Starting phenix.real_space_refine on Fri Mar 6 02:30:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7krr_23011/03_2026/7krr_23011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7krr_23011/03_2026/7krr_23011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7krr_23011/03_2026/7krr_23011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7krr_23011/03_2026/7krr_23011.map" model { file = "/net/cci-nas-00/data/ceres_data/7krr_23011/03_2026/7krr_23011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7krr_23011/03_2026/7krr_23011.cif" } resolution = 3.5 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= 0.001 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 118 5.16 5 C 17267 2.51 5 N 4402 2.21 5 O 5405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27192 Number of models: 1 Model: "" Number of chains: 35 Chain: "B" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8540 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 52, 'TRANS': 1038} Chain breaks: 5 Chain: "C" Number of atoms: 8687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8687 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 53, 'TRANS': 1056} Chain breaks: 4 Chain: "A" Number of atoms: 8665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 8665 Classifications: {'peptide': 1109} Link IDs: {'PTRANS': 52, 'TRANS': 1056} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.58, per 1000 atoms: 0.24 Number of scatterers: 27192 At special positions: 0 Unit cell: (149.325, 150.15, 217.8, 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 118 16.00 O 5405 8.00 N 4402 7.00 C 17267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.57 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=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.93 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.00 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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=2.94 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.00 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.94 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.01 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 A 840 " - pdb=" SG CYS A 851 " distance=2.06 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM26854 O5 NAG B1404 .*. O " rejected from bonding due to valence issues. Atom "HETATM26938 O5 NAG C1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM27064 O5 NAG A1402 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 234 " " NAG A1406 " - " ASN A 282 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 657 " " NAG A1410 " - " ASN A 709 " " NAG A1411 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG 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 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG E 1 " - " ASN B 122 " " NAG F 1 " - " ASN B 165 " " NAG G 1 " - " ASN B 282 " " NAG H 1 " - " ASN B 616 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 17 " " NAG O 1 " - " ASN C 122 " " NAG P 1 " - " ASN C 165 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 282 " " NAG S 1 " - " ASN C 616 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1074 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN A 17 " " NAG Z 1 " - " ASN A 331 " " NAG a 1 " - " ASN A 616 " " NAG b 1 " - " ASN A 717 " " NAG c 1 " - " ASN A 801 " " NAG d 1 " - " ASN A1074 " " NAG e 1 " - " ASN A1098 " " NAG f 1 " - " ASN A1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6198 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 51 sheets defined 27.3% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.800A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.663A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.849A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.506A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.114A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 852 through 856 removed outlier: 3.938A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 852 through 856' Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.539A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.590A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.530A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.552A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.182A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.849A 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 342 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.522A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.230A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.940A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.849A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.518A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.492A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.251A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.503A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.686A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.599A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.589A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.887A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.629A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.374A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.129A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.603A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.649A pdb=" N ILE A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 411' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 623 Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.929A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.137A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.745A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 removed outlier: 4.117A pdb=" N ALA A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 842 through 847' Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.571A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.522A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.790A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.543A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.798A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 988 through 1033 removed outlier: 3.893A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1161 removed outlier: 4.158A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.683A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 