 19.84 ( 865) hydrogen bonds : angle 9.83884 / 6.74 ( 2448) link_ALPHA1-4 : bond 0.00442 / 0.21 ( 6) link_ALPHA1-4 : angle 1.75582 / 1.07 ( 18) link_BETA1-4 : bond 0.00521 / 0.29 ( 28) link_BETA1-4 : angle 1.49025 / 0.96 ( 84) link_BETA1-6 : bond 0.00485 / 0.24 ( 3) link_BETA1-6 : angle 1.58418 / 0.98 ( 9) link_NAG-ASN : bond 0.01293 / 0.92 ( 52) link_NAG-ASN : angle 4.76086 / 3.23 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 340 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.1291 (tpt) cc_final: -0.1712 (tpt) REVERT: A 461 LEU cc_start: 0.4209 (pp) cc_final: 0.3633 (mm) REVERT: A 508 TYR cc_start: 0.5571 (m-80) cc_final: 0.5242 (m-80) REVERT: B 258 TRP cc_start: -0.2661 (t60) cc_final: -0.3010 (t60) REVERT: B 663 ASP cc_start: 0.7290 (m-30) cc_final: 0.7032 (m-30) REVERT: C 99 ASN cc_start: 0.4809 (m-40) cc_final: 0.4151 (m110) REVERT: C 266 TYR cc_start: 0.5016 (m-80) cc_final: 0.4213 (m-80) REVERT: C 369 TYR cc_start: 0.5954 (t80) cc_final: 0.5683 (t80) REVERT: C 420 ASP cc_start: 0.5475 (t0) cc_final: 0.5086 (t70) REVERT: C 1115 ILE cc_start: 0.4105 (mm) cc_final: 0.3833 (mm) outliers start: 9 outliers final: 2 residues processed: 348 average time/residue: 0.1676 time to fit residues: 94.0050 Evaluate side-chains 193 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 207 HIS A 644 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 448 ASN C 481 ASN C 606 ASN C 675 GLN C 804 GLN C 935 GLN C 955 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.157008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120046 restraints weight = 63991.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118128 restraints weight = 47149.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118369 restraints weight = 58177.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119161 restraints weight = 38194.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121019 restraints weight = 32058.772| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 27204 Z= 0.311 Angle : 0.901 16.752 37165 Z= 0.447 Chirality : 0.056 1.135 4416 Planarity : 0.006 0.060 4640 Dihedral : 5.729 47.264 3460 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 1.95 % Allowed : 10.22 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.14), residues: 3189 helix: -0.25 (0.18), residues: 720 sheet: -0.65 (0.20), residues: 622 loop : -1.84 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.039 0.003 TYR B1067 PHE 0.038 0.003 PHE A1089 TRP 0.030 0.003 TRP C 436 HIS 0.010 0.002 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.31 (27073) covalent geometry : angle 0.85082 / 0.44 (36814) SS BOND : bond 0.00610 / 0.41 ( 42) SS BOND : angle 1.61684 / 1.12 ( 84) hydrogen bonds : bond 0.07039 / 4.67 ( 865) hydrogen bonds : angle 7.00533 / 4.78 ( 2448) link_ALPHA1-4 : bond 0.00588 / 0.32 ( 6) link_ALPHA1-4 : angle 1.98408 / 1.25 ( 18) link_BETA1-4 : bond 0.00519 / 0.37 ( 28) link_BETA1-4 : angle 1.70485 / 1.12 ( 84) link_BETA1-6 : bond 0.00214 / 0.11 ( 3) link_BETA1-6 : angle 1.86088 / 1.21 ( 9) link_NAG-ASN : bond 0.00958 / 0.68 ( 52) link_NAG-ASN : angle 4.33058 / 2.84 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 224 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5462 (m-90) cc_final: 0.4948 (m-90) REVERT: A 177 MET cc_start: -0.2319 (tpt) cc_final: -0.2606 (tpt) REVERT: A 329 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6632 (m-10) REVERT: A 1030 SER cc_start: 0.9242 (OUTLIER) cc_final: 0.8911 (t) REVERT: B 216 LEU cc_start: 0.8780 (mt) cc_final: 0.8537 (mp) REVERT: B 228 ASP cc_start: 0.7821 (m-30) cc_final: 0.7166 (t70) REVERT: B 258 TRP cc_start: -0.2468 (t60) cc_final: -0.3235 (t60) REVERT: B 663 ASP cc_start: 0.7638 (m-30) cc_final: 0.7351 (m-30) REVERT: B 901 