Starting phenix.real_space_refine on Sun Jul 5 10:49:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7krr_23011/07_2026/7krr_23011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7krr_23011/07_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_23011/07_2026/7krr_23011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7krr_23011/07_2026/7krr_23011.map" model { file = "/net/cci-nas-00/data/ceres_data/7krr_23011/07_2026/7krr_23011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7krr_23011/07_2026/7krr_23011.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7krr_23011/07_2026/7krr_23011.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7krr_23011/07_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-6108/lib/python3.11/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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 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 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 chiralities: 11 Time building chain proxies: 6.07, per 1000 atoms: 0.22 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: 2.52 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: 1.32 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: 6.44 Time building geometry restraints manager: 3.25 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 - 17.94: 14502 17.94 - 35.88: 1002 35.88 - 53.82: 209 53.82 - 71.76: 64 71.76 - 89.70: 25 Dihedral angle restraints: 15802 sinusoidal: 6165 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 15799 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: 9.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.180 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.080 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 13.841 89.704 9475 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/Z covalent geometry : bond 0.01550 / 0.90 (27790) covalent geometry : angle 1.96572 / 1.30 (37801) SS BOND : bond 0.25384 / 14.28 ( 43) SS BOND : angle 4.15978 / 3.15 ( 86) hydrogen bonds : bond 0.18168 / 12.07 ( 1103) hydrogen bonds : angle 9.44305 / 6.51 ( 3105) Misc. bond : bond 0.53911 / 28.37 ( 1) link_ALPHA1-4 : bond 0.03164 / 1.63 ( 6) link_ALPHA1-4 : angle 5.01599 / 3.20 ( 18) link_BETA1-4 : bond 0.01453 / 0.88 ( 29) link_BETA1-4 : angle 2.84106 / 1.90 ( 87) link_BETA1-6 : bond 0.02218 / 1.11 ( 3) link_BETA1-6 : angle 2.54291 / 1.82 ( 9) link_NAG-ASN : bond 0.18942 / 12.62 ( 55) link_NAG-ASN : angle 13.31796 / 9.52 ( 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 : 0.745 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: 0.2062 time to fit residues: 177.7711 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 : 1.037 ------------------------------------------------------------------------------- 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... B 164 ASN B 422 ASN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.070081 restraints weight = 75285.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071653 restraints weight = 41741.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.072384 restraints weight = 24672.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.072783 restraints weight = 23165.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072856 restraints weight = 20376.621| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27927 Z= 0.186 Angle : 0.815 11.064 38166 Z= 0.405 Chirality : 0.049 0.413 4548 Planarity : 0.005 0.088 4761 Dihedral : 6.531 64.771 3580 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 1.84 % Allowed : 10.39 % Favored : 87.78 % 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: -0.82 (0.14), residues: 3278 helix: 0.39 (0.18), residues: 714 sheet: 0.06 (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 0.052 0.002 TYR A 495 PHE 0.031 0.002 PHE A 342 TRP 0.030 0.003 TRP B 152 HIS 0.011 0.002 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (27790) covalent geometry : angle 0.76535 / 0.39 (37801) SS BOND : bond 0.00349 / 0.22 ( 43) SS BOND : angle 1.67158 / 1.23 ( 86) hydrogen bonds : bond 0.04956 / 3.31 ( 1103) hydrogen bonds : angle 6.57955 / 4.58 ( 3105) Misc. bond : bond 0.00206 / 0.11 ( 1) link_ALPHA1-4 : bond 0.01131 / 0.65 ( 6) link_ALPHA1-4 : angle 3.28998 / 2.04 ( 18) link_BETA1-4 : bond 0.00508 / 0.31 ( 29) link_BETA1-4 : angle 1.82558 / 1.28 ( 87) link_BETA1-6 : bond 0.00653 / 0.33 ( 3) link_BETA1-6 : angle 1.67642 / 0.93 ( 9) link_NAG-ASN : bond 0.00529 / 0.36 ( 55) link_NAG-ASN : angle 3.85173 / 2.57 ( 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 315 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 1.019 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: B 990 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8230 (mm-30) REVERT: C 99 ASN cc_start: 0.8763 (m-40) cc_final: 0.8524 (m-40) REVERT: C 137 ASN cc_start: 0.7449 (m-40) cc_final: 0.7150 (m-40) REVERT: C 317 ASN cc_start: 0.7987 (m-40) cc_final: 0.7740 (m110) REVERT: C 370 ASN cc_start: 0.8441 (m-40) cc_final: 0.8013 (p0) REVERT: C 402 ILE cc_start: 0.8457 (pt) cc_final: 0.8225 (pt) REVERT: C 436 TRP cc_start: 0.7922 (p90) cc_final: 0.7324 (p90) REVERT: C 551 VAL cc_start: 0.9156 (t) cc_final: 0.8923 (m) REVERT: C 627 