Starting phenix.real_space_refine on Fri Feb 6 17:42:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n1x_24126/02_2026/7n1x_24126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n1x_24126/02_2026/7n1x_24126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n1x_24126/02_2026/7n1x_24126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n1x_24126/02_2026/7n1x_24126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n1x_24126/02_2026/7n1x_24126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n1x_24126/02_2026/7n1x_24126.map" } resolution = 4.0 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= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 17037 2.51 5 N 4338 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26810 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8434 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 52, 'TRANS': 1024} Chain breaks: 5 Chain: "B" Number of atoms: 8522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8522 Classifications: {'peptide': 1088} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8554 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 53, 'TRANS': 1038} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.68, per 1000 atoms: 0.25 Number of scatterers: 26810 At special positions: 0 Unit cell: (155.938, 154.288, 216.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5321 8.00 N 4338 7.00 C 17037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.01 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.06 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 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=2.00 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 234 " " NAG A1406 " - " ASN A 282 " " NAG A1407 " - " ASN A 343 " " 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 C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.3 seconds 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6102 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 48 sheets defined 26.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 368 removed outlier: 4.646A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.516A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.638A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.931A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.119A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.614A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 866 through 882 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.775A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.570A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.794A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 954 " --> pdb=" O ASP A 950 " (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 977 through 982 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.999A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1161 removed outlier: 3.853A pdb=" N LYS A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.092A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.878A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 5.447A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.013A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.672A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (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 760 through 783 removed outlier: 3.808A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 3.570A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.633A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.568A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.258A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 978 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.003A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.510A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.675A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.046A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.531A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.614A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.620A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.516A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.585A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.731A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.582A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 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: 3.758A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.555A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.167A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 4.134A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.789A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 11.218A pdb=" N SER A 221 