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7828 (tp40) REVERT: C 177 MET cc_start: -0.4440 (ttt) cc_final: -0.5239 (ttt) REVERT: C 1105 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8405 (p) outliers start: 55 outliers final: 30 residues processed: 267 average time/residue: 0.1605 time to fit residues: 70.2902 Evaluate side-chains 205 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 199 optimal weight: 0.5980 chunk 43 optimal weight: 20.0000 chunk 219 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 192 optimal weight: 0.3980 chunk 309 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 281 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 564 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 474 GLN C 606 ASN C 920 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.160203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.123441 restraints weight = 63641.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120215 restraints weight = 45017.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121377 restraints weight = 49963.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121344 restraints weight = 39211.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122052 restraints weight = 33161.550| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27204 Z= 0.138 Angle : 0.683 16.264 37165 Z= 0.332 Chirality : 0.047 0.499 4416 Planarity : 0.004 0.052 4640 Dihedral : 5.008 31.008 3458 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 1.92 % Allowed : 13.35 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3189 helix: 0.43 (0.19), residues: 724 sheet: -0.36 (0.20), residues: 632 loop : -1.72 (0.13), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.019 0.001 TYR C 396 PHE 0.023 0.001 PHE A 392 TRP 0.021 0.001 TRP B 353 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (27073) covalent geometry : angle 0.62765 / 0.32 (36814) SS BOND : bond 0.00372 / 0.20 ( 42) SS BOND : angle 1.82357 / 1.15 ( 84) hydrogen bonds : bond 0.06035 / 3.98 ( 865) hydrogen bonds : angle 6.24609 / 4.26 ( 2448) link_ALPHA1-4 : bond 0.00520 / 0.26 ( 6) link_ALPHA1-4 : angle 1.28764 / 0.82 ( 18) link_BETA1-4 : bond 0.00502 / 0.29 ( 28) link_BETA1-4 : angle 1.25853 / 0.81 ( 84) link_BETA1-6 : bond 0.00408 / 0.21 ( 3) link_BETA1-6 : angle 1.37762 / 0.88 ( 9) link_NAG-ASN : bond 0.00833 / 0.54 ( 52) link_NAG-ASN : angle 3.88174 / 2.58 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5257 (m-90) cc_final: 0.4636 (m-90) REVERT: A 189 LEU cc_start: 0.6793 (mt) cc_final: 0.6586 (mt) REVERT: A 329 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.6266 (m-10) REVERT: A 351 TYR cc_start: 0.7060 (p90) cc_final: 0.6272 (t80) REVERT: A 1030 SER cc_start: 0.9039 (p) cc_final: 0.8792 (t) REVERT: B 216 LEU cc_start: 0.8668 (mt) cc_final: 0.8441 (mp) REVERT: B 228 ASP cc_start: 0.7820 (m-30) cc_final: 0.7215 (t70) REVERT: B 237 ARG cc_start: 0.5939 (ptt90) cc_final: 0.5648 (ptt-90) REVERT: B 258 TRP cc_start: -0.2677 (t60) cc_final: -0.3406 (t60) REVERT: B 663 ASP cc_start: 0.7666 (m-30) cc_final: 0.7389 (m-30) REVERT: B 990 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: C 266 TYR cc_start: 0.6450 (m-80) cc_final: 0.5895 (m-80) REVERT: C 392 PHE cc_start: 0.8247 (m-80) cc_final: 0.7995 (m-80) REVERT: C 926 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: C 1105 THR cc_start: 0.8721 (p) cc_final: 0.8437 (p) outliers start: 54 outliers final: 24 residues processed: 244 average time/residue: 0.1496 time to fit residues: 61.2867 Evaluate side-chains 193 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 297 optimal weight: 4.9990 chunk 314 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 252 optimal weight: 0.3980 chunk 316 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 305 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1036 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.160737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.123775 restraints weight = 63116.