11.462A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.439A pdb=" N PHE B 43 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.554A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.516A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.481A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.337A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.725A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.970A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.256A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.034A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.988A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.199A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.754A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.659A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.113A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.428A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 787 through 790 removed outlier: 3.552A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.219A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.764A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.826A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.889A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.446A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 13.014A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.179A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.760A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.644A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 310 through 319 removed outlier: 4.436A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.041A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 354 through 358 removed outlier: 7.217A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.677A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.585A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.004A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 701 through 704 Processing sheet with id=AD5, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.038A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.044A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.273A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.489A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.235A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.235A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.625A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.188A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.177A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.704A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.082A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.082A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.759A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.156A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.036A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.528A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.408A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.408A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6604 1.33 - 1.46: 7015 1.46 - 1.59: 14023 1.59 - 1.72: 0 1.72 - 1.85: 148 Bond restraints: 27790 Sorted by residual: bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.560 -0.043 6.70e-03 2.23e+04 4.10e+01 bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.514 1.548 -0.034 5.50e-03 3.31e+04 3.75e+01 bond pdb=" CA PRO B 792 " pdb=" C PRO B 792 " ideal model delta sigma weight residual 1.514 1.547 -0.033 5.50e-03 3.31e+04 3.59e+01 bond pdb=" C3 MAN X 3 " pdb=" O3 MAN X 3 " ideal model delta sigma weight residual 1.408 1.509 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.508 -0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 27785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 29003 2.27 - 4.55: 7785 4.55 - 6.82: 939 6.82 - 9.10: 70 9.10 - 11.37: 4 Bond angle restraints: 37801 Sorted by residual: angle pdb=" N PRO A 665 " pdb=" CA PRO A 665 " pdb=" CB PRO A 665 " ideal model delta sigma weight residual 102.92 107.47 -4.55 5.60e-01 3.19e+00 6.60e+01 angle pdb=" CA ASP C 80 " pdb=" CB ASP C 80 " pdb=" CG ASP C 80 " ideal model delta sigma weight residual 112.60 120.06 -7.46 1.00e+00 1.00e+00 5.56e+01 angle pdb=" N ILE A 850 " pdb=" CA ILE A 850 " pdb=" C ILE A 850 " ideal model delta sigma weight residual 110.62 117.98 -7.36 1.02e+00 9.61e-01 5.21e+01 angle pdb=" N LEU A 452 " pdb=" CA LEU A 452 " pdb=" C LEU A 452 " ideal model delta sigma weight residual 109.85 121.22 -11.37 1.58e+00 4.01e-01 5.18e+01 angle pdb=" CA GLY C 601 " pdb=" C GLY C 601 " pdb=" O GLY C 601 " ideal model delta sigma weight residual 122.57 116.09 6.48 9.20e-01 1.18e+00 4.96e+01 ... (remaining 37796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 16923 24.59 - 49.19: 665 49.19 - 73.78: 138 73.78 - 98.37: 30 98.37 - 122.96: 17 Dihedral angle restraints: 17773 sinusoidal: 8136 harmonic: 9637 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -158.70 72.70 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.10 69.10 1 1.00e+01 1.00e-02 6.18e+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 -86.00 -152.71 66.71 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 17770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.761: 4532 0.761 - 1.522: 13 1.522 - 2.283: 2 2.283 - 3.044: 0 3.044 - 3.805: 1 Chirality restraints: 4548 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 1.41 -3.81 2.00e-01 2.50e+01 3.62e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.60e+01 chirality pdb=" C1 MAN W 3 " pdb=" O4 NAG W 2 " pdb=" C2 MAN W 3 " pdb=" O5 MAN W 3 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-02 2.50e+03 7.29e+01 ... (remaining 4545 not shown) Planarity restraints: 4816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " -0.149 2.00e-02 2.50e+03 1.50e-01 2.81e+02 pdb=" CG ASN A 282 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " 0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " 0.235 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " -0.108 2.00e-02 2.50e+03 1.42e-01 2.54e+02 pdb=" CG ASN C 616 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " -0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " 0.247 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.117 2.00e-02 2.50e+03 1.26e-01 1.98e+02 pdb=" CG ASN C 234 