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.148A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.562A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.353A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.045A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.109A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.780A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.525A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.769A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.769A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.451A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.424A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.256A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.256A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.503A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 9.249A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.244A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.077A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.212A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.953A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.811A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.220A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.334A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.551A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.243A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.765A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.621A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.352A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.627A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 142 through 144 removed outlier: 6.300A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.090A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.308A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.181A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.371A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.514A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.514A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.447A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.416A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2898 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: 6.83 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4356 1.30 - 1.43: 7337 1.43 - 1.56: 15563 1.56 - 1.70: 4 1.70 - 1.83: 144 Bond restraints: 27404 Sorted by residual: bond pdb=" C ARG B1014 " pdb=" O ARG B1014 " ideal model delta sigma weight residual 1.237 1.172 0.064 1.19e-02 7.06e+03 2.91e+01 bond pdb=" N ARG C1000 " pdb=" CA ARG C1000 " ideal model delta sigma weight residual 1.459 1.401 0.059 1.20e-02 6.94e+03 2.39e+01 bond pdb=" CA ARG A1014 " pdb=" CB ARG A1014 " ideal model delta sigma weight residual 1.529 1.451 0.077 1.62e-02 3.81e+03 2.28e+01 bond pdb=" N ARG A 509 " pdb=" CA ARG A 509 " ideal model delta sigma weight residual 1.457 1.515 -0.058 1.23e-02 6.61e+03 2.20e+01 bond pdb=" CA ARG C 466 " pdb=" C ARG C 466 " ideal model delta sigma weight residual 1.520 1.575 -0.055 1.20e-02 6.94e+03 2.09e+01 ... (remaining 27399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 31093 2.60 - 5.21: 5804 5.21 - 7.81: 359 7.81 - 10.42: 17 10.42 - 13.02: 5 Bond angle restraints: 37278 Sorted by residual: angle pdb=" OD1 ASN C 61 " pdb=" CG ASN C 61 " pdb=" ND2 ASN C 61 " ideal model delta sigma weight residual 122.60 114.14 8.46 1.00e+00 1.00e+00 7.15e+01 angle pdb=" OD1 ASN B 331 " pdb=" CG ASN B 331 " pdb=" ND2 ASN B 331 " ideal model delta sigma weight residual 122.60 114.92 7.68 1.00e+00 1.00e+00 5.90e+01 angle pdb=" CB ASN C 61 " pdb=" CG ASN C 61 " pdb=" ND2 ASN C 61 " ideal model delta sigma weight residual 116.40 127.55 -11.15 1.50e+00 4.44e-01 5.53e+01 angle pdb=" CB ASN B 331 " pdb=" CG ASN B 331 " pdb=" ND2 ASN B 331 " ideal model delta sigma weight residual 116.40 127.25 -10.85 1.50e+00 4.44e-01 5.24e+01 angle pdb=" CA ASP A 570 " pdb=" CB ASP A 570 " pdb=" CG ASP A 570 " ideal model delta sigma weight residual 112.60 119.67 -7.07 1.00e+00 1.00e+00 5.00e+01 ... (remaining 37273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.75: 16685 25.75 - 51.50: 662 51.50 - 77.25: 131 77.25 - 103.00: 43 103.00 - 128.75: 16 Dihedral angle restraints: 17537 sinusoidal: 8052 harmonic: 9485 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.73 69.73 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 156.66 -63.66 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CA GLY B 526 " pdb=" C GLY B 526 " pdb=" N PRO B 527 " pdb=" CA PRO B 527 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 17534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.684: 4477 0.684 - 1.369: 6 1.369 - 2.053: 1 2.053 - 2.738: 3 2.738 - 3.422: 1 Chirality restraints: 4488 Sorted by residual: chirality pdb=" C1 NAG A1402 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1402 " pdb=" O5 NAG A1402 " both_signs ideal model delta sigma weight residual False -2.40 1.02 -3.42 2.00e-01 2.50e+01 2.93e+02 chirality pdb=" C1 NAG B1405 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1405 " pdb=" O5 NAG B1405 " both_signs ideal model delta sigma weight residual False -2.40 0.32 -2.72 2.00e-01 2.50e+01 1.85e+02 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 0.20 -2.60 2.00e-01 2.50e+01 1.69e+02 ... (remaining 4485 not shown) Planarity restraints: 4745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.343 2.00e-02 2.50e+03 3.70e-01 1.71e+03 pdb=" CG ASN A 343 " 0.119 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.614 