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6318 (p0) REVERT: A 201 PHE cc_start: 0.8444 (t80) cc_final: 0.7851 (t80) REVERT: A 241 LEU cc_start: 0.7830 (mt) cc_final: 0.7549 (pp) REVERT: A 319 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7774 (ptm160) REVERT: A 574 ASP cc_start: 0.8102 (p0) cc_final: 0.7815 (p0) REVERT: A 640 SER cc_start: 0.7695 (OUTLIER) cc_final: 0.7375 (p) REVERT: A 902 MET cc_start: 0.9076 (tpp) cc_final: 0.8682 (tpt) REVERT: A 921 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8450 (ttpt) outliers start: 53 outliers final: 21 residues processed: 306 average time/residue: 0.1743 time to fit residues: 85.7852 Evaluate side-chains 198 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 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 282 ASN 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: 2.9990 chunk 166 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 327 optimal weight: 0.0040 chunk 105 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 185 optimal weight: 0.0040 chunk 224 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 overall best weight: 1.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN B 394 ASN C 125 ASN C 394 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN A 99 ASN A 121 ASN A 955 ASN A1011 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.101742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067964 restraints weight = 76015.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069811 restraints weight = 37779.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.070054 restraints weight = 24417.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.070376 restraints weight = 25443.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070699 restraints weight = 22087.273| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3510 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= 0.148 Angle : 0.672 11.659 38166 Z= 0.333 Chirality : 0.045 0.332 4548 Planarity : 0.004 0.080 4761 Dihedral : 5.618 55.019 3560 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 2.04 % Allowed : 11.60 % Favored : 86.36 % 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: -0.36 (0.14), residues: 3278 helix: 1.21 (0.19), residues: 733 sheet: 0.14 (0.19), residues: 708 loop : -1.01 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 102 TYR 0.020 0.002 TYR B1067 PHE 0.028 0.002 PHE A 342 TRP 0.027 0.002 TRP B 152 HIS 0.007 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (27790) covalent geometry : angle 0.64092 / 0.33 (37801) SS BOND : bond 0.00325 / 0.20 ( 43) SS BOND : angle 1.18639 / 0.89 ( 86) hydrogen bonds : bond 0.04327 / 2.87 ( 1103) hydrogen bonds : angle 6.03805 / 4.20 ( 3105) Misc. bond : bond 0.00032 / 0.02 ( 1) link_ALPHA1-4 : bond 0.01048 / 0.55 ( 6) link_ALPHA1-4 : angle 2.26626 / 1.47 ( 18) link_BETA1-4 : bond 0.00367 / 0.23 ( 29) link_BETA1-4 : angle 1.43418 / 1.04 ( 87) link_BETA1-6 : bond 0.00620 / 0.31 ( 3) link_BETA1-6 : angle 1.14991 / 0.69 ( 9) link_NAG-ASN : bond 0.00405 / 0.28 ( 55) link_NAG-ASN : angle 2.82955 / 1.83 ( 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 276 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9024 (t) cc_final: 0.8623 (m) REVERT: B 495 TYR cc_start: 0.7189 (m-10) cc_final: 0.6810 (m-80) REVERT: B 516 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7845 (mm-30) REVERT: C 140 PHE cc_start: 0.8467 (p90) cc_final: 0.7685 (p90) REVERT: C 317 ASN cc_start: 0.8023 (m-40) cc_final: 0.7776 (m-40) REVERT: C 370 ASN cc_start: 0.8445 (m-40) cc_final: 0.8012 (p0) REVERT: C 402 ILE cc_start: 0.8509 (pt) cc_final: 0.8244 (pt) REVERT: C 436 TRP cc_start: 0.7949 (p90) cc_final: 0.7644 (p90) REVERT: C 551 VAL cc_start: 0.9219 (t) cc_final: 0.9000 (m) REVERT: C 627 ASP cc_start: 0.6898 (OUTLIER) cc_final: 0.6382 (p0) REVERT: C 836 GLN cc_start: 0.3995 (OUTLIER) cc_final: 0.2863 (pm20) REVERT: C 1019 ARG cc_start: 0.8071 (tpt90) cc_final: 0.7762 (tpt90) REVERT: C 1148 PHE cc_start: 0.5515 (OUTLIER) cc_final: 0.4910 (m-80) REVERT: A 168 PHE cc_start: 0.6459 (t80) cc_final: 0.6234 (t80) REVERT: A 201 PHE cc_start: 0.8223 (t80) cc_final: 0.7821 (t80) REVERT: A 319 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7754 (ptm160) REVERT: A 428 ASP cc_start: 0.8328 (p0) cc_final: 0.6903 (t0) REVERT: A 574 ASP cc_start: 0.8125 (p0) cc_final: 0.7884 (p0) REVERT: A 921 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8421 (ttpt) outliers start: 59 outliers final: 26 residues processed: 263 average time/residue: 0.1566 time to fit residues: 68.9066 Evaluate side-chains 204 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 216 LEU 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 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 836 GLN Chi-restraints excluded: chain C residue 850 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 59 optimal weight: 0.5980 chunk 198 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 79 optimal weight: 0.0170 chunk 320 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 328 optimal weight: 0.0980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN C 188 ASN C 580 GLN C 907 ASN C 955 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 = 0.3809 r_free = 0.3809 target = 0.102364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068727 restraints weight = 75518.