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.199 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.152 2.00e-02 2.50e+03 ... (remaining 4813 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 12 2.28 - 2.93: 11102 2.93 - 3.59: 36201 3.59 - 4.24: 63549 4.24 - 4.90: 105506 Nonbonded interactions: 216370 Sorted by model distance: nonbonded pdb=" CG GLN C 321 " pdb=" O GLN C 628 " model vdw 1.621 3.440 nonbonded pdb=" CB GLN C 321 " pdb=" O GLN C 628 " model vdw 1.630 3.440 nonbonded pdb=" O ASP A 839 " pdb=" CG1 ILE A 844 " model vdw 1.890 3.440 nonbonded pdb=" O THR A 124 " pdb=" CD1 PHE A 175 " model vdw 1.996 3.340 nonbonded pdb=" O ASP A 839 " pdb=" CB ILE A 844 " model vdw 2.024 3.470 ... (remaining 216365 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 68 or resid 77 through 828 or resid 851 through \ 1408)) selection = (chain 'B' and (resid 14 through 623 or resid 636 through 1408)) selection = (chain 'C' and (resid 14 through 68 or resid 77 through 623 or resid 636 through \ 828 or resid 851 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.310 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.020 0.912 27927 Z= 1.159 Angle : 2.160 38.713 38166 Z= 1.334 Chirality : 0.148 3.805 4548 Planarity : 0.013 0.129 4761 Dihedral : 14.462 122.964 11446 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.07 % Rotamer: Outliers : 2.53 % Allowed : 4.16 % Favored : 93.32 % Cbeta Deviations : 0.58 % 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: -2.17 (0.13), residues: 3278 helix: -2.25 (0.14), residues: 725 sheet: 0.11 (0.20), residues: 611 loop : -1.67 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG B 21 TYR 0.113 0.018 TYR A 365 PHE 0.099 0.017 PHE A 718 TRP 0.105 0.027 TRP A1102 HIS 0.028 0.007 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01550 (27790) covalent geometry : angle 1.96572 (37801) SS BOND : bond 0.25384 ( 43) SS BOND : angle 4.15978 ( 86) hydrogen bonds : bond 0.18168 ( 1103) hydrogen bonds : angle 9.44305 ( 3105) Misc. bond : bond 0.53911 ( 1) link_ALPHA1-4 : bond 0.03164 ( 6) link_ALPHA1-4 : angle 5.01599 ( 18) link_BETA1-4 : bond 0.01453 ( 29) link_BETA1-4 : angle 2.84106 ( 87) link_BETA1-6 : bond 0.02218 ( 3) link_BETA1-6 : angle 2.54291 ( 9) link_NAG-ASN : bond 0.18942 ( 55) link_NAG-ASN : angle 13.31796 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 508 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 VAL cc_start: 0.8014 (t) cc_final: 0.7517 (t) REVERT: B 167 THR cc_start: 0.7345 (OUTLIER) cc_final: 0.7079 (m) REVERT: B 434 ILE cc_start: 0.8574 (mt) cc_final: 0.7996 (mt) REVERT: B 823 PHE cc_start: 0.8261 (m-80) cc_final: 0.7920 (m-80) REVERT: C 128 ILE cc_start: 0.7737 (mt) cc_final: 0.7501 (mt) REVERT: C 551 VAL cc_start: 0.9145 (t) cc_final: 0.8865 (m) REVERT: C 627 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5678 (p0) REVERT: C 737 ASP cc_start: 0.7959 (t0) cc_final: 0.7637 (t0) REVERT: C 985 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7049 (p0) REVERT: A 335 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7607 (tp) REVERT: A 434 ILE cc_start: 0.6583 (mt) cc_final: 0.6076 (mt) outliers start: 73 outliers final: 10 residues processed: 572 average time/residue: 0.2164 time to fit residues: 185.7608 Evaluate side-chains 232 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 854 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 564 GLN B 658 ASN B 957 GLN B1005 GLN C 121 ASN C 164 ASN C 388 ASN C 394 ASN C 501 ASN C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 955 ASN A 52 GLN A 239 GLN A 556 ASN A 955 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1119 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.070062 restraints weight = 75306.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071640 restraints weight = 41646.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072338 restraints weight = 24672.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072929 restraints weight = 23265.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.072945 restraints weight = 20453.877| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27927 Z= 0.175 Angle : 0.812 11.246 38166 Z= 0.402 Chirality : 0.049 0.450 4548 Planarity : 0.005 0.087 4761 Dihedral : 10.155 108.146 5551 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 1.80 % Allowed : 10.25 % Favored : 87.95 % 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: -0.84 (0.14), residues: 3278 helix: 0.37 (0.18), residues: 714 sheet: 0.05 (0.19), residues: 692 loop : -1.17 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 214 TYR 0.049 0.002 TYR A 495 PHE 0.032 0.002 PHE A 342 TRP 0.031 0.003 TRP B 152 HIS 0.011 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00388 (27790) covalent geometry : angle 0.76207 (37801) SS BOND : bond 0.00315 ( 43) SS BOND : angle 1.63839 ( 86) hydrogen bonds : bond 0.04947 ( 1103) hydrogen bonds : angle 6.58149 ( 3105) Misc. bond : bond 0.00308 ( 1) link_ALPHA1-4 : bond 0.01462 ( 6) link_ALPHA1-4 : angle 3.32340 ( 18) link_BETA1-4 : bond 0.00426 ( 29) link_BETA1-4 : angle 1.90121 ( 87) link_BETA1-6 : bond 0.01296 ( 3) link_BETA1-6 : angle 2.10901 ( 9) link_NAG-ASN : bond 0.00556 ( 55) link_NAG-ASN : angle 3.84608 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 1.057 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: B 990 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8148 (mm-30) REVERT: C 99 ASN cc_start: 0.8768 (m-40) cc_final: 0.8517 (m-40) REVERT: C 317 ASN cc_start: 0.7983 (m-40) cc_final: 0.7728 (m110) REVERT: C 370 ASN cc_start: 0.8434 (m-40) cc_final: 0.8022 (p0) REVERT: C 402 ILE cc_start: 0.8464 (pt) cc_final: 0.8228 (pt) REVERT: C 436 TRP cc_start: 0.7916 (p90) cc_final: 0.7313 (p90) REVERT: C 473 TYR cc_start: 0.7956 (t80) cc_final: 0.7752 (t80) REVERT: C 551 VAL cc_start: 0.9156 (t) cc_final: 0.8925 (m) REVERT: C 627 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6265 (p0) REVERT: A 201 PHE cc_start: 0.8438 (t80) cc_final: 0.7856 (t80) REVERT: A 241 LEU cc_start: 0.7828 (mt) cc_final: 0.7544 (pp) REVERT: A 319 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7730 (ptm160) REVERT: A 565 PHE cc_start: 0.8491 (m-80) cc_final: 0.8207 (m-80) REVERT: A 574 ASP cc_start: 0.8104 (p0) cc_final: 0.7824 (p0) REVERT: A 640 SER cc_start: 0.7655 (OUTLIER) cc_final: 0.7336 (p) REVERT: A 902 MET cc_start: 0.9073 (tpp) cc_final: 0.8658 (tpt) REVERT: A 921 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8457 (ttpt) outliers start: 52 outliers final: 21 residues processed: 306 average time/residue: 0.1832 time to fit residues: 90.3878 Evaluate side-chains 197 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 921 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 211 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 327 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 185 optimal weight: 0.0870 chunk 224 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 137 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 188 ASN C 955 ASN A 99 ASN A 121 ASN A 955 ASN A1005 GLN A1011 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.100462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.066644 restraints weight = 76079.