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.121237 restraints weight = 44024.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122315 restraints weight = 49062.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122511 restraints weight = 35374.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.123267 restraints weight = 30860.429| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27204 Z= 0.118 Angle : 0.649 15.568 37165 Z= 0.311 Chirality : 0.046 0.486 4416 Planarity : 0.004 0.047 4640 Dihedral : 4.728 29.982 3458 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 1.85 % Allowed : 14.45 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 3189 helix: 0.71 (0.19), residues: 730 sheet: -0.25 (0.20), residues: 644 loop : -1.66 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1107 TYR 0.026 0.001 TYR A1047 PHE 0.032 0.001 PHE C 201 TRP 0.017 0.001 TRP B 436 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (27073) covalent geometry : angle 0.58759 / 0.30 (36814) SS BOND : bond 0.00273 / 0.17 ( 42) SS BOND : angle 1.68479 / 1.09 ( 84) hydrogen bonds : bond 0.05146 / 3.40 ( 865) hydrogen bonds : angle 5.78934 / 3.95 ( 2448) link_ALPHA1-4 : bond 0.00456 / 0.22 ( 6) link_ALPHA1-4 : angle 1.31625 / 0.84 ( 18) link_BETA1-4 : bond 0.00337 / 0.23 ( 28) link_BETA1-4 : angle 1.18983 / 0.77 ( 84) link_BETA1-6 : bond 0.00369 / 0.19 ( 3) link_BETA1-6 : angle 1.29750 / 0.84 ( 9) link_NAG-ASN : bond 0.00659 / 0.41 ( 52) link_NAG-ASN : angle 4.04673 / 2.76 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.7918 (p0) cc_final: 0.7563 (m-30) REVERT: A 189 LEU cc_start: 0.6826 (mt) cc_final: 0.6621 (mt) REVERT: A 237 ARG cc_start: 0.7094 (ptt90) cc_final: 0.6782 (ptt90) REVERT: A 351 TYR cc_start: 0.6842 (p90) cc_final: 0.6340 (t80) REVERT: A 904 TYR cc_start: 0.7403 (m-80) cc_final: 0.7124 (m-10) REVERT: B 216 LEU cc_start: 0.8611 (mt) cc_final: 0.8268 (mp) REVERT: B 228 ASP cc_start: 0.7859 (m-30) cc_final: 0.7409 (t70) REVERT: B 258 TRP cc_start: -0.2831 (t60) cc_final: -0.3528 (t60) REVERT: B 365 TYR cc_start: 0.7825 (m-80) cc_final: 0.6790 (m-80) REVERT: B 512 VAL cc_start: 0.7781 (t) cc_final: 0.7517 (t) REVERT: B 663 ASP cc_start: 0.7621 (m-30) cc_final: 0.7353 (m-30) REVERT: C 41 LYS cc_start: 0.7660 (tptm) cc_final: 0.7341 (tptp) REVERT: C 225 PRO cc_start: 0.6846 (Cg_exo) cc_final: 0.6173 (Cg_endo) REVERT: C 266 TYR cc_start: 0.6388 (m-80) cc_final: 0.5817 (m-80) REVERT: C 392 PHE cc_start: 0.8212 (m-80) cc_final: 0.7881 (m-80) REVERT: C 1105 THR cc_start: 0.8709 (p) cc_final: 0.8398 (p) outliers start: 52 outliers final: 31 residues processed: 239 average time/residue: 0.1549 time to fit residues: 62.0115 Evaluate side-chains 193 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 208 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 180 optimal weight: 0.0050 chunk 166 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 270 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.161226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.123882 restraints weight = 63447.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121815 restraints weight = 45010.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123189 restraints weight = 45692.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.123167 restraints weight = 34137.