2.00e-02 2.50e+03 pdb=" C1 NAG A1407 " -0.420 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.279 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" CG ASN B 343 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.479 2.00e-02 2.50e+03 pdb=" C1 NAG B1405 " -0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 17 " -0.243 2.00e-02 2.50e+03 2.41e-01 7.29e+02 pdb=" CG ASN B 17 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN B 17 " 0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN B 17 " 0.381 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.277 2.00e-02 2.50e+03 ... (remaining 4742 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 18 2.17 - 2.85: 7546 2.85 - 3.53: 37581 3.53 - 4.22: 63806 4.22 - 4.90: 105353 Nonbonded interactions: 214304 Sorted by model distance: nonbonded pdb=" NH2 ARG B 905 " pdb=" O LEU B1049 " model vdw 1.484 3.120 nonbonded pdb=" O MET B 900 " pdb=" CD2 TYR B 904 " model vdw 1.609 3.340 nonbonded pdb=" O HIS C 66 " pdb=" NH1 ARG C 78 " model vdw 1.711 3.120 nonbonded pdb=" OE1 GLU B 132 " pdb=" ND2 ASN B 165 " model vdw 1.725 3.120 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 1.823 3.120 ... (remaining 214299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 826 or resid 855 through 1408)) selection = (chain 'B' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1408)) selection = (chain 'C' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.230 Find NCS groups from input model: 0.620 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: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 : 0.016 0.462 27539 Z= 0.884 Angle : 2.044 46.420 37641 Z= 1.266 Chirality : 0.142 3.422 4488 Planarity : 0.014 0.120 4690 Dihedral : 15.454 128.749 11309 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.13 % Favored : 91.25 % Rotamer: Outliers : 1.97 % Allowed : 6.22 % Favored : 91.82 % Cbeta Deviations : 0.43 % 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: -2.39 (0.13), residues: 3223 helix: -2.19 (0.16), residues: 704 sheet: -0.17 (0.21), residues: 546 loop : -1.83 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A1000 TYR 0.107 0.020 TYR A 674 PHE 0.117 0.016 PHE A1121 TRP 0.197 0.039 TRP C 258 HIS 0.016 0.004 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.01410 (27404) covalent geometry : angle 1.89450 (37278) SS BOND : bond 0.01282 ( 42) SS BOND : angle 2.41078 ( 84) hydrogen bonds : bond 0.17129 ( 1034) hydrogen bonds : angle 9.23249 ( 2898) link_ALPHA1-4 : bond 0.02746 ( 6) link_ALPHA1-4 : angle 3.79525 ( 18) link_BETA1-4 : bond 0.01872 ( 29) link_BETA1-4 : angle 3.53109 ( 87) link_BETA1-6 : bond 0.03503 ( 3) link_BETA1-6 : angle 3.35661 ( 9) link_NAG-ASN : bond 0.17293 ( 55) link_NAG-ASN : angle 11.42239 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 797 time to evaluate : 1.128 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: A 40 ASP cc_start: 0.6386 (p0) cc_final: 0.6131 (p0) REVERT: A 81 ASN cc_start: 0.7920 (p0) cc_final: 0.7693 (p0) REVERT: A 144 TYR cc_start: 0.7887 (m-80) cc_final: 0.7559 (m-80) REVERT: A 304 LYS cc_start: 0.7982 (tptt) cc_final: 0.7719 (tptt) REVERT: A 364 ASP cc_start: 0.6241 (t0) cc_final: 0.5999 (t70) REVERT: A 551 VAL cc_start: 0.7927 (t) cc_final: 0.7689 (p) REVERT: A 565 PHE cc_start: 0.6760 (m-80) cc_final: 0.6434 (m-10) REVERT: A 571 ASP cc_start: 0.7124 (m-30) cc_final: 0.6551 (m-30) REVERT: A 740 MET cc_start: 0.7666 (mtm) cc_final: 0.7332 (mtm) REVERT: A 755 GLN cc_start: 0.7277 (tp-100) cc_final: 0.7039 (tp-100) REVERT: A 777 ASN cc_start: 0.7834 (m-40) cc_final: 0.7579 (m-40) REVERT: A 779 GLN cc_start: 0.7765 (tt0) cc_final: 0.7518 (tt0) REVERT: A 788 ILE cc_start: 0.7874 (mm) cc_final: 0.7665 (mp) REVERT: A 806 LEU cc_start: 0.8648 (mm) cc_final: 0.8380 (mm) REVERT: A 825 LYS cc_start: 0.7469 (mttm) cc_final: 0.7050 (tttp) REVERT: A 870 ILE cc_start: 0.8341 (mt) cc_final: 0.7990 (mp) REVERT: A 935 GLN cc_start: 0.7054 (mt0) cc_final: 0.6781 (mt0) REVERT: A 936 ASP cc_start: 0.7865 (t0) cc_final: 0.7625 (t70) REVERT: A 957 GLN cc_start: 0.7073 (tp40) cc_final: 0.6778 (tp40) REVERT: A 1005 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7246 (mm-40) REVERT: A 1148 PHE cc_start: 0.6268 (m-80) cc_final: 0.5954 (m-10) REVERT: B 48 LEU cc_start: 0.8138 (mp) cc_final: 0.7759 (mt) REVERT: B 53 ASP cc_start: 0.7327 (m-30) cc_final: 0.6827 (m-30) REVERT: B 129 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7546 (mmtt) REVERT: B 141 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6255 (tp) REVERT: B 152 TRP cc_start: 0.3053 (m100) cc_final: 0.1911 (m100) REVERT: B 157 PHE cc_start: 0.5838 (t80) cc_final: 0.5065 (t80) REVERT: B 226 LEU cc_start: 0.7633 (mp) cc_final: 0.7369 (mp) REVERT: B 227 VAL cc_start: 0.7851 (p) cc_final: 0.7539 (t) REVERT: B 238 PHE cc_start: 0.6764 (p90) cc_final: 0.5698 (p90) REVERT: B 286 THR cc_start: 0.7599 (m) cc_final: 0.7363 (p) REVERT: B 293 LEU cc_start: 0.7897 (tt) cc_final: 0.7681 (tt) REVERT: B 304 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7295 (tmmt) REVERT: B 310 LYS cc_start: 0.8791 (tttt) cc_final: 0.8402 (tmtt) REVERT: B 313 TYR cc_start: 