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068351 restraints weight = 38037.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068639 restraints weight = 24872.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068948 restraints weight = 26078.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069143 restraints weight = 22321.816| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27927 Z= 0.190 Angle : 0.708 11.919 38166 Z= 0.346 Chirality : 0.046 0.399 4548 Planarity : 0.004 0.079 4761 Dihedral : 9.101 104.216 5529 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 2.18 % Allowed : 11.36 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3278 helix: 1.14 (0.19), residues: 732 sheet: 0.11 (0.19), residues: 691 loop : -1.03 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 214 TYR 0.022 0.002 TYR C1067 PHE 0.028 0.002 PHE A 342 TRP 0.027 0.002 TRP B 152 HIS 0.006 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00431 (27790) covalent geometry : angle 0.67411 (37801) SS BOND : bond 0.00458 ( 43) SS BOND : angle 1.16276 ( 86) hydrogen bonds : bond 0.04471 ( 1103) hydrogen bonds : angle 6.08601 ( 3105) Misc. bond : bond 0.00053 ( 1) link_ALPHA1-4 : bond 0.01674 ( 6) link_ALPHA1-4 : angle 3.14238 ( 18) link_BETA1-4 : bond 0.00298 ( 29) link_BETA1-4 : angle 1.61056 ( 87) link_BETA1-6 : bond 0.01764 ( 3) link_BETA1-6 : angle 2.20781 ( 9) link_NAG-ASN : bond 0.00436 ( 55) link_NAG-ASN : angle 2.90640 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 195 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9027 (t) cc_final: 0.8608 (m) REVERT: B 173 GLN cc_start: 0.8873 (mt0) cc_final: 0.8605 (pm20) REVERT: B 495 TYR cc_start: 0.7123 (m-10) cc_final: 0.6823 (m-80) REVERT: B 516 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7870 (mm-30) REVERT: C 113 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7455 (mtmm) REVERT: C 140 PHE cc_start: 0.8512 (p90) cc_final: 0.7715 (p90) REVERT: C 370 ASN cc_start: 0.8428 (m-40) cc_final: 0.7994 (p0) REVERT: C 402 ILE cc_start: 0.8487 (pt) cc_final: 0.8226 (pt) REVERT: C 436 TRP cc_start: 0.7973 (p90) cc_final: 0.7716 (p90) REVERT: C 551 VAL cc_start: 0.9228 (t) cc_final: 0.9010 (m) REVERT: C 627 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6368 (p0) REVERT: C 836 GLN cc_start: 0.3791 (OUTLIER) cc_final: 0.2801 (pm20) REVERT: C 1002 GLN cc_start: 0.8093 (tp40) cc_final: 0.7761 (tp40) REVERT: C 1148 PHE cc_start: 0.5462 (OUTLIER) cc_final: 0.4766 (m-80) REVERT: A 201 PHE cc_start: 0.8225 (t80) cc_final: 0.7843 (t80) REVERT: A 319 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7943 (ptm160) REVERT: A 428 ASP cc_start: 0.8325 (p0) cc_final: 0.6884 (t0) REVERT: A 574 ASP cc_start: 0.8151 (p0) cc_final: 0.7917 (p0) REVERT: A 921 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8461 (ttpt) outliers start: 63 outliers final: 29 residues processed: 247 average time/residue: 0.1682 time to fit residues: 69.7952 Evaluate side-chains 196 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 836 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 955 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 59 optimal weight: 0.3980 chunk 198 optimal weight: 3.9990 chunk 322 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 320 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 501 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.100875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067133 restraints weight = 75376.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069060 restraints weight = 39368.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069431 restraints weight = 23844.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.069936 restraints weight = 23968.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.069989 restraints weight = 20590.424| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27927 Z= 0.135 Angle : 0.647 11.636 38166 Z= 0.316 Chirality : 0.044 0.363 4548 Planarity : 0.004 0.076 4761 Dihedral : 8.619 105.747 5524 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 1.84 % Allowed : 12.19 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3278 helix: 1.57 (0.19), residues: 723 sheet: 0.10 (0.18), residues: 715 loop : -0.93 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 102 TYR 0.021 0.001 TYR C 495 PHE 0.015 0.001 PHE A 429 TRP 0.025 0.001 TRP B 152 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00302 (27790) covalent geometry : angle 0.61509 (37801) SS BOND : bond 0.00223 ( 43) SS BOND : angle 1.39379 ( 86) hydrogen bonds : bond 0.03993 ( 1103) hydrogen bonds : angle 5.82846 ( 3105) Misc. bond : bond 0.00011 ( 1) link_ALPHA1-4 : bond 0.01600 ( 6) link_ALPHA1-4 : angle 3.06010 ( 18) link_BETA1-4 : bond 0.00329 ( 29) link_BETA1-4 : angle 1.48377 ( 87) link_BETA1-6 : bond 0.01842 ( 3) link_BETA1-6 : angle 2.10498 ( 9) link_NAG-ASN : bond 0.00362 ( 55) link_NAG-ASN : angle 2.60552 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9017 (t) cc_final: 0.8569 (m) REVERT: B 173 GLN cc_start: 0.9012 (mt0) cc_final: 0.8806 (pm20) REVERT: B 495 TYR cc_start: 0.7214 (m-10) cc_final: 0.6893 (m-80) REVERT: B 1017 GLU cc_start: 0.7873 (tt0) cc_final: 0.7485 (tt0) REVERT: C 140 PHE cc_start: 0.8532 (p90) cc_final: 0.7629 (p90) REVERT: C 168 PHE cc_start: 0.8542 (t80) cc_final: 0.8264 (t80) REVERT: C 177 MET cc_start: 0.7369 (ppp) cc_final: 0.6126 (ptt) REVERT: C 188 ASN cc_start: 0.8740 (m110) cc_final: 0.8458 (p0) REVERT: C 370 ASN cc_start: 0.8454 (m-40) cc_final: 0.8020 (p0) REVERT: C 402 ILE cc_start: 0.8630 (pt) cc_final: 0.8408 (pt) REVERT: C 436 TRP cc_start: 0.8007 (p90) cc_final: 