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123813 restraints weight = 30341.978| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27204 Z= 0.113 Angle : 0.620 15.879 37165 Z= 0.297 Chirality : 0.045 0.471 4416 Planarity : 0.004 0.046 4640 Dihedral : 4.528 30.543 3458 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 1.95 % Allowed : 15.58 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3189 helix: 1.00 (0.20), residues: 728 sheet: -0.21 (0.20), residues: 652 loop : -1.56 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.017 0.001 TYR B 91 PHE 0.024 0.001 PHE A 377 TRP 0.017 0.001 TRP B 436 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (27073) covalent geometry : angle 0.55902 / 0.28 (36814) SS BOND : bond 0.00251 / 0.15 ( 42) SS BOND : angle 1.54712 / 0.98 ( 84) hydrogen bonds : bond 0.04769 / 3.14 ( 865) hydrogen bonds : angle 5.51026 / 3.75 ( 2448) link_ALPHA1-4 : bond 0.00486 / 0.24 ( 6) link_ALPHA1-4 : angle 1.34580 / 0.84 ( 18) link_BETA1-4 : bond 0.00375 / 0.25 ( 28) link_BETA1-4 : angle 1.07317 / 0.69 ( 84) link_BETA1-6 : bond 0.00410 / 0.21 ( 3) link_BETA1-6 : angle 1.31929 / 0.83 ( 9) link_NAG-ASN : bond 0.00700 / 0.41 ( 52) link_NAG-ASN : angle 3.94560 / 2.62 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.7759 (p0) cc_final: 0.7517 (m-30) REVERT: A 237 ARG cc_start: 0.7162 (ptt90) cc_final: 0.6835 (ptt90) REVERT: A 351 TYR cc_start: 0.6679 (p90) cc_final: 0.6376 (t80) REVERT: A 904 TYR cc_start: 0.7414 (m-80) cc_final: 0.7120 (m-10) REVERT: B 216 LEU cc_start: 0.8585 (mt) cc_final: 0.8258 (mp) REVERT: B 228 ASP cc_start: 0.7840 (m-30) cc_final: 0.7471 (t70) REVERT: B 240 THR cc_start: 0.5569 (t) cc_final: 0.5206 (m) REVERT: B 258 TRP cc_start: -0.2827 (t60) cc_final: -0.3478 (t60) REVERT: B 365 TYR cc_start: 0.8035 (m-80) cc_final: 0.7134 (m-80) REVERT: B 512 VAL cc_start: 0.7738 (t) cc_final: 0.7377 (t) REVERT: B 663 ASP cc_start: 0.7640 (m-30) cc_final: 0.7394 (m-30) REVERT: B 725 GLU cc_start: 0.7778 (pt0) cc_final: 0.7564 (pt0) REVERT: C 41 LYS cc_start: 0.7561 (tptm) cc_final: 0.7091 (tptt) REVERT: C 225 PRO cc_start: 0.6508 (Cg_exo) cc_final: 0.6243 (Cg_endo) REVERT: C 266 TYR cc_start: 0.6464 (m-80) cc_final: 0.5882 (m-80) REVERT: C 354 ASN cc_start: 0.7348 (t0) cc_final: 0.7057 (t0) REVERT: C 552 LEU cc_start: 0.8400 (pt) cc_final: 0.8104 (pp) REVERT: C 1105 THR cc_start: 0.8672 (p) cc_final: 0.8398 (p) outliers start: 55 outliers final: 36 residues processed: 226 average time/residue: 0.1473 time to fit residues: 56.3293 Evaluate side-chains 194 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 46 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 239 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 360 ASN B 564 GLN C 498 GLN C 606 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.152180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113302 restraints weight = 62420.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110827 restraints weight = 46178.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111585 restraints weight = 48917.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112119 restraints weight = 34536.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112703 restraints weight = 31865.497| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 27204 Z= 0.248 Angle : 0.767 14.519 37165 Z= 0.375 Chirality : 0.049 0.494 4416 Planarity : 0.005 0.055 4640 Dihedral : 5.139 33.950 3458 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 3.02 % Allowed : 15.94 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3189 helix: 0.49 (0.19), residues: 724 sheet: -0.35 (0.20), residues: 612 loop : -1.76 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1107 TYR 0.027 0.002 TYR C 873 PHE 0.041 0.002 PHE A 392 TRP 0.023 0.002 TRP B 353 HIS 0.009 0.002 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (27073) covalent geometry : angle 0.71692 / 0.36 (36814) SS BOND : bond 0.00436 / 0.29 ( 42) SS BOND : angle 1.77154 / 1.19 ( 84) hydrogen bonds : bond 0.06512 / 4.31 ( 865) hydrogen bonds : angle 6.04032 / 4.12 ( 2448) link_ALPHA1-4 : bond 0.00419 / 0.21 ( 6) link_ALPHA1-4 : angle 1.66937 / 1.09 ( 18) link_BETA1-4 : bond 0.00375 / 0.25 ( 28) link_BETA1-4 : angle 1.41493 / 0.91 ( 84) link_BETA1-6 : bond 0.00184 / 0.09 ( 3) link_BETA1-6 : angle 1.61370 / 1.04 ( 9) link_NAG-ASN : bond 0.00665 / 0.42 ( 52) link_NAG-ASN : angle 3.95285 / 2.69 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 180 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7575 (ptt90) cc_final: 0.7105 (ptt90) REVERT: A 392 PHE cc_start: 0.6852 (m-80) cc_final: 0.6264 (m-10) REVERT: A 763 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8665 (mp) REVERT: B 127 VAL cc_start: 0.6439 (OUTLIER) cc_final: 0.6201 (m) REVERT: B 216 LEU cc_start: 0.8724 (mt) cc_final: 0.8523 (mp) REVERT: B 258 TRP cc_start: -0.2587 (t60) cc_final: -0.3664 (t60) REVERT: B 353 TRP cc_start: 0.6312 (p-90) cc_final: 0.5668 (p-90) REVERT: B 546 LEU cc_start: 0.8647 (tt) cc_final: 0.8427 (tt) REVERT: B 663 ASP cc_start: 0.7605 (m-30) cc_final: 0.7324 (m-30) REVERT: C 225 PRO cc_start: 0.6666 (Cg_exo) cc_final: 0.6282 (Cg_endo) REVERT: C 354 ASN cc_start: 0.7501 (t0) cc_final: 0.7048 (t0) REVERT: C 505 TYR cc_start: 0.6937 (m-80) cc_final: 0.6726 (m-80) outliers start: 85 outliers final: 63 residues processed: 249 average time/residue: 0.1525 time to fit residues: 63.7917 Evaluate side-chains 220 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 155 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 221 optimal weight: 10.0000 chunk 289 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 300 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN C 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.152057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113709 restraints weight = 61571.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110877 restraints weight = 48546.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111795 restraints weight = 47308.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112369 restraints weight = 34672.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.112984 restraints weight = 32183.174| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27204 Z= 0.172 Angle : 0.682 14.092 37165 Z= 0.331 Chirality : 0.047 0.469 4416 Planarity : 0.004 0.053 4640 Dihedral : 4.919 30.187 3456 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 2.73 % Allowed : 17.15 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3189 helix: 0.72 (0.19), residues: 734 sheet: -0.24 (0.20), residues: 612 loop : -1.81 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 190 TYR 0.023 0.002 TYR B 495 PHE 0.020 0.002 PHE A 392 TRP 0.015 0.001 TRP B 353 HIS 0.007 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (27073) covalent geometry : angle 0.63186 / 0.32 (36814) SS BOND : bond 0.00335 / 0.21 ( 42) SS BOND : angle 1.66619 / 1.09 ( 84) hydrogen bonds : bond 0.05627 / 3.71 ( 865) hydrogen bonds : angle 5.71924 / 3.88 ( 2448) link_ALPHA1-4 : bond 0.00454 / 0.21 ( 6) link_ALPHA1-4 : angle 1.38671 / 0.90 ( 18) link_BETA1-4 : bond 0.00353 / 0.26 ( 28) link_BETA1-4 : angle 1.18337 / 0.75 ( 84) link_BETA1-6 : bond 0.00257 / 0.13 ( 3) link_BETA1-6 : angle 1.48287 / 0.96 ( 9) link_NAG-ASN : bond 0.00639 / 0.38 ( 52) link_NAG-ASN : angle 3.72376 / 2.52 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 164 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6412 (m-80) cc_final: 0.6203 (m-10) REVERT: B 258 TRP cc_start: -0.2593 (t60) cc_final: -0.3650 (t60) REVERT: B 353 TRP cc_start: 0.6419 (p-90) cc_final: 0.5791 (p-90) REVERT: B 365 TYR cc_start: 0.7993 (m-80) cc_final: 0.5890 (m-80) REVERT: B 546 LEU cc_start: 0.8656 (tt) cc_final: 0.8435 (tt) REVERT: B 580 