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070635 restraints weight = 39403.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071147 restraints weight = 23843.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071668 restraints weight = 23990.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071685 restraints weight = 20546.346| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3835 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= 0.116 Angle : 0.621 11.555 38166 Z= 0.307 Chirality : 0.044 0.286 4548 Planarity : 0.004 0.076 4761 Dihedral : 5.136 52.441 3553 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 1.94 % Allowed : 12.19 % Favored : 85.87 % 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: -0.14 (0.14), residues: 3278 helix: 1.68 (0.20), residues: 723 sheet: 0.09 (0.18), residues: 709 loop : -0.91 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.022 0.001 TYR C 495 PHE 0.019 0.001 PHE A 133 TRP 0.024 0.001 TRP B 152 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (27790) covalent geometry : angle 0.59324 / 0.30 (37801) SS BOND : bond 0.00329 / 0.23 ( 43) SS BOND : angle 1.39120 / 1.07 ( 86) hydrogen bonds : bond 0.03860 / 2.58 ( 1103) hydrogen bonds : angle 5.73587 / 3.99 ( 3105) Misc. bond : bond 0.00027 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00913 / 0.48 ( 6) link_ALPHA1-4 : angle 1.90679 / 1.24 ( 18) link_BETA1-4 : bond 0.00395 / 0.25 ( 29) link_BETA1-4 : angle 1.32210 / 0.95 ( 87) link_BETA1-6 : bond 0.00582 / 0.30 ( 3) link_BETA1-6 : angle 1.00510 / 0.57 ( 9) link_NAG-ASN : bond 0.00355 / 0.25 ( 55) link_NAG-ASN : angle 2.46908 / 1.58 ( 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 252 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8985 (t) cc_final: 0.8541 (m) REVERT: B 177 MET cc_start: 0.6169 (ppp) cc_final: 0.5447 (ppp) REVERT: B 516 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7790 (mm-30) REVERT: C 63 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8439 (p) REVERT: C 168 PHE cc_start: 0.8470 (t80) cc_final: 0.8215 (t80) REVERT: C 177 MET cc_start: 0.7204 (ppp) cc_final: 0.6066 (ptt) REVERT: C 370 ASN cc_start: 0.8418 (m-40) cc_final: 0.8028 (p0) REVERT: C 402 ILE cc_start: 0.8637 (pt) cc_final: 0.8331 (pt) REVERT: C 436 TRP cc_start: 0.7958 (p90) cc_final: 0.7716 (p90) REVERT: C 627 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6363 (p0) REVERT: C 878 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8963 (tt) REVERT: C 881 THR cc_start: 0.8903 (m) cc_final: 0.8397 (p) REVERT: C 907 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8648 (m110) REVERT: C 1019 ARG cc_start: 0.8066 (tpt90) cc_final: 0.7733 (tpt90) REVERT: C 1148 PHE cc_start: 0.5621 (OUTLIER) cc_final: 0.5132 (m-80) REVERT: A 191 GLU cc_start: 0.8711 (mt-10) cc_final: 0.7962 (mt-10) REVERT: A 201 PHE cc_start: 0.8472 (t80) cc_final: 0.7966 (t80) REVERT: A 319 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7771 (ptm160) REVERT: A 428 ASP cc_start: 0.8370 (p0) cc_final: 0.7107 (t0) REVERT: A 430 THR cc_start: 0.7527 (OUTLIER) cc_final: 0.7231 (p) REVERT: A 574 ASP cc_start: 0.8097 (p0) cc_final: 0.7879 (p0) REVERT: A 637 SER cc_start: 0.1547 (OUTLIER) cc_final: 0.1045 (p) REVERT: A 900 MET cc_start: 0.8625 (mtp) cc_final: 0.8393 (mtm) REVERT: A 921 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8396 (ttpt) outliers start: 56 outliers final: 21 residues processed: 239 average time/residue: 0.1496 time to fit residues: 60.5658 Evaluate side-chains 201 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 113 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 216 LEU 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 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 907 ASN 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 637 SER Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 955 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 280 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 907 ASN C 14 GLN C 115 GLN C 314 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3723 r_free = 0.3723 target = 0.097362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.063411 restraints weight = 76039.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065173 restraints weight = 38021.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.065267 restraints weight = 24700.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.065580 restraints weight = 25785.