0.7822 (m-80) cc_final: 0.7604 (m-80) REVERT: B 402 ILE cc_start: 0.7584 (tp) cc_final: 0.7333 (mm) REVERT: B 421 TYR cc_start: 0.3912 (p90) cc_final: 0.3384 (p90) REVERT: B 468 ILE cc_start: 0.7122 (pt) cc_final: 0.6894 (tp) REVERT: B 540 ASN cc_start: 0.7504 (t0) cc_final: 0.7301 (t0) REVERT: B 581 THR cc_start: 0.7079 (p) cc_final: 0.6737 (p) REVERT: B 611 LEU cc_start: 0.8620 (tp) cc_final: 0.8319 (tp) REVERT: B 613 GLN cc_start: 0.7547 (mt0) cc_final: 0.7156 (mt0) REVERT: B 644 GLN cc_start: 0.6620 (tp40) cc_final: 0.6414 (tp40) REVERT: B 659 SER cc_start: 0.7594 (m) cc_final: 0.7391 (t) REVERT: B 664 ILE cc_start: 0.8135 (mm) cc_final: 0.7586 (mm) REVERT: B 693 ILE cc_start: 0.8213 (pt) cc_final: 0.8004 (pt) REVERT: B 720 ILE cc_start: 0.8560 (mm) cc_final: 0.8139 (mm) REVERT: B 776 LYS cc_start: 0.8406 (tmtt) cc_final: 0.8133 (tttt) REVERT: B 806 LEU cc_start: 0.8811 (mt) cc_final: 0.8432 (mt) REVERT: B 877 LEU cc_start: 0.8438 (mt) cc_final: 0.8195 (mt) REVERT: B 895 GLN cc_start: 0.7615 (pm20) cc_final: 0.7224 (pm20) REVERT: B 907 ASN cc_start: 0.8152 (m-40) cc_final: 0.7322 (m110) REVERT: B 918 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7473 (tp30) REVERT: B 950 ASP cc_start: 0.7425 (m-30) cc_final: 0.7156 (m-30) REVERT: B 953 ASN cc_start: 0.7760 (m-40) cc_final: 0.7544 (m-40) REVERT: B 957 GLN cc_start: 0.7966 (tt0) cc_final: 0.7752 (tt0) REVERT: B 1037 SER cc_start: 0.8399 (t) cc_final: 0.8061 (p) REVERT: B 1096 VAL cc_start: 0.8336 (m) cc_final: 0.7914 (p) REVERT: B 1135 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7826 (m-40) REVERT: C 36 VAL cc_start: 0.7942 (t) cc_final: 0.7716 (m) REVERT: C 170 TYR cc_start: 0.6533 (m-80) cc_final: 0.6230 (m-80) REVERT: C 186 PHE cc_start: 0.6841 (m-80) cc_final: 0.6552 (m-80) REVERT: C 190 ARG cc_start: 0.7020 (mmt180) cc_final: 0.6679 (mmm-85) REVERT: C 271 GLN cc_start: 0.7954 (mp10) cc_final: 0.7646 (mp10) REVERT: C 278 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7736 (ttpt) REVERT: C 290 ASP cc_start: 0.6874 (t0) cc_final: 0.6596 (t0) REVERT: C 298 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8043 (mm-30) REVERT: C 313 TYR cc_start: 0.7445 (m-80) cc_final: 0.7230 (m-10) REVERT: C 353 TRP cc_start: 0.3185 (p-90) cc_final: 0.2690 (p-90) REVERT: C 355 ARG cc_start: 0.6715 (mtp85) cc_final: 0.6266 (mtp85) REVERT: C 388 ASN cc_start: 0.7289 (p0) cc_final: 0.6922 (p0) REVERT: C 392 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: C 402 ILE cc_start: 0.7444 (pt) cc_final: 0.7187 (pt) REVERT: C 403 ARG cc_start: 0.5329 (OUTLIER) cc_final: 0.4490 (ttp-170) REVERT: C 429 PHE cc_start: 0.7476 (t80) cc_final: 0.7146 (t80) REVERT: C 466 ARG cc_start: 0.4125 (OUTLIER) cc_final: 0.3279 (ttp80) REVERT: C 568 ASP cc_start: 0.6037 (t0) cc_final: 0.5217 (t0) REVERT: C 585 LEU cc_start: 0.7172 (mm) cc_final: 0.6924 (mp) REVERT: C 673 SER cc_start: 0.7018 (t) cc_final: 0.6160 (m) REVERT: C 699 LEU cc_start: 0.7517 (mp) cc_final: 0.7301 (mp) REVERT: C 779 GLN cc_start: 0.8041 (pp30) cc_final: 0.7470 (pp30) REVERT: C 864 LEU cc_start: 0.8005 (tp) cc_final: 0.7771 (tt) REVERT: C 873 TYR cc_start: 0.7851 (m-80) cc_final: 0.7302 (m-80) REVERT: C 877 LEU cc_start: 0.8521 (mt) cc_final: 0.8146 (mt) REVERT: C 915 VAL cc_start: 0.8348 (t) cc_final: 0.8099 (t) REVERT: C 919 ASN cc_start: 0.8100 (m-40) cc_final: 0.7700 (m110) REVERT: C 1008 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8057 (p) REVERT: C 1067 TYR cc_start: 0.8063 (t80) cc_final: 0.7545 (t80) REVERT: C 1145 LEU cc_start: 0.7857 (tp) cc_final: 0.7482 (tp) outliers start: 56 outliers final: 19 residues processed: 834 average time/residue: 0.1934 time to fit residues: 249.9596 Evaluate side-chains 659 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 634 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 1008 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 99 ASN A 317 ASN A 580 GLN A 655 HIS ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 804 GLN A 901 GLN A 926 GLN A 935 GLN A 954 GLN A 965 GLN B 164 ASN B 317 ASN B 409 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 925 ASN B 954 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN B1135 ASN C 52 GLN C 360 ASN C 954 GLN C 955 ASN C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.085813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.070194 restraints weight = 106991.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072310 restraints weight = 59619.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.073711 restraints weight = 39144.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074668 restraints weight = 28853.