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7282 (mm-40) REVERT: B 663 ASP cc_start: 0.7607 (m-30) cc_final: 0.7311 (m-30) REVERT: B 767 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8761 (mt) REVERT: C 225 PRO cc_start: 0.6636 (Cg_exo) cc_final: 0.6338 (Cg_endo) REVERT: C 354 ASN cc_start: 0.7388 (t0) cc_final: 0.6974 (t0) REVERT: C 505 TYR cc_start: 0.7094 (m-80) cc_final: 0.6772 (m-80) REVERT: C 869 MET cc_start: 0.8679 (mtp) cc_final: 0.8445 (mtm) outliers start: 77 outliers final: 53 residues processed: 229 average time/residue: 0.1547 time to fit residues: 58.7570 Evaluate side-chains 206 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 30 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 119 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 606 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.153038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115312 restraints weight = 62524.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112145 restraints weight = 46237.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113084 restraints weight = 52775.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113172 restraints weight = 38297.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113369 restraints weight = 33184.881| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27204 Z= 0.134 Angle : 0.643 13.850 37165 Z= 0.311 Chirality : 0.046 0.455 4416 Planarity : 0.004 0.050 4640 Dihedral : 4.706 29.517 3456 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 2.77 % Allowed : 17.47 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3189 helix: 0.96 (0.20), residues: 728 sheet: -0.19 (0.20), residues: 621 loop : -1.69 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.018 0.001 TYR C1067 PHE 0.018 0.001 PHE A 400 TRP 0.041 0.002 TRP C 64 HIS 0.009 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (27073) covalent geometry : angle 0.59345 / 0.30 (36814) SS BOND : bond 0.00275 / 0.17 ( 42) SS BOND : angle 1.57308 / 1.03 ( 84) hydrogen bonds : bond 0.05168 / 3.40 ( 865) hydrogen bonds : angle 5.53322 / 3.75 ( 2448) link_ALPHA1-4 : bond 0.00437 / 0.21 ( 6) link_ALPHA1-4 : angle 1.39730 / 0.91 ( 18) link_BETA1-4 : bond 0.00358 / 0.26 ( 28) link_BETA1-4 : angle 1.09841 / 0.70 ( 84) link_BETA1-6 : bond 0.00328 / 0.17 ( 3) link_BETA1-6 : angle 1.39348 / 0.89 ( 9) link_NAG-ASN : bond 0.00624 / 0.37 ( 52) link_NAG-ASN : angle 3.59556 / 2.44 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 164 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 258 TRP cc_start: -0.2546 (t60) cc_final: -0.3664 (t60) REVERT: B 580 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7332 (mm-40) REVERT: B 663 ASP cc_start: 0.7637 (m-30) cc_final: 0.7354 (m-30) REVERT: B 973 ILE cc_start: 0.9014 (mm) cc_final: 0.8803 (mm) REVERT: C 225 PRO cc_start: 0.6642 (Cg_exo) cc_final: 0.6351 (Cg_endo) REVERT: C 298 GLU cc_start: 0.8493 (tp30) cc_final: 0.8285 (tp30) REVERT: C 354 ASN cc_start: 0.7504 (t0) cc_final: 0.7047 (t0) REVERT: C 505 TYR cc_start: 0.7131 (m-80) cc_final: 0.6915 (m-80) REVERT: C 965 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8497 (tm-30) outliers start: 78 outliers final: 61 residues processed: 232 average time/residue: 0.1462 time to fit residues: 57.3448 Evaluate side-chains 213 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 150 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 269 optimal weight: 6.9990 chunk 175 optimal weight: 0.0670 chunk 167 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 127 optimal weight: 50.0000 chunk 233 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.154335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.115731 restraints weight = 61749.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113260 restraints weight = 45328.