0.7739 (p90) REVERT: C 627 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6400 (p0) REVERT: C 1002 GLN cc_start: 0.8115 (tp40) cc_final: 0.7689 (tp40) REVERT: C 1148 PHE cc_start: 0.5549 (OUTLIER) cc_final: 0.4979 (m-80) REVERT: A 191 GLU cc_start: 0.8743 (mt-10) cc_final: 0.7966 (mt-10) REVERT: A 201 PHE cc_start: 0.8490 (t80) cc_final: 0.8004 (t80) REVERT: A 319 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7909 (ptm160) REVERT: A 428 ASP cc_start: 0.8369 (p0) cc_final: 0.7077 (t0) REVERT: A 430 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7289 (p) REVERT: A 574 ASP cc_start: 0.8147 (p0) cc_final: 0.7918 (p0) REVERT: A 921 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8420 (ttpt) outliers start: 53 outliers final: 24 residues processed: 230 average time/residue: 0.1607 time to fit residues: 63.3882 Evaluate side-chains 193 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 921 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 280 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 261 optimal weight: 30.0000 chunk 141 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 314 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN A 317 ASN A 907 ASN A 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.097331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062192 restraints weight = 75793.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064680 restraints weight = 35668.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066233 restraints weight = 23292.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067144 restraints weight = 18263.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067646 restraints weight = 15940.581| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 27927 Z= 0.292 Angle : 0.738 12.139 38166 Z= 0.358 Chirality : 0.047 0.362 4548 Planarity : 0.005 0.069 4761 Dihedral : 8.392 103.626 5520 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 2.98 % Allowed : 12.12 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3278 helix: 1.31 (0.19), residues: 737 sheet: 0.14 (0.18), residues: 722 loop : -1.00 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 646 TYR 0.024 0.002 TYR C1067 PHE 0.018 0.002 PHE A 168 TRP 0.021 0.002 TRP A 436 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00673 (27790) covalent geometry : angle 0.70886 (37801) SS BOND : bond 0.00408 ( 43) SS BOND : angle 1.48932 ( 86) hydrogen bonds : bond 0.04442 ( 1103) hydrogen bonds : angle 5.92040 ( 3105) Misc. bond : bond 0.00001 ( 1) link_ALPHA1-4 : bond 0.01606 ( 6) link_ALPHA1-4 : angle 3.09489 ( 18) link_BETA1-4 : bond 0.00250 ( 29) link_BETA1-4 : angle 1.62369 ( 87) link_BETA1-6 : bond 0.01861 ( 3) link_BETA1-6 : angle 1.98763 ( 9) link_NAG-ASN : bond 0.00417 ( 55) link_NAG-ASN : angle 2.66345 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 166 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9163 (t) cc_final: 0.8790 (m) REVERT: B 129 LYS cc_start: 0.8524 (mmtm) cc_final: 0.7899 (tppt) REVERT: B 495 TYR cc_start: 0.7337 (m-80) cc_final: 0.7020 (m-80) REVERT: B 516 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7587 (mm-30) REVERT: C 63 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8590 (p) REVERT: C 66 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7849 (p90) REVERT: C 140 PHE cc_start: 0.8600 (p90) cc_final: 0.7800 (p90) REVERT: C 402 ILE cc_start: 0.8619 (pt) cc_final: 0.8417 (pt) REVERT: C 517 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7781 (mp) REVERT: C 836 GLN cc_start: 0.4450 (OUTLIER) cc_final: 0.3491 (pm20) REVERT: C 1148 PHE cc_start: 0.5466 (OUTLIER) cc_final: 0.4724 (m-10) REVERT: A 168 PHE cc_start: 0.6873 (t80) cc_final: 0.6516 (t80) REVERT: A 175 PHE cc_start: 0.6771 (p90) cc_final: 0.6330 (p90) REVERT: A 191 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 319 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8029 (ptm160) REVERT: A 428 ASP cc_start: 0.8447 (p0) cc_final: 0.7188 (t0) REVERT: A 430 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7216 (p) REVERT: A 637 SER cc_start: 0.1088 (OUTLIER) cc_final: 0.0616 (p) REVERT: A 1155 TYR cc_start: -0.1325 (OUTLIER) cc_final: -0.2362 (m-80) outliers start: 86 outliers final: 48 residues processed: 238 average time/residue: 0.1642 time to fit residues: 67.0592 Evaluate side-chains 201 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 144 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 836 GLN Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1155 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 256 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 292 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 309 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 ASN C 519 HIS C 580 GLN C 613 GLN C 907 ASN A 188 ASN A 207 HIS A 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.099105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.064914 restraints weight = 75136.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068133 restraints weight = 36851.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068725 restraints weight = 20205.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069139 restraints weight = 18959.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069162 restraints weight = 17001.072| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27927 Z= 0.135 Angle : 0.637 14.034 38166 Z= 0.308 Chirality : 0.044 0.334 4548 Planarity : 0.004 0.067 4761 Dihedral : 7.910 102.403 5518 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 2.18 % Allowed : 13.16 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3278 helix: 1.74 (0.20), residues: 728 sheet: 0.15 (0.18), residues: 716 loop : -0.92 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.019 0.001 TYR B1067 PHE 0.027 0.001 PHE B 79 TRP 0.020 0.001 TRP A 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00301 (27790) covalent geometry : angle 0.60951 (37801) SS BOND : bond 0.00359 ( 43) SS BOND : angle 1.23536 ( 86) hydrogen bonds : bond 0.03865 ( 1103) hydrogen bonds : angle 5.65131 ( 3105) Misc. bond : bond 0.00003 ( 1) link_ALPHA1-4 : bond 0.01634 ( 6) link_ALPHA1-4 : angle 3.05489 ( 18) link_BETA1-4 : bond 0.00306 ( 29) link_BETA1-4 : angle 1.40275 ( 87) link_BETA1-6 : bond 0.01956 ( 3) link_BETA1-6 : angle 1.90779 ( 9) link_NAG-ASN : bond 0.00393 ( 55) link_NAG-ASN : angle 2.36066 