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.075329 restraints weight = 23116.973| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27539 Z= 0.185 Angle : 0.908 18.752 37641 Z= 0.443 Chirality : 0.053 0.699 4488 Planarity : 0.005 0.098 4690 Dihedral : 11.713 110.614 5509 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.23 % Allowed : 11.73 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3223 helix: -0.37 (0.19), residues: 714 sheet: -0.19 (0.20), residues: 615 loop : -1.39 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 905 TYR 0.027 0.002 TYR A1067 PHE 0.033 0.003 PHE C 157 TRP 0.025 0.002 TRP A 64 HIS 0.012 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00392 (27404) covalent geometry : angle 0.83419 (37278) SS BOND : bond 0.00624 ( 42) SS BOND : angle 2.31612 ( 84) hydrogen bonds : bond 0.05097 ( 1034) hydrogen bonds : angle 6.92718 ( 2898) link_ALPHA1-4 : bond 0.01248 ( 6) link_ALPHA1-4 : angle 2.33793 ( 18) link_BETA1-4 : bond 0.00456 ( 29) link_BETA1-4 : angle 2.13806 ( 87) link_BETA1-6 : bond 0.01476 ( 3) link_BETA1-6 : angle 1.98880 ( 9) link_NAG-ASN : bond 0.00659 ( 55) link_NAG-ASN : angle 4.98260 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 659 time to evaluate : 0.929 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: A 121 ASN cc_start: 0.5630 (t0) cc_final: 0.5272 (t0) REVERT: A 146 HIS cc_start: 0.5009 (p-80) cc_final: 0.3620 (m-70) REVERT: A 317 ASN cc_start: 0.5885 (OUTLIER) cc_final: 0.5346 (p0) REVERT: A 388 ASN cc_start: 0.4996 (m-40) cc_final: 0.4331 (t0) REVERT: A 466 ARG cc_start: 0.4788 (mtp85) cc_final: 0.4181 (ttt90) REVERT: A 551 VAL cc_start: 0.8168 (t) cc_final: 0.7821 (p) REVERT: A 565 PHE cc_start: 0.6758 (m-80) cc_final: 0.6539 (m-10) REVERT: A 661 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6706 (mm-30) REVERT: A 697 MET cc_start: 0.6942 (tpt) cc_final: 0.6706 (tpt) REVERT: A 779 GLN cc_start: 0.7749 (tt0) cc_final: 0.7501 (tt0) REVERT: A 806 LEU cc_start: 0.8661 (mm) cc_final: 0.8391 (mm) REVERT: A 870 ILE cc_start: 0.8271 (mt) cc_final: 0.7917 (mp) REVERT: A 1146 ASP cc_start: 0.8047 (m-30) cc_final: 0.6704 (m-30) REVERT: A 1148 PHE cc_start: 0.5916 (m-80) cc_final: 0.5696 (m-80) REVERT: B 43 PHE cc_start: 0.7384 (t80) cc_final: 0.7034 (t80) REVERT: B 152 TRP cc_start: 0.2678 (m100) cc_final: 0.2096 (m100) REVERT: B 157 PHE cc_start: 0.5559 (t80) cc_final: 0.5013 (t80) REVERT: B 227 VAL cc_start: 0.7705 (p) cc_final: 0.7235 (t) REVERT: B 238 PHE cc_start: 0.6871 (p90) cc_final: 0.5882 (p90) REVERT: B 286 THR cc_start: 0.7793 (m) cc_final: 0.7475 (p) REVERT: B 293 LEU cc_start: 0.7760 (tt) cc_final: 0.7549 (tt) REVERT: B 396 TYR cc_start: 0.5405 (m-80) cc_final: 0.5079 (m-80) REVERT: B 409 GLN cc_start: 0.5990 (OUTLIER) cc_final: 0.5765 (tt0) REVERT: B 439 ASN cc_start: 0.6974 (t0) cc_final: 0.5848 (p0) REVERT: B 462 LYS cc_start: 0.6969 (tptt) cc_final: 0.6497 (tttp) REVERT: B 468 ILE cc_start: 0.7091 (pt) cc_final: 0.6842 (tp) REVERT: B 480 CYS cc_start: 0.4454 (OUTLIER) cc_final: 0.3402 (t) REVERT: B 495 TYR cc_start: 0.6083 (m-80) cc_final: 0.5309 (m-80) REVERT: B 540 ASN cc_start: 0.7332 (t0) cc_final: 0.7065 (t0) REVERT: B 565 PHE cc_start: 0.6590 (m-80) cc_final: 0.6137 (m-80) REVERT: B 567 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.5462 (mmm160) REVERT: B 611 LEU cc_start: 0.8680 (tp) cc_final: 0.8456 (tp) REVERT: B 693 ILE cc_start: 0.8081 (pt) cc_final: 0.7856 (pt) REVERT: B 748 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: B 776 LYS cc_start: 0.8395 (tmtt) cc_final: 0.8130 (tptp) REVERT: B 788 ILE cc_start: 0.7854 (mm) cc_final: 0.7651 (mm) REVERT: B 806 LEU cc_start: 0.8766 (mt) cc_final: 0.8553 (mt) REVERT: B 918 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7377 (tp30) REVERT: B 950 ASP cc_start: 0.7338 (m-30) cc_final: 0.6983 (m-30) REVERT: B 957 GLN cc_start: 0.8028 (tt0) cc_final: 0.7808 (tt0) REVERT: B 1037 SER cc_start: 0.8375 (t) cc_final: 0.8081 (p) REVERT: C 63 THR cc_start: 0.7311 (p) cc_final: 0.6987 (p) REVERT: C 190 ARG cc_start: 0.7084 (mmt180) cc_final: 0.6755 (mmm-85) REVERT: C 204 TYR cc_start: 0.6875 (m-80) cc_final: 0.6508 (m-80) REVERT: C 237 ARG cc_start: 0.6542 (ptt180) cc_final: 0.6182 (ptt-90) REVERT: C 274 THR cc_start: 0.7669 (m) cc_final: 0.7284 (t) REVERT: C 290 ASP cc_start: 0.6978 (t0) cc_final: 0.6584 (t0) REVERT: C 298 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7883 (mm-30) REVERT: C 324 GLU cc_start: 0.6134 (pm20) cc_final: 0.5881 (pm20) REVERT: C 355 ARG cc_start: 0.7002 (mtp85) cc_final: 0.6700 (mtp85) REVERT: C 466 ARG cc_start: 0.3935 (OUTLIER) cc_final: 0.3470 (ttp80) REVERT: C 510 VAL cc_start: 0.7220 (t) cc_final: 0.6959 (t) REVERT: C 517 LEU cc_start: 0.5247 (mp) cc_final: 0.4976 (mp) REVERT: C 541 PHE cc_start: 0.7828 (p90) cc_final: 0.7580 (p90) REVERT: C 576 VAL cc_start: 0.8048 (p) cc_final: 0.7837 (t) REVERT: C 588 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7970 (p) REVERT: C 673 SER cc_start: 0.6955 (t) cc_final: 0.6268 (m) REVERT: C 779 GLN cc_start: 0.7973 (pp30) cc_final: 0.7690 (pp30) REVERT: C 919 ASN cc_start: 0.8013 (m-40) cc_final: 0.7621 (m110) REVERT: C 991 VAL cc_start: 0.8495 (t) cc_final: 0.7861 (t) REVERT: C 1058 HIS cc_start: 0.7573 (m-70) cc_final: 0.7336 (m170) outliers start: 92 outliers final: 39 residues processed: 712 average time/residue: 0.1680 time to fit residues: 188.5706 Evaluate side-chains 617 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 571 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 311 optimal weight: 0.4980 chunk 131 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 194 optimal weight: 0.4980 chunk 155 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 173 GLN A 493 GLN A 580 GLN A 613 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 164 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 644 GLN B 703 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 360 ASN C 388 ASN C 474 GLN C 603 ASN C 935 GLN C 960 ASN C1054 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.085089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.069581 restraints weight = 106572.