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114084 restraints weight = 45239.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.114668 restraints weight = 33431.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115465 restraints weight = 30761.089| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27204 Z= 0.115 Angle : 0.628 13.396 37165 Z= 0.302 Chirality : 0.045 0.441 4416 Planarity : 0.004 0.095 4640 Dihedral : 4.574 37.618 3456 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 1.95 % Allowed : 18.35 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3189 helix: 1.17 (0.20), residues: 728 sheet: -0.17 (0.20), residues: 632 loop : -1.59 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.016 0.001 TYR C1067 PHE 0.031 0.001 PHE A 347 TRP 0.028 0.001 TRP C 64 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (27073) covalent geometry : angle 0.58221 / 0.29 (36814) SS BOND : bond 0.00241 / 0.14 ( 42) SS BOND : angle 1.46875 / 0.94 ( 84) hydrogen bonds : bond 0.04709 / 3.10 ( 865) hydrogen bonds : angle 5.32308 / 3.60 ( 2448) link_ALPHA1-4 : bond 0.00469 / 0.23 ( 6) link_ALPHA1-4 : angle 1.35229 / 0.87 ( 18) link_BETA1-4 : bond 0.00358 / 0.24 ( 28) link_BETA1-4 : angle 1.02643 / 0.65 ( 84) link_BETA1-6 : bond 0.00411 / 0.21 ( 3) link_BETA1-6 : angle 1.33238 / 0.84 ( 9) link_NAG-ASN : bond 0.00636 / 0.38 ( 52) link_NAG-ASN : angle 3.45879 / 2.34 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6381 (m-80) cc_final: 0.5922 (m-80) REVERT: A 1050 MET cc_start: 0.8645 (ptp) cc_final: 0.8319 (ptt) REVERT: B 258 TRP cc_start: -0.2635 (t60) cc_final: -0.3647 (t60) REVERT: B 663 ASP cc_start: 0.7599 (m-30) cc_final: 0.7326 (m-30) REVERT: B 725 GLU cc_start: 0.7764 (pt0) cc_final: 0.7493 (pt0) REVERT: B 973 ILE cc_start: 0.8945 (mm) cc_final: 0.8744 (mm) REVERT: B 1115 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7338 (mt) REVERT: C 354 ASN cc_start: 0.7520 (t0) cc_final: 0.7004 (t0) REVERT: C 552 LEU cc_start: 0.8278 (pt) cc_final: 0.7967 (pp) REVERT: C 965 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8561 (tm-30) REVERT: C 1130 ILE cc_start: 0.7131 (mp) cc_final: 0.6783 (pt) outliers start: 55 outliers final: 45 residues processed: 221 average time/residue: 0.1458 time to fit residues: 54.6571 Evaluate side-chains 199 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 208 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 306 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.154944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118360 restraints weight = 63026.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115731 restraints weight = 44946.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116836 restraints weight = 51993.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117150 restraints weight = 35591.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118053 restraints weight = 31964.922| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27204 Z= 0.150 Angle : 0.656 13.150 37165 Z= 0.317 Chirality : 0.046 0.446 4416 Planarity : 0.004 0.091 4640 Dihedral : 4.604 32.975 3456 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.67 % Rotamer: Outliers : 2.20 % Allowed : 18.42 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3189 helix: 1.15 (0.20), residues: 722 sheet: -0.22 (0.20), residues: 643 loop : -1.56 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 454 TYR 0.022 0.001 TYR C1067 PHE 0.026 0.002 PHE A 400 TRP 0.029 0.001 TRP C 64 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (27073) covalent geometry : angle 0.61142 / 0.31 (36814) SS BOND : bond 0.00307 / 0.18 ( 42) SS BOND : angle 1.62583 / 1.05 ( 84) hydrogen bonds : bond 0.05123 / 3.37 ( 865) hydrogen bonds : angle 5.39382 / 3.66 ( 2448) link_ALPHA1-4 : bond 0.00454 / 0.21 ( 6) link_ALPHA1-4 : angle 1.48038 / 0.96 ( 18) link_BETA1-4 : bond 0.00320 / 0.22 ( 28) link_BETA1-4 : angle 1.10105 / 0.71 ( 84) link_BETA1-6 : bond 0.00300 / 0.15 ( 3) link_BETA1-6 : angle 1.43274 / 0.92 ( 9) link_NAG-ASN : bond 0.00592 / 0.36 ( 52) link_NAG-ASN : angle 3.46314 / 2.35 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 158 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8022 (mt) cc_final: 0.7514 (mp) REVERT: A 1050 MET cc_start: 0.8807 (ptp) cc_final: 0.8499 (ptt) REVERT: A 1115 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8037 (mt) REVERT: B 203 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8263 (mt) REVERT: B 258 TRP cc_start: -0.2428 (t60) cc_final: -0.3509 (t60) REVERT: B 663 ASP cc_start: 0.7706 (m-30) cc_final: 0.7400 (m-30) REVERT: B 725 GLU cc_start: 0.7762 (pt0) cc_final: 0.7378 (pt0) REVERT: B 973 ILE cc_start: 0.8991 (mm) cc_final: 0.8780 (mm) REVERT: C 90 VAL cc_start: 0.8872 (t) cc_final: 0.8279 (m) REVERT: C 169 GLU cc_start: 0.8304 (mp0) cc_final: 0.7855 (tp30) REVERT: C 354 ASN cc_start: 0.7554 (t0) cc_final: 0.7046 (t0) REVERT: C 489 TYR cc_start: 0.7815 (m-10) cc_final: 0.7608 (m-80) REVERT: C 552 LEU cc_start: 0.8214 (pt) cc_final: 0.7914 (pp) REVERT: C 965 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8516 (tm-30) outliers start: 62 outliers final: 51 residues processed: 211 average time/residue: 0.1514 time to fit residues: 54.4050 Evaluate side-chains 205 residues out of total 2821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 986 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 210 optimal weight: 3.9990 chunk 127 optimal weight: 50.0000 chunk 189 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 272 optimal weight: 0.0050 chunk 136 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 253 optimal weight: 0.0870 chunk 244 optimal weight: 6.9990 overall best weight: 1.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 544 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.152721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114427 restraints weight = 61531.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.111838 restraints weight = 44683.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112575 restraints weight = 46777.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113456 restraints weight = 34226.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113577 restraints weight = 32196.189| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27204 Z= 0.124 Angle : 0.633 12.904 37165 Z= 0.305 Chirality : 0.045 0.441 4416 Planarity : 0.004 0.074 4640 Dihedral : 4.528 32.927 3456 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 1.95 % Allowed : 18.67 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3189 helix: 1.19 (0.20), residues: 731 sheet: -0.17 (0.20), residues: 640 loop : -1.53 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 454 TYR 0.018 0.001 TYR C1067 PHE 0.035 0.001 PHE A 400 TRP 0.023 0.001 TRP C 64 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (27073) covalent geometry : angle 0.58949 / 0.29 (36814) SS BOND : bond 0.00275 / 0.16 ( 42) SS BOND : angle 1.52485 / 0.97 ( 84) hydrogen bonds : bond 0.04804 / 3.17 ( 865) hydrogen bonds : angle 5.25945 / 3.57 ( 2448) link_ALPHA1-4 : bond 0.00466 / 0.23 ( 6) link_ALPHA1-4 : angle 1.39340 / 0.90 ( 18) link_BETA1-4 : bond 0.00344 / 0.24 ( 28) link_BETA1-4 : angle 1.02203 / 0.65 ( 84) link_BETA1-6 : bond 0.00372 / 0.19 ( 3) link_BETA1-6 : angle 1.36531 / 0.87 ( 9) link_NAG-ASN : bond 0.00604 / 0.36 ( 52) link_NAG-ASN : angle 3.36326 / 2.28 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.93 seconds wall clock time: 68 minutes 6.44 seconds (4086.44 seconds total)