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 174 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9118 (t) cc_final: 0.8680 (m) REVERT: B 129 LYS cc_start: 0.8591 (mmtm) cc_final: 0.7927 (tppt) REVERT: B 177 MET cc_start: 0.5774 (tmm) cc_final: 0.5545 (tmm) REVERT: B 342 PHE cc_start: 0.7492 (m-80) cc_final: 0.7261 (m-80) REVERT: B 495 TYR cc_start: 0.7399 (m-80) cc_final: 0.7029 (m-80) REVERT: B 516 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7523 (mm-30) REVERT: C 63 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8653 (p) REVERT: C 66 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7880 (p90) REVERT: C 127 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8603 (m) REVERT: C 140 PHE cc_start: 0.8611 (p90) cc_final: 0.7703 (p90) REVERT: C 177 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.6977 (ppp) REVERT: C 402 ILE cc_start: 0.8708 (pt) cc_final: 0.8462 (pt) REVERT: C 637 SER cc_start: 0.6267 (OUTLIER) cc_final: 0.5949 (t) REVERT: C 1041 ASP cc_start: 0.8037 (t70) cc_final: 0.7691 (t70) REVERT: C 1148 PHE cc_start: 0.5530 (OUTLIER) cc_final: 0.4708 (m-80) REVERT: A 168 PHE cc_start: 0.6784 (t80) cc_final: 0.6482 (t80) REVERT: A 175 PHE cc_start: 0.6770 (p90) cc_final: 0.6405 (p90) REVERT: A 191 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8305 (mt-10) REVERT: A 428 ASP cc_start: 0.8340 (p0) cc_final: 0.7048 (t0) REVERT: A 430 THR cc_start: 0.7111 (OUTLIER) cc_final: 0.6768 (p) REVERT: A 637 SER cc_start: 0.1521 (OUTLIER) cc_final: 0.0834 (p) outliers start: 63 outliers final: 34 residues processed: 224 average time/residue: 0.1558 time to fit residues: 60.3702 Evaluate side-chains 198 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 955 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 85 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 290 optimal weight: 0.0670 chunk 34 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 300 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN C 856 ASN A 125 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062824 restraints weight = 75796.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.064539 restraints weight = 38379.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.064615 restraints weight = 25311.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.064936 restraints weight = 25671.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.065092 restraints weight = 22693.623| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 27927 Z= 0.300 Angle : 0.734 13.386 38166 Z= 0.354 Chirality : 0.046 0.343 4548 Planarity : 0.004 0.062 4761 Dihedral : 7.847 100.251 5518 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.45 % Rotamer: Outliers : 2.67 % Allowed : 13.16 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3278 helix: 1.33 (0.19), residues: 741 sheet: -0.05 (0.18), residues: 751 loop : -1.00 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 408 TYR 0.023 0.002 TYR C1067 PHE 0.022 0.002 PHE B 79 TRP 0.019 0.002 TRP A 436 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00682 (27790) covalent geometry : angle 0.70598 (37801) SS BOND : bond 0.00396 ( 43) SS BOND : angle 1.35767 ( 86) hydrogen bonds : bond 0.04394 ( 1103) hydrogen bonds : angle 5.84273 ( 3105) Misc. bond : bond 0.00016 ( 1) link_ALPHA1-4 : bond 0.01828 ( 6) link_ALPHA1-4 : angle 3.27556 ( 18) link_BETA1-4 : bond 0.00241 ( 29) link_BETA1-4 : angle 1.60498 ( 87) link_BETA1-6 : bond 0.01932 ( 3) link_BETA1-6 : angle 2.16848 ( 9) link_NAG-ASN : bond 0.00452 ( 55) link_NAG-ASN : angle 2.56159 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 161 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9202 (t) cc_final: 0.8816 (m) REVERT: B 95 THR cc_start: 0.8664 (p) cc_final: 0.8450 (p) REVERT: B 125 ASN cc_start: 0.6882 (OUTLIER) cc_final: 0.6420 (p0) REVERT: B 177 MET cc_start: 0.5776 (tmm) cc_final: 0.5545 (tmm) REVERT: B 495 TYR cc_start: 0.7535 (m-80) cc_final: 0.7206 (m-80) REVERT: B 516 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7801 (tm-30) REVERT: C 63 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 66 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7814 (p90) REVERT: C 127 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8728 (m) REVERT: C 131 CYS cc_start: 0.3743 (OUTLIER) cc_final: 0.3260 (m) REVERT: C 140 PHE cc_start: 0.8720 (p90) cc_final: 0.7843 (p90) REVERT: C 177 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6928 (ppp) REVERT: C 402 ILE cc_start: 0.8702 (pt) cc_final: 0.8481 (pt) REVERT: C 517 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7703 (mp) REVERT: C 637 SER cc_start: 0.6200 (OUTLIER) cc_final: 0.5954 (t) REVERT: C 1141 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8537 (tt) REVERT: C 1148 PHE cc_start: 0.5299 (OUTLIER) cc_final: 0.4677 (m-10) REVERT: A 144 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.7183 (m-10) REVERT: A 175 PHE cc_start: 0.6853 (p90) cc_final: 0.6426 (p90) REVERT: A 314 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7859 (tp-100) REVERT: A 428 ASP cc_start: 0.8296 (p0) cc_final: 0.7020 (t0) REVERT: A 430 THR cc_start: 0.6882 (OUTLIER) cc_final: 0.6475 (p) REVERT: A 637 SER cc_start: 0.2226 (OUTLIER) cc_final: 0.1316 (p) REVERT: A 661 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 1155 TYR cc_start: -0.1473 (OUTLIER) cc_final: -0.2465 (m-80) outliers start: 77 outliers final: 44 residues processed: 223 average time/residue: 0.1596 time to fit residues: 61.5096 Evaluate side-chains 202 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 144 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1155 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 277 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 229 optimal weight: 0.9990 chunk 193 optimal weight: 0.3980 chunk 190 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 303 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 836 GLN A 66 HIS ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** 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 = 0.3749 r_free = 0.3749 target = 0.098748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.066094 restraints weight = 75663.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.067339 restraints weight = 37352.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067986 restraints weight = 25583.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068164 restraints weight = 25741.