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065783 restraints weight = 22481.155| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 27927 Z= 0.325 Angle : 0.752 12.154 38166 Z= 0.371 Chirality : 0.047 0.303 4548 Planarity : 0.005 0.065 4761 Dihedral : 5.209 41.712 3549 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 2.56 % Allowed : 12.40 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3278 helix: 1.34 (0.19), residues: 723 sheet: 0.19 (0.18), residues: 698 loop : -0.99 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 646 TYR 0.024 0.002 TYR B 636 PHE 0.026 0.002 PHE A 168 TRP 0.020 0.002 TRP A 436 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.33 (27790) covalent geometry : angle 0.72709 / 0.37 (37801) SS BOND : bond 0.00335 / 0.22 ( 43) SS BOND : angle 1.52075 / 1.21 ( 86) hydrogen bonds : bond 0.04613 / 3.10 ( 1103) hydrogen bonds : angle 5.96009 / 4.13 ( 3105) Misc. bond : bond 0.00006 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00881 / 0.47 ( 6) link_ALPHA1-4 : angle 1.82043 / 1.24 ( 18) link_BETA1-4 : bond 0.00263 / 0.16 ( 29) link_BETA1-4 : angle 1.56761 / 1.10 ( 87) link_BETA1-6 : bond 0.00535 / 0.27 ( 3) link_BETA1-6 : angle 1.34604 / 0.82 ( 9) link_NAG-ASN : bond 0.00443 / 0.31 ( 55) link_NAG-ASN : angle 2.61348 / 1.71 ( 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 249 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 175 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9142 (t) cc_final: 0.8764 (m) REVERT: B 177 MET cc_start: 0.6301 (ppp) cc_final: 0.5791 (ppp) REVERT: C 66 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7758 (p90) REVERT: C 140 PHE cc_start: 0.8643 (p90) cc_final: 0.7841 (p90) REVERT: C 177 MET cc_start: 0.7517 (ppp) cc_final: 0.6285 (ptt) REVERT: C 338 PHE cc_start: 0.7765 (m-80) cc_final: 0.7531 (m-80) REVERT: C 402 ILE cc_start: 0.8564 (pt) cc_final: 0.8362 (pt) REVERT: C 517 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7856 (mp) REVERT: C 584 ILE cc_start: 0.8354 (mm) cc_final: 0.8075 (mm) REVERT: C 977 LEU cc_start: 0.8795 (tp) cc_final: 0.8391 (mp) REVERT: C 1148 PHE cc_start: 0.5500 (OUTLIER) cc_final: 0.4778 (m-10) REVERT: A 191 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8381 (mt-10) REVERT: A 201 PHE cc_start: 0.8527 (t80) cc_final: 0.8148 (t80) REVERT: A 428 ASP cc_start: 0.8348 (p0) cc_final: 0.6996 (t0) REVERT: A 430 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.7011 (p) REVERT: A 434 ILE cc_start: 0.7589 (mp) cc_final: 0.7378 (mm) REVERT: A 637 SER cc_start: 0.1512 (OUTLIER) cc_final: 0.1017 (p) outliers start: 74 outliers final: 44 residues processed: 236 average time/residue: 0.1566 time to fit residues: 63.3885 Evaluate side-chains 197 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 147 LYS 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 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 216 LEU 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 457 ARG 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 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 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 377 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 833 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 912 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 256 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 292 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 148 optimal weight: 0.1980 chunk 309 optimal weight: 0.8980 chunk 296 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 519 HIS C 613 GLN C 836 GLN A 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.099743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066281 restraints weight = 75236.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068124 restraints weight = 37049.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068188 restraints weight = 23964.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.068526 restraints weight = 24904.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068726 restraints weight = 21790.049| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27927 Z= 0.124 Angle : 0.616 13.077 38166 Z= 0.305 Chirality : 0.044 0.262 4548 Planarity : 0.004 0.066 4761 Dihedral : 4.800 28.186 3547 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 1.77 % Allowed : 13.57 % 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: -0.06 (0.14), residues: 3278 helix: 1.83 (0.20), residues: 722 sheet: 0.10 (0.18), residues: 722 loop : -0.88 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.019 0.001 TYR B1067 PHE 0.029 0.001 PHE B 79 TRP 0.024 0.001 TRP A 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (27790) covalent geometry : angle 0.59397 / 0.30 (37801) SS BOND : bond 0.00257 / 0.16 ( 43) SS BOND : angle 1.35820 / 1.07 ( 86) hydrogen bonds : bond 0.03830 / 2.55 ( 1103) hydrogen bonds : angle 5.62390 / 3.90 ( 3105) Misc. bond : bond 0.00008 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00798 / 0.43 ( 6) link_ALPHA1-4 : angle 1.61111 / 1.06 ( 18) link_BETA1-4 : bond 0.00332 / 0.21 ( 29) link_BETA1-4 : angle 1.23722 / 0.88 ( 87) link_BETA1-6 : bond 0.00636 / 0.32 ( 3) link_BETA1-6 : angle 1.07855 / 0.65 ( 9) link_NAG-ASN : bond 0.00327 / 0.23 ( 55) link_NAG-ASN : angle 2.22278 / 1.41 ( 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 225 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9053 (t) cc_final: 0.8598 (m) REVERT: B 129 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8009 (tppt) REVERT: B 177 MET cc_start: 0.6218 (ppp) cc_final: 0.5764 (ppp) REVERT: B 430 THR cc_start: 0.9181 (m) cc_final: 0.8917 (t) REVERT: C 66 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7852 (p90) REVERT: C 140 PHE cc_start: 0.8612 (p90) cc_final: 0.7733 (p90) REVERT: C 177 