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.071663 restraints weight = 60187.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.073043 restraints weight = 39705.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073981 restraints weight = 29344.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.074608 restraints weight = 23577.758| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27539 Z= 0.193 Angle : 0.840 18.071 37641 Z= 0.409 Chirality : 0.051 0.632 4488 Planarity : 0.005 0.049 4690 Dihedral : 11.136 111.708 5485 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.83 % Allowed : 14.19 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3223 helix: 0.05 (0.19), residues: 716 sheet: -0.47 (0.19), residues: 648 loop : -1.37 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 408 TYR 0.029 0.002 TYR A 365 PHE 0.024 0.002 PHE C 157 TRP 0.021 0.002 TRP A 353 HIS 0.009 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00420 (27404) covalent geometry : angle 0.78543 (37278) SS BOND : bond 0.00426 ( 42) SS BOND : angle 1.84184 ( 84) hydrogen bonds : bond 0.04746 ( 1034) hydrogen bonds : angle 6.69520 ( 2898) link_ALPHA1-4 : bond 0.01537 ( 6) link_ALPHA1-4 : angle 2.42322 ( 18) link_BETA1-4 : bond 0.00469 ( 29) link_BETA1-4 : angle 2.03322 ( 87) link_BETA1-6 : bond 0.01500 ( 3) link_BETA1-6 : angle 2.22466 ( 9) link_NAG-ASN : bond 0.00611 ( 55) link_NAG-ASN : angle 4.07455 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 614 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.7594 (m-80) cc_final: 0.7306 (m-10) REVERT: A 146 HIS cc_start: 0.4961 (p-80) cc_final: 0.3486 (m-70) REVERT: A 153 MET cc_start: 0.6973 (tpt) cc_final: 0.6204 (tpp) REVERT: A 304 LYS cc_start: 0.7985 (tptt) cc_final: 0.7672 (tptt) REVERT: A 317 ASN cc_start: 0.6499 (OUTLIER) cc_final: 0.5645 (p0) REVERT: A 319 ARG cc_start: 0.6686 (mpp80) cc_final: 0.6295 (mpp80) REVERT: A 388 ASN cc_start: 0.4949 (m-40) cc_final: 0.4239 (t0) REVERT: A 396 TYR cc_start: 0.5789 (m-80) cc_final: 0.4522 (m-80) REVERT: A 779 GLN cc_start: 0.7863 (tt0) cc_final: 0.7560 (tt0) REVERT: A 780 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7377 (mm-30) REVERT: A 870 ILE cc_start: 0.8286 (mt) cc_final: 0.7937 (mp) REVERT: A 1031 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: A 1145 LEU cc_start: 0.7046 (pp) cc_final: 0.6759 (mp) REVERT: A 1146 ASP cc_start: 0.7096 (m-30) cc_final: 0.6446 (m-30) REVERT: B 43 PHE cc_start: 0.7182 (t80) cc_final: 0.6877 (t80) REVERT: B 49 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7143 (t-170) REVERT: B 94 SER cc_start: 0.6161 (p) cc_final: 0.5946 (m) REVERT: B 141 LEU cc_start: 0.6908 (tp) cc_final: 0.6530 (mm) REVERT: B 152 TRP cc_start: 0.2911 (m100) cc_final: 0.2295 (m100) REVERT: B 157 PHE cc_start: 0.5561 (t80) cc_final: 0.4887 (t80) REVERT: B 286 THR cc_start: 0.7839 (m) cc_final: 0.7508 (p) REVERT: B 293 LEU cc_start: 0.8058 (tt) cc_final: 0.7698 (tt) REVERT: B 297 SER cc_start: 0.8512 (m) cc_final: 0.8114 (p) REVERT: B 354 ASN cc_start: 0.7298 (OUTLIER) cc_final: 0.6922 (m-40) REVERT: B 387 LEU cc_start: 0.8140 (mt) cc_final: 0.7722 (tp) REVERT: B 439 ASN cc_start: 0.7007 (t0) cc_final: 0.6011 (p0) REVERT: B 480 CYS cc_start: 0.4404 (OUTLIER) cc_final: 0.3388 (t) REVERT: B 540 ASN cc_start: 0.7288 (t0) cc_final: 0.7045 (t0) REVERT: B 567 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.5410 (mmm160) REVERT: B 664 ILE cc_start: 0.8136 (mm) cc_final: 0.7784 (mm) REVERT: B 693 ILE cc_start: 0.8060 (pt) cc_final: 0.7854 (pt) REVERT: B 776 LYS cc_start: 0.8409 (tmtt) cc_final: 0.8146 (ttpt) REVERT: B 873 TYR cc_start: 0.7949 (m-10) cc_final: 0.7699 (m-10) REVERT: B 900 MET cc_start: 0.8101 (mmp) cc_final: 0.7819 (mmp) REVERT: B 916 LEU cc_start: 0.8643 (tt) cc_final: 0.8443 (tp) REVERT: B 918 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7336 (tp30) REVERT: B 950 ASP cc_start: 0.7257 (m-30) cc_final: 0.6951 (m-30) REVERT: B 1014 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7442 (mtt90) REVERT: B 1037 SER cc_start: 0.8372 (t) cc_final: 0.8087 (p) REVERT: C 204 TYR cc_start: 0.6500 (m-80) cc_final: 0.6294 (m-80) REVERT: C 242 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7495 (mp) REVERT: C 271 GLN cc_start: 0.7960 (mp10) cc_final: 0.7713 (mp10) REVERT: C 274 THR cc_start: 0.7706 (m) cc_final: 0.7348 (t) REVERT: C 290 ASP cc_start: 0.7142 (t0) cc_final: 0.6716 (t0) REVERT: C 298 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8005 (mm-30) REVERT: C 319 ARG cc_start: 0.7461 (mpt-90) cc_final: 0.7119 (mmt90) REVERT: C 324 GLU cc_start: 0.6055 (pm20) cc_final: 0.5852 (pm20) REVERT: C 576 VAL cc_start: 0.8176 (p) cc_final: 0.7925 (t) REVERT: C 588 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7960 (p) REVERT: C 673 SER cc_start: 0.6982 (t) cc_final: 0.6327 (m) REVERT: C 819 GLU cc_start: 0.8209 (mp0) cc_final: 0.7967 (mp0) REVERT: C 825 LYS cc_start: 0.7239 (tppt) cc_final: 0.6781 (tppt) REVERT: C 919 ASN cc_start: 0.8029 (m-40) cc_final: 0.7672 (m110) REVERT: C 1058 HIS cc_start: 0.7600 (m-70) cc_final: 0.7380 (m170) outliers start: 109 outliers final: 66 residues processed: 675 average time/residue: 0.1690 time to fit residues: 179.8872 Evaluate side-chains 633 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 557 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 275 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 180 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 183 optimal weight: 0.4980 chunk 300 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 493 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 360 ASN C 388 ASN C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.085905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.070327 restraints weight = 106218.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072432 restraints weight = 59495.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073823 restraints weight = 39146.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.074784 restraints weight = 28890.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.075424 restraints weight = 23170.921| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27539 Z= 0.143 Angle : 0.770 16.516 37641 Z= 0.372 Chirality : 0.049 0.587 4488 Planarity : 0.004 0.061 4690 Dihedral : 10.361 108.471 5481 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.83 % Allowed : 16.19 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3223 helix: 0.48 (0.20), residues: 703 sheet: -0.45 (0.20), residues: 614 loop : -1.28 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 466 TYR 0.024 0.002 TYR A1067 PHE 0.032 0.002 PHE B 306 TRP 0.027 0.002 TRP A 353 HIS 0.007 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00304 (27404) covalent geometry : angle 0.71970 (37278) SS BOND : bond 0.00426 ( 42) SS BOND : angle 2.23776 ( 84) hydrogen bonds : bond 0.04155 ( 1034) hydrogen bonds : angle 6.40582 ( 2898) link_ALPHA1-4 : bond 0.01535 ( 6) link_ALPHA1-4 : angle 2.42140 ( 18) link_BETA1-4 : bond 0.00368 ( 29) link_BETA1-4 : angle 1.75526 ( 87) link_BETA1-6 : bond 0.01570 ( 3) link_BETA1-6 : angle 2.09776 ( 9) link_NAG-ASN : bond 0.00541 ( 55) link_NAG-ASN : angle 3.62178 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 605 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6894 (p0) cc_final: 0.6343 (t0) REVERT: A 144 TYR cc_start: 0.7668 (m-80) cc_final: 0.7337 (m-10) REVERT: A 146 HIS cc_start: 0.4645 (p-80) cc_final: 0.3219 (m-70) REVERT: A 237 ARG cc_start: 0.7397 (mtm180) cc_final: 0.7139 (mtp85) REVERT: A 304 LYS cc_start: 0.8006 (tptt) cc_final: 0.7635 (tptt) REVERT: A 317 ASN cc_start: 0.6430 (OUTLIER) cc_final: 0.5598 (p0) REVERT: A 319 ARG cc_start: 0.6416 (mpp80) cc_final: 0.6094 (mpp80) REVERT: A 326 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6653 (mm) REVERT: A 388 ASN cc_start: 0.4967 (m-40) cc_final: 0.4302 (t0) REVERT: A 697 MET cc_start: 0.6788 (tpt) cc_final: 0.6572 (tpt) REVERT: A 779 GLN cc_start: 0.7870 (tt0) cc_final: 0.7563 (tt0) REVERT: A 780 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: A 800 PHE cc_start: 0.8071 (m-80) cc_final: 0.7869 (m-10) REVERT: A 870 ILE cc_start: 0.8198 (mt) cc_final: 0.7919 (mt) REVERT: A 904 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7174 (m-10) REVERT: A 1146 ASP cc_start: 0.7322 (m-30) cc_final: 0.6935 (m-30) REVERT: B 43 PHE cc_start: 0.7219 (t80) cc_final: 0.6873 (t80) REVERT: B 141 LEU cc_start: 0.6874 (tp) cc_final: 0.6496 (mm) REVERT: B 152 TRP cc_start: 0.2593 (m100) cc_final: 0.2148 (m100) REVERT: B 157 PHE cc_start: 0.5529 (t80) cc_final: 0.4862 (t80) REVERT: B 206 LYS cc_start: 0.7712 (tptt) cc_final: 0.7383 (tppt) REVERT: B 286 THR cc_start: 0.7748 (m) cc_final: 0.7424 (p) REVERT: B 293 LEU cc_start: 0.8073 (tt) cc_final: 0.7711 (tt) REVERT: B 297 SER cc_start: 0.8385 (m) cc_final: 0.8083 (p) REVERT: B 354 ASN cc_start: 0.7292 (OUTLIER) cc_final: 0.6912 (m-40) REVERT: B 387 LEU cc_start: 0.8108 (mt) cc_final: 0.7660 (tp) REVERT: B 439 ASN cc_start: 0.6965 (t0) cc_final: 0.6094 (p0) REVERT: B 457 ARG cc_start: 0.4773 (tpt90) cc_final: 0.4320 (tmt170) REVERT: B 462 LYS cc_start: 0.7432 (tppt) cc_final: 0.7071 (tttp) REVERT: B 540 ASN cc_start: 0.7304 (t0) cc_final: 0.7015 (t0) REVERT: B 567 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5658 (mmm-85) REVERT: B 663 ASP cc_start: 0.6591 (t0) cc_final: 0.5830 (t0) REVERT: B 664 ILE cc_start: 0.8068 (mm) cc_final: 0.7665 (mm) REVERT: B 704 SER cc_start: 0.7196 (t) cc_final: 0.6936 (m) REVERT: B 748 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: B 776 LYS cc_start: 0.8436 (tmtt) cc_final: 0.8134 (ttpp) REVERT: B 873 TYR cc_start: 0.7954 (m-10) cc_final: 0.7668 (m-10) REVERT: B 900 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7695 (mmt) REVERT: B 916 LEU cc_start: 0.8635 (tt) cc_final: 0.8324 (tp) REVERT: B 918 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7366 (tp30) REVERT: B 950 ASP cc_start: 0.7252 (m-30) cc_final: 0.6984 (m-30) REVERT: B 1014 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7476 (mtt90) REVERT: B 1037 SER cc_start: 0.8388 (t) cc_final: 0.8102 (p) REVERT: C 41 LYS cc_start: 0.7662 (mttp) cc_final: 0.7269 (mtmm) REVERT: C 121 ASN cc_start: 0.5755 (OUTLIER) cc_final: 0.5357 (t0) REVERT: C 200 TYR cc_start: 0.5764 (m-80) cc_final: 0.5457 (m-80) REVERT: C 204 TYR cc_start: 0.6607 (m-80) cc_final: 0.6366 (m-80) REVERT: C 242 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7375 (mp) REVERT: C 271 GLN cc_start: 0.8026 (mp10) cc_final: 0.7810 (mp10) REVERT: C 274 THR cc_start: 0.7752 (m) cc_final: 0.7226 (t) REVERT: C 290 ASP cc_start: 0.7098 (t0) cc_final: 0.6821 (t0) REVERT: C 298 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7941 (mm-30) REVERT: C 319 ARG cc_start: 0.7422 (mpt-90) cc_final: 0.6890 (mmt90) REVERT: C 324 GLU cc_start: 0.6040 (pm20) cc_final: 0.5820 (pm20) REVERT: C 588 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7905 (p) REVERT: C 673 SER cc_start: 0.7021 (t) cc_final: 0.6364 (m) REVERT: C 825 LYS cc_start: 0.7203 (tppt) cc_final: 0.6737 (tppt) REVERT: C 919 ASN cc_start: 0.7982 (m-40) cc_final: 0.7619 (m110) REVERT: C 970 PHE cc_start: 0.7473 (m-80) cc_final: 0.7068 (m-80) outliers start: 109 outliers final: 70 residues processed: 669 average time/residue: 0.1699 time to fit residues: 179.5153 Evaluate side-chains 643 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 561 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 229 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 309 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 580 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 360 ASN C 960 ASN C1058 HIS ** C1106 GLN ** 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 = 0.3644 r_free = 0.3644 target = 0.085444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.070147 restraints weight = 105933.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072205 restraints weight = 59534.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.073566 restraints weight = 39197.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074499 restraints weight = 28980.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.075127 restraints weight = 23289.592| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27539 Z= 0.156 Angle : 0.765 15.271 37641 Z= 0.369 Chirality : 0.048 0.541 4488 Planarity : 0.005 0.069 4690 Dihedral : 10.123 109.339 5480 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.29 % Allowed : 17.25 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3223 helix: 0.59 (0.20), residues: 702 sheet: -0.50 (0.20), residues: 632 loop : -1.28 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1019 TYR 0.026 0.002 TYR A1067 PHE 0.031 0.002 PHE B 306 TRP 0.021 0.002 TRP A 353 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00338 (27404) covalent geometry : angle 0.71950 (37278) SS BOND : bond 0.00476 ( 42) SS BOND : angle 1.88544 ( 84) hydrogen bonds : bond 0.04159 ( 1034) hydrogen bonds : angle 6.31756 ( 2898) link_ALPHA1-4 : bond 0.01513 ( 6) link_ALPHA1-4 : angle 2.47118 ( 18) link_BETA1-4 : bond 0.00379 ( 29) link_BETA1-4 : angle 1.80298 ( 87) link_BETA1-6 : bond 0.01648 ( 3) link_BETA1-6 : angle 2.13592 ( 9) link_NAG-ASN : bond 0.00544 ( 55) link_NAG-ASN : angle 3.46135 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 593 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6978 (p0) cc_final: 0.6341 (t0) REVERT: A 144 TYR cc_start: 0.7669 (m-80) cc_final: 0.7405 (m-10) REVERT: A 146 HIS cc_start: 0.4607 (p-80) cc_final: 0.3261 (m-70) REVERT: A 287 ASP cc_start: 0.7857 (t0) cc_final: 0.7637 (t70) REVERT: A 306 PHE cc_start: 0.6862 (m-10) cc_final: 0.6416 (m-10) REVERT: A 319 ARG cc_start: 0.6437 (mpp80) cc_final: 0.6193 (mpp80) REVERT: A 388 ASN cc_start: 0.4967 (m-40) cc_final: 0.4343 (t0) REVERT: A 697 MET cc_start: 0.6769 (tpt) cc_final: 0.6521 (tpt) REVERT: A 779 GLN cc_start: 0.7864 (tt0) cc_final: 0.7573 (tt0) REVERT: A 780 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: A 904 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7081 (m-10) REVERT: A 1031 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: A 1142 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7750 (tp-100) REVERT: A 1146 ASP cc_start: 0.7467 (m-30) cc_final: 0.7020 (m-30) REVERT: B 43 PHE cc_start: 0.7211 (t80) cc_final: 0.6870 (t80) REVERT: B 104 TRP cc_start: 0.6591 (m-90) cc_final: 0.6338 (m-90) REVERT: B 119 ILE cc_start: 0.6720 (mp) cc_final: 0.6391 (tt) REVERT: B 141 LEU cc_start: 0.6830 (tp) cc_final: 0.6481 (mm) REVERT: B 152 TRP cc_start: 0.2738 (m100) cc_final: 0.2207 (m100) REVERT: B 157 PHE cc_start: 0.5566 (t80) cc_final: 0.4849 (t80) REVERT: B 206 LYS cc_start: 0.7654 (tptt) cc_final: 0.7332 (tppt) REVERT: B 286 THR cc_start: 0.7773 (m) cc_final: 0.7436 (p) REVERT: B 293 LEU cc_start: 0.8086 (tt) cc_final: 0.7458 (tt) REVERT: B 297 SER cc_start: 0.8389 (m) cc_final: 0.8106 (p) REVERT: B 387 LEU cc_start: 0.8156 