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068468 restraints weight = 22053.497| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27927 Z= 0.132 Angle : 0.639 12.574 38166 Z= 0.308 Chirality : 0.044 0.308 4548 Planarity : 0.004 0.065 4761 Dihedral : 7.223 101.866 5518 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.23 % Favored : 96.71 % Rotamer: Outliers : 2.08 % Allowed : 13.78 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3278 helix: 1.75 (0.20), residues: 735 sheet: 0.04 (0.18), residues: 732 loop : -0.93 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 408 TYR 0.019 0.001 TYR B1067 PHE 0.030 0.001 PHE A 497 TRP 0.023 0.001 TRP A 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00292 (27790) covalent geometry : angle 0.61367 (37801) SS BOND : bond 0.00349 ( 43) SS BOND : angle 1.12352 ( 86) hydrogen bonds : bond 0.03805 ( 1103) hydrogen bonds : angle 5.57631 ( 3105) Misc. bond : bond 0.00004 ( 1) link_ALPHA1-4 : bond 0.01866 ( 6) link_ALPHA1-4 : angle 3.31858 ( 18) link_BETA1-4 : bond 0.00338 ( 29) link_BETA1-4 : angle 1.35350 ( 87) link_BETA1-6 : bond 0.02039 ( 3) link_BETA1-6 : angle 2.04942 ( 9) link_NAG-ASN : bond 0.00383 ( 55) link_NAG-ASN : angle 2.24905 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9114 (t) cc_final: 0.8753 (m) REVERT: B 129 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8297 (mmmt) REVERT: B 495 TYR cc_start: 0.7379 (m-80) cc_final: 0.7081 (m-80) REVERT: B 516 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7761 (tm-30) REVERT: B 740 MET cc_start: 0.8189 (tpp) cc_final: 0.7958 (tpp) REVERT: C 63 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8731 (p) REVERT: C 66 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7776 (p90) REVERT: C 140 PHE cc_start: 0.8665 (p90) cc_final: 0.7803 (p90) REVERT: C 177 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.6792 (ppp) REVERT: C 402 ILE cc_start: 0.8693 (pt) cc_final: 0.8477 (pt) REVERT: C 517 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7677 (mp) REVERT: C 637 SER cc_start: 0.6082 (OUTLIER) cc_final: 0.5761 (t) REVERT: C 955 ASN cc_start: 0.8551 (t0) cc_final: 0.8338 (t0) REVERT: C 1041 ASP cc_start: 0.8021 (t70) cc_final: 0.7673 (t70) REVERT: C 1141 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8513 (tt) REVERT: C 1148 PHE cc_start: 0.5096 (OUTLIER) cc_final: 0.4605 (m-80) REVERT: A 144 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.7153 (m-10) REVERT: A 175 PHE cc_start: 0.6754 (p90) cc_final: 0.6331 (p90) REVERT: A 191 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 314 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7787 (tp-100) REVERT: A 380 TYR cc_start: 0.6802 (m-80) cc_final: 0.6393 (m-80) REVERT: A 428 ASP cc_start: 0.8225 (p0) cc_final: 0.7060 (t0) REVERT: A 430 THR cc_start: 0.6794 (OUTLIER) cc_final: 0.6384 (p) REVERT: A 855 PHE cc_start: 0.8690 (m-10) cc_final: 0.8484 (m-80) REVERT: A 1155 TYR cc_start: -0.1636 (OUTLIER) cc_final: -0.2589 (m-80) outliers start: 60 outliers final: 37 residues processed: 216 average time/residue: 0.1562 time to fit residues: 58.9533 Evaluate side-chains 199 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1155 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 52 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 252 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 360 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.098614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066373 restraints weight = 76006.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067631 restraints weight = 38651.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.068420 restraints weight = 26437.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068594 restraints weight = 27170.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068693 restraints weight = 22544.107| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 27927 Z= 0.226 Angle : 0.678 11.939 38166 Z= 0.325 Chirality : 0.045 0.321 4548 Planarity : 0.004 0.062 4761 Dihedral : 6.880 99.684 5518 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 2.25 % Allowed : 13.95 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3278 helix: 1.58 (0.20), residues: 748 sheet: 0.04 (0.18), residues: 705 loop : -0.96 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 408 TYR 0.030 0.002 TYR B 269 PHE 0.033 0.002 PHE A 497 TRP 0.022 0.002 TRP A 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00517 (27790) covalent geometry : angle 0.65066 (37801) SS BOND : bond 0.00319 ( 43) SS BOND : angle 1.26299 ( 86) hydrogen bonds : bond 0.04035 ( 1103) hydrogen bonds : angle 5.62924 ( 3105) Misc. bond : bond 0.00010 ( 1) link_ALPHA1-4 : bond 0.01927 ( 6) link_ALPHA1-4 : angle 3.73444 ( 18) link_BETA1-4 : bond 0.00239 ( 29) link_BETA1-4 : angle 1.46168 ( 87) link_BETA1-6 : bond 0.01819 ( 3) link_BETA1-6 : angle 2.25900 ( 9) link_NAG-ASN : bond 0.00364 ( 55) link_NAG-ASN : angle 2.34530 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 155 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9067 (t) cc_final: 0.8575 (p) REVERT: B 125 ASN cc_start: 0.6983 (OUTLIER) cc_final: 0.6483 (p0) REVERT: B 129 LYS cc_start: 0.8665 (mmtm) cc_final: 0.7940 (tppt) REVERT: B 495 TYR cc_start: 0.7426 (m-80) cc_final: 0.7146 (m-80) REVERT: B 740 MET cc_start: 0.8088 (tpp) cc_final: 0.7837 (tpp) REVERT: B 1084 ASP cc_start: 0.8075 (t0) cc_final: 0.7874 (t0) REVERT: C 63 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8753 (p) REVERT: C 66 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7689 (p90) REVERT: C 127 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8867 (m) REVERT: C 131 CYS cc_start: 0.3677 (OUTLIER) cc_final: 0.3152 (m) REVERT: C 140 PHE cc_start: 0.8686 (p90) cc_final: 0.7821 (p90) REVERT: C 177 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6834 (ppp) REVERT: C 402 ILE cc_start: 0.8659 (pt) cc_final: 0.8436 (pt) REVERT: C 517 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7720 (mp) REVERT: C 637 SER cc_start: 0.6028 (OUTLIER) cc_final: 0.5744 (t) REVERT: C 1041 ASP cc_start: 0.8051 (t70) cc_final: 0.7680 (t0) REVERT: C 1141 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8494 (tt) REVERT: C 1148 PHE cc_start: 0.5165 (OUTLIER) cc_final: 0.4560 (m-80) REVERT: A 144 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.7178 (m-10) REVERT: A 175 PHE cc_start: 0.6746 (p90) cc_final: 0.6258 (p90) REVERT: A 314 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7852 (tp-100) REVERT: A 380 TYR cc_start: 0.6761 (m-80) cc_final: 0.6456 (m-80) REVERT: A 1155 TYR cc_start: -0.1584 (OUTLIER) cc_final: -0.2577 (m-80) outliers start: 65 outliers final: 44 residues processed: 207 average time/residue: 0.1558 time to fit residues: 56.1563 Evaluate side-chains 195 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 139 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1155 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 214 optimal weight: 0.8980 chunk 263 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 254 optimal weight: 0.4980 chunk 211 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 280 optimal weight: 0.0970 chunk 136 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.098911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065869 restraints weight = 75390.