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6267 (ptt) REVERT: C 338 PHE cc_start: 0.7800 (m-80) cc_final: 0.7536 (m-80) REVERT: C 402 ILE cc_start: 0.8608 (pt) cc_final: 0.8357 (pt) REVERT: C 637 SER cc_start: 0.6336 (OUTLIER) cc_final: 0.6017 (t) REVERT: C 977 LEU cc_start: 0.8684 (tp) cc_final: 0.8288 (mp) REVERT: C 1041 ASP cc_start: 0.8033 (t70) cc_final: 0.7696 (t70) REVERT: C 1148 PHE cc_start: 0.5546 (OUTLIER) cc_final: 0.5004 (m-80) REVERT: A 175 PHE cc_start: 0.6698 (p90) cc_final: 0.6302 (p90) REVERT: A 191 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 314 GLN cc_start: 0.7972 (tp-100) cc_final: 0.7719 (tp-100) REVERT: A 428 ASP cc_start: 0.8296 (p0) cc_final: 0.6970 (t0) REVERT: A 430 THR cc_start: 0.7016 (OUTLIER) cc_final: 0.6633 (p) REVERT: A 637 SER cc_start: 0.1700 (OUTLIER) cc_final: 0.1070 (p) REVERT: A 921 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8433 (ttpt) outliers start: 51 outliers final: 26 residues processed: 213 average time/residue: 0.1512 time to fit residues: 55.3420 Evaluate side-chains 188 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 147 LYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 113 LYS 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 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 1043 CYS 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 227 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 231 ILE 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 921 LYS 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: 2.9990 chunk 290 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 300 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN C 856 ASN C 965 GLN A 99 ASN A 121 ASN A 125 ASN A 188 ASN A 207 HIS ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.095733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.060728 restraints weight = 75995.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.063162 restraints weight = 36118.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064678 restraints weight = 23737.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.065568 restraints weight = 18691.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.066066 restraints weight = 16361.427| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.138 27927 Z= 0.394 Angle : 0.810 13.431 38166 Z= 0.396 Chirality : 0.049 0.289 4548 Planarity : 0.005 0.060 4761 Dihedral : 5.294 24.790 3547 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 2.25 % Allowed : 13.68 % Favored : 84.07 % 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: -0.54 (0.14), residues: 3278 helix: 1.16 (0.19), residues: 742 sheet: -0.13 (0.18), residues: 737 loop : -1.11 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 408 TYR 0.025 0.002 TYR B1067 PHE 0.022 0.002 PHE B 79 TRP 0.022 0.002 TRP C 64 HIS 0.006 0.002 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.39 (27790) covalent geometry : angle 0.78453 / 0.39 (37801) SS BOND : bond 0.00574 / 0.40 ( 43) SS BOND : angle 1.58278 / 1.26 ( 86) hydrogen bonds : bond 0.04751 / 3.17 ( 1103) hydrogen bonds : angle 6.03294 / 4.19 ( 3105) Misc. bond : bond 0.00013 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00820 / 0.45 ( 6) link_ALPHA1-4 : angle 1.74636 / 1.21 ( 18) link_BETA1-4 : bond 0.00285 / 0.19 ( 29) link_BETA1-4 : angle 1.74596 / 1.20 ( 87) link_BETA1-6 : bond 0.00565 / 0.28 ( 3) link_BETA1-6 : angle 1.39003 / 0.87 ( 9) link_NAG-ASN : bond 0.00586 / 0.41 ( 55) link_NAG-ASN : angle 2.70357 / 1.81 ( 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 228 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 163 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9258 (t) cc_final: 0.8811 (p) REVERT: B 95 THR cc_start: 0.8629 (p) cc_final: 0.8416 (p) REVERT: B 129 LYS cc_start: 0.8300 (mmtm) cc_final: 0.7635 (mmtm) REVERT: B 147 LYS cc_start: 0.5279 (OUTLIER) cc_final: 0.4310 (mmtp) REVERT: B 177 MET cc_start: 0.6258 (ppp) cc_final: 0.5937 (ppp) REVERT: B 316 SER cc_start: 0.9456 (t) cc_final: 0.8881 (p) REVERT: C 66 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.7649 (p90) REVERT: C 127 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8838 (m) REVERT: C 131 CYS cc_start: 0.3597 (OUTLIER) cc_final: 0.3116 (m) REVERT: C 140 PHE cc_start: 0.8708 (p90) cc_final: 0.7861 (p90) REVERT: C 177 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6606 (ptt) REVERT: C 402 ILE cc_start: 0.8604 (pt) cc_final: 0.8391 (pt) REVERT: C 517 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7776 (mp) REVERT: C 1148 PHE cc_start: 0.5419 (OUTLIER) cc_final: 0.4692 (m-80) REVERT: A 144 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: A 168 PHE cc_start: 0.6947 (t80) cc_final: 0.6555 (t80) REVERT: A 175 PHE cc_start: 0.6890 (p90) cc_final: 0.6472 (p90) REVERT: A 314 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7820 (tp-100) REVERT: A 428 ASP cc_start: 0.8449 (p0) cc_final: 0.7266 (t0) REVERT: A 430 THR cc_start: 0.6773 (OUTLIER) cc_final: 0.6376 (p) REVERT: A 637 SER cc_start: 0.1921 (OUTLIER) cc_final: 0.1056 (p) REVERT: A 1145 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8963 (tt) REVERT: A 1155 TYR cc_start: -0.1613 (OUTLIER) cc_final: -0.2684 (m-80) outliers start: 65 outliers final: 36 residues processed: 215 average time/residue: 0.1444 time to fit residues: 53.4717 Evaluate side-chains 189 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 147 LYS 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 637 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1141 LEU 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 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 341 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 495 TYR 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 1148 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 ASP 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 596 SER Chi-restraints excluded: chain A residue 637 SER 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 833 PHE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1145 LEU 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: 0.8980 chunk 67 optimal weight: 0.7980 chunk 229 optimal weight: 9.9990 chunk 193 optimal weight: 0.5980 chunk 190 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 303 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN A 66 HIS A 99 ASN A 137 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.099958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068214 restraints weight = 75628.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.069651 restraints weight = 36261.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.069586 restraints weight = 24499.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070109 restraints weight = 26599.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.070206 restraints weight = 22225.740| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27927 Z= 0.132 Angle : 0.635 12.296 38166 Z= 0.313 Chirality : 0.044 0.253 4548 Planarity : 0.004 0.063 4761 Dihedral : 4.865 21.226 3547 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 1.73 % Allowed : 14.40 % Favored : 83.86 % 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: 1.67 (0.20), residues: 737 sheet: 0.02 (0.18), residues: 722 loop : -0.98 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 408 TYR 0.019 0.001 TYR C1067 PHE 0.027 0.001 PHE A 497 TRP 0.025 0.001 TRP A 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (27790) covalent geometry : angle 0.61448 / 0.31 (37801) SS BOND : bond 0.00436 / 0.27 ( 43) SS BOND : angle 1.34427 / 1.11 ( 86) hydrogen bonds : bond 0.03893 / 2.58 ( 1103) hydrogen bonds : angle 5.65350 / 3.92 ( 3105) Misc. bond : bond 0.00001 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00816 / 0.47 ( 6) link_ALPHA1-4 : angle 1.50533 / 0.99 ( 18) link_BETA1-4 : bond 0.00306 / 0.19 ( 29) link_BETA1-4 : angle 1.23749 / 0.86 ( 87) link_BETA1-6 : bond 0.00656 / 0.33 ( 3) link_BETA1-6 : angle 1.22571 / 0.75 ( 9) link_NAG-ASN : bond 0.00351 / 0.26 ( 55) link_NAG-ASN : angle 2.17447 / 1.39 ( 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 217 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9112 (t) cc_final: 0.8737 (m) REVERT: B 95 THR cc_start: 0.8572 (p) cc_final: 0.8369 (p) REVERT: B 129 LYS cc_start: 0.8313 (mmtm) cc_final: 0.7633 (mmtm) REVERT: B 177 MET cc_start: 0.6206 (ppp) cc_final: 0.5902 (ppp) REVERT: C 63 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8754 (p) REVERT: C 66 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.7620 (p90) REVERT: C 131 CYS cc_start: 0.3645 (OUTLIER) cc_final: 0.3115 (m) REVERT: C 140 PHE cc_start: 0.8656 (p90) cc_final: 0.7821 (p90) REVERT: C 177 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6575 (ptt) REVERT: C 402 ILE cc_start: 0.8633 (pt) cc_final: 0.8422 (pt) REVERT: C 517 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7756 (mp) REVERT: C 1041 ASP cc_start: 0.8018 (t70) cc_final: 0.7673 (t70) REVERT: C 1148 PHE cc_start: 0.5444 (OUTLIER) cc_final: 0.4846 (m-80) REVERT: A 144 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.7181 (m-10) REVERT: A 168 PHE cc_start: 0.6708 (t80) cc_final: 0.6421 (t80) REVERT: A 175 PHE cc_start: 0.6748 (p90) cc_final: 0.6308 (p90) REVERT: A 191 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8210 (mt-10) REVERT: A 314 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7757 (tp-100) REVERT: A 428 ASP cc_start: 0.8240 (p0) cc_final: 0.7146 (t0) REVERT: A 430 THR cc_start: 0.6552 (OUTLIER) cc_final: 0.6122 (p) REVERT: A 434 ILE cc_start: 0.7348 (mm) cc_final: 0.6991 (mm) REVERT: A 1145 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8882 (tt) REVERT: A 1155 TYR cc_start: -0.1674 (OUTLIER) cc_final: -0.2658 (m-80) outliers start: 50 outliers final: 30 residues processed: 206 average time/residue: 0.1582 time to fit residues: 56.0684 Evaluate side-chains 190 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 858 LEU 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 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR 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 341 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 740 MET 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 144 TYR Chi-restraints excluded: chain A residue 227 VAL 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 430 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 739 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 1043 CYS Chi-restraints excluded: chain A residue 1145 LEU 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: 3.9990 chunk 84 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 250 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.098501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066649 restraints weight = 76136.