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068035 restraints weight = 37997.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068867 restraints weight = 23159.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069165 restraints weight = 24045.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069218 restraints weight = 19253.419| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27927 Z= 0.118 Angle : 0.625 11.731 38166 Z= 0.301 Chirality : 0.044 0.290 4548 Planarity : 0.004 0.065 4761 Dihedral : 6.411 100.106 5518 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 1.84 % Allowed : 14.51 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3278 helix: 1.88 (0.20), residues: 740 sheet: 0.05 (0.18), residues: 723 loop : -0.89 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 408 TYR 0.031 0.001 TYR C 904 PHE 0.047 0.001 PHE A 497 TRP 0.026 0.001 TRP A 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00256 (27790) covalent geometry : angle 0.59891 (37801) SS BOND : bond 0.00358 ( 43) SS BOND : angle 1.10776 ( 86) hydrogen bonds : bond 0.03646 ( 1103) hydrogen bonds : angle 5.47569 ( 3105) Misc. bond : bond 0.00012 ( 1) link_ALPHA1-4 : bond 0.01886 ( 6) link_ALPHA1-4 : angle 3.94005 ( 18) link_BETA1-4 : bond 0.00336 ( 29) link_BETA1-4 : angle 1.31184 ( 87) link_BETA1-6 : bond 0.01877 ( 3) link_BETA1-6 : angle 2.14789 ( 9) link_NAG-ASN : bond 0.00345 ( 55) link_NAG-ASN : angle 2.13611 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6556 Ramachandran restraints generated. 3278 Oldfield, 0 Emsley, 3278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9044 (t) cc_final: 0.8728 (m) REVERT: B 129 LYS cc_start: 0.8634 (mmtm) cc_final: 0.7893 (tppt) REVERT: B 421 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.5269 (p90) REVERT: B 495 TYR cc_start: 0.7458 (m-80) cc_final: 0.7162 (m-80) REVERT: B 740 MET cc_start: 0.8182 (tpp) cc_final: 0.7966 (tpp) REVERT: B 1084 ASP cc_start: 0.8141 (t0) cc_final: 0.7936 (t0) REVERT: C 63 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8734 (p) REVERT: C 66 HIS cc_start: 0.8406 (OUTLIER) cc_final: 0.7746 (p90) REVERT: C 131 CYS cc_start: 0.3683 (OUTLIER) cc_final: 0.3128 (m) REVERT: C 177 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6786 (ppp) REVERT: C 402 ILE cc_start: 0.8719 (pt) cc_final: 0.8502 (pt) REVERT: C 517 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7673 (mp) REVERT: C 637 SER cc_start: 0.5952 (OUTLIER) cc_final: 0.5646 (t) REVERT: C 740 MET cc_start: 0.7925 (ttp) cc_final: 0.7659 (ttp) REVERT: C 904 TYR cc_start: 0.7686 (m-10) cc_final: 0.7424 (m-10) REVERT: C 1041 ASP cc_start: 0.8010 (t70) cc_final: 0.7652 (t70) REVERT: C 1141 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8502 (tt) REVERT: C 1148 PHE cc_start: 0.5210 (OUTLIER) cc_final: 0.4761 (m-80) REVERT: A 144 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: A 175 PHE cc_start: 0.6765 (p90) cc_final: 0.6303 (p90) REVERT: A 191 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 314 GLN cc_start: 0.8015 (tp-100) cc_final: 0.7722 (tp-100) REVERT: A 380 TYR cc_start: 0.6730 (m-80) cc_final: 0.6400 (m-80) REVERT: A 1155 TYR cc_start: -0.1548 (OUTLIER) cc_final: -0.2490 (m-80) outliers start: 53 outliers final: 38 residues processed: 204 average time/residue: 0.1581 time to fit residues: 55.4951 Evaluate side-chains 194 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1155 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 167 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 327 optimal weight: 0.7980 chunk 254 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 135 optimal weight: 0.5980 chunk 207 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 907 ASN C 913 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.098840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.065826 restraints weight = 74901.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067881 restraints weight = 37537.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068632 restraints weight = 22880.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068886 restraints weight = 23995.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.068952 restraints weight = 19888.539| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.212 27927 Z= 0.169 Angle : 0.758 59.146 38166 Z= 0.401 Chirality : 0.045 0.744 4548 Planarity : 0.004 0.064 4761 Dihedral : 6.425 100.103 5518 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 1.90 % Allowed : 14.75 % Favored : 83.34 % Cbeta Deviations : 0.03 % 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: -0.04 (0.14), residues: 3278 helix: 1.88 (0.20), residues: 740 sheet: 0.05 (0.18), residues: 723 loop : -0.89 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 408 TYR 0.045 0.001 TYR B 144 PHE 0.041 0.001 PHE A 497 TRP 0.023 0.001 TRP A 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00341 (27790) covalent geometry : angle 0.72500 (37801) SS BOND : bond 0.02104 ( 43) SS BOND : angle 3.15487 ( 86) hydrogen bonds : bond 0.03644 ( 1103) hydrogen bonds : angle 5.47619 ( 3105) Misc. bond : bond 0.00010 ( 1) link_ALPHA1-4 : bond 0.01818 ( 6) link_ALPHA1-4 : angle 3.94436 ( 18) link_BETA1-4 : bond 0.00342 ( 29) link_BETA1-4 : angle 1.34526 ( 87) link_BETA1-6 : bond 0.01885 ( 3) link_BETA1-6 : angle 2.14832 ( 9) link_NAG-ASN : bond 0.00341 ( 55) link_NAG-ASN : angle 2.13685 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4984.36 seconds wall clock time: 87 minutes 11.52 seconds (5231.52 seconds total)