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067985 restraints weight = 37200.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067945 restraints weight = 25253.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.068440 restraints weight = 27267.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.068523 restraints weight = 22857.184| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 27927 Z= 0.225 Angle : 0.667 12.018 38166 Z= 0.327 Chirality : 0.045 0.264 4548 Planarity : 0.004 0.061 4761 Dihedral : 4.889 20.749 3547 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 1.80 % Allowed : 14.51 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3278 helix: 1.53 (0.20), residues: 749 sheet: -0.07 (0.18), residues: 734 loop : -0.96 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 408 TYR 0.029 0.002 TYR B 269 PHE 0.035 0.002 PHE A 497 TRP 0.026 0.002 TRP A 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.23 (27790) covalent geometry : angle 0.64512 / 0.32 (37801) SS BOND : bond 0.00314 / 0.20 ( 43) SS BOND : angle 1.35785 / 1.11 ( 86) hydrogen bonds : bond 0.04080 / 2.70 ( 1103) hydrogen bonds : angle 5.68244 / 3.95 ( 3105) Misc. bond : bond 0.00013 / 0.01 ( 1) link_ALPHA1-4 : bond 0.00763 / 0.42 ( 6) link_ALPHA1-4 : angle 1.55024 / 1.06 ( 18) link_BETA1-4 : bond 0.00206 / 0.12 ( 29) link_BETA1-4 : angle 1.38507 / 0.96 ( 87) link_BETA1-6 : bond 0.00565 / 0.29 ( 3) link_BETA1-6 : angle 1.31109 / 0.81 ( 9) link_NAG-ASN : bond 0.00375 / 0.28 ( 55) link_NAG-ASN : angle 2.27594 / 1.47 ( 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 206 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9078 (t) cc_final: 0.8585 (p) REVERT: B 177 MET cc_start: 0.6240 (ppp) cc_final: 0.5947 (ppp) REVERT: C 63 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8752 (p) REVERT: C 66 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.7620 (p90) REVERT: C 127 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8948 (m) REVERT: C 131 CYS cc_start: 0.3622 (OUTLIER) cc_final: 0.3092 (m) REVERT: C 140 PHE cc_start: 0.8681 (p90) cc_final: 0.7838 (p90) REVERT: C 177 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.6752 (ptt) REVERT: C 317 ASN cc_start: 0.7947 (m-40) cc_final: 0.7151 (m110) REVERT: C 402 ILE cc_start: 0.8607 (pt) cc_final: 0.8383 (pt) REVERT: C 517 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7805 (mp) REVERT: C 1148 PHE cc_start: 0.5512 (OUTLIER) cc_final: 0.4880 (m-80) REVERT: A 144 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: A 168 PHE cc_start: 0.7037 (t80) cc_final: 0.6575 (t80) REVERT: A 175 PHE cc_start: 0.6741 (p90) cc_final: 0.6255 (p90) REVERT: A 314 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7799 (tp-100) REVERT: A 380 TYR cc_start: 0.5919 (m-80) cc_final: 0.5580 (m-80) REVERT: A 434 ILE cc_start: 0.7326 (mm) cc_final: 0.6943 (mm) REVERT: A 855 PHE cc_start: 0.8598 (m-10) cc_final: 0.8370 (m-80) REVERT: A 902 MET cc_start: 0.9205 (mmt) cc_final: 0.8994 (tpt) REVERT: A 1155 TYR cc_start: -0.1685 (OUTLIER) cc_final: -0.2678 (m-80) outliers start: 52 outliers final: 38 residues processed: 192 average time/residue: 0.1546 time to fit residues: 52.0520 Evaluate side-chains 190 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 231 ILE Chi-restraints excluded: chain B residue 633 TRP 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 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR 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 341 VAL Chi-restraints excluded: chain C residue 389 ASP 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 740 MET 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 227 VAL 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 596 SER Chi-restraints excluded: chain A residue 739 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 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: 3.9990 chunk 263 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 280 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.098986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067301 restraints weight = 75712.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.068650 restraints weight = 36692.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.068596 restraints weight = 24968.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.068974 restraints weight = 26742.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.069176 restraints weight = 22911.263| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27927 Z= 0.183 Angle : 0.634 11.942 38166 Z= 0.312 Chirality : 0.044 0.264 4548 Planarity : 0.004 0.064 4761 Dihedral : 4.789 22.182 3547 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 1.66 % Allowed : 14.85 % Favored : 83.48 % 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: -0.18 (0.14), residues: 3278 helix: 1.66 (0.20), residues: 748 sheet: 0.04 (0.18), residues: 712 loop : -0.96 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1107 TYR 0.022 0.001 TYR C 904 PHE 0.040 0.001 PHE A 497 TRP 0.028 0.001 TRP A 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (27790) covalent geometry : angle 0.61470 / 0.31 (37801) SS BOND : bond 0.00428 / 0.28 ( 43) SS BOND : angle 1.20878 / 0.96 ( 86) hydrogen bonds : bond 0.03891 / 2.58 ( 1103) hydrogen bonds : angle 5.59466 / 3.89 ( 3105) Misc. bond : bond 0.00003 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00752 / 0.41 ( 6) link_ALPHA1-4 : angle 1.49312 / 1.00 ( 18) link_BETA1-4 : bond 0.00250 / 0.15 ( 29) link_BETA1-4 : angle 1.25798 / 0.87 ( 87) link_BETA1-6 : bond 0.00599 / 0.30 ( 3) link_BETA1-6 : angle 1.27996 / 0.79 ( 9) link_NAG-ASN : bond 0.00318 / 0.24 ( 55) link_NAG-ASN : angle 2.13518 / 1.37 ( 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 201 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.9079 (t) cc_final: 0.8571 (p) REVERT: B 177 MET cc_start: 0.6257 (ppp) cc_final: 0.5976 (ppp) REVERT: B 1084 ASP cc_start: 0.8151 (t0) cc_final: 0.7932 (t0) REVERT: C 63 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8751 (p) REVERT: C 66 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7742 (p90) REVERT: C 95 THR cc_start: 0.9221 (p) cc_final: 0.8945 (p) REVERT: C 131 CYS cc_start: 0.3645 (OUTLIER) cc_final: 0.3132 (m) REVERT: C 177 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.6787 (ptt) REVERT: C 402 ILE cc_start: 0.8618 (pt) cc_final: 0.8377 (pt) REVERT: C 517 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7779 (mp) REVERT: C 904 TYR cc_start: 0.7700 (m-10) cc_final: 0.6889 (m-10) REVERT: C 1148 PHE cc_start: 0.5465 (OUTLIER) cc_final: 0.4857 (m-80) REVERT: A 144 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.7233 (m-10) REVERT: A 168 PHE cc_start: 0.6998 (t80) cc_final: 0.6477 (t80) REVERT: A 175 PHE cc_start: 0.6737 (p90) cc_final: 0.6246 (p90) REVERT: A 314 GLN cc_start: 0.8059 (tp-100) cc_final: 0.7772 (tp-100) REVERT: A 380 TYR cc_start: 0.5771 (m-80) cc_final: 0.5553 (m-80) REVERT: A 434 ILE cc_start: 0.7357 (mm) cc_final: 0.6991 (mm) REVERT: A 1155 TYR cc_start: -0.1643 (OUTLIER) cc_final: -0.2612 (m-80) outliers start: 48 outliers final: 36 residues processed: 190 average time/residue: 0.1548 time to fit residues: 50.8552 Evaluate side-chains 191 residues out of total 2888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 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 858 LEU 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 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR 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 177 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 389 ASP 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 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 227 VAL 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 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 841 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1043 CYS 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: 1.9990 chunk 208 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 136 optimal weight: 0.1980 chunk 135 optimal weight: 1.9990 chunk 207 optimal weight: 0.2980 chunk 120 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.099195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.067555 restraints weight = 75209.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.068688 restraints weight = 36765.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.068878 restraints weight = 25691.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.069326 restraints weight = 26930.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.069380 restraints weight = 23068.469| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.295 27927 Z= 0.206 Angle : 0.758 59.186 38166 Z= 0.406 Chirality : 0.045 0.796 4548 Planarity : 0.004 0.062 4761 Dihedral : 4.825 36.314 3547 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 1.87 % Allowed : 14.82 % Favored : 83.31 % 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: -0.17 (0.14), residues: 3278 helix: 1.68 (0.20), residues: 748 sheet: 0.04 (0.18), residues: 712 loop : -0.96 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG A 190 TYR 0.023 0.001 TYR C 904 PHE 0.063 0.002 PHE C 497 TRP 0.024 0.001 TRP A 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (27790) covalent geometry : angle 0.74291 / 0.40 (37801) SS BOND : bond 0.00296 / 0.20 ( 43) SS BOND : angle 1.19918 / 0.95 ( 86) hydrogen bonds : bond 0.03865 / 2.56 ( 1103) hydrogen bonds : angle 5.59774 / 3.89 ( 3105) Misc. bond : bond 0.00006 / 0.00 ( 1) link_ALPHA1-4 : bond 0.00725 / 0.39 ( 6) link_ALPHA1-4 : angle 1.49171 / 1.00 ( 18) link_BETA1-4 : bond 0.00250 / 0.15 ( 29) link_BETA1-4 : angle 1.25608 / 0.86 ( 87) link_BETA1-6 : bond 0.00553 / 0.28 ( 3) link_BETA1-6 : angle 1.26347 / 0.77 ( 9) link_NAG-ASN : bond 0.00315 / 0.24 ( 55) link_NAG-ASN : angle 2.13675 / 1.37 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4711.89 seconds wall clock time: 82 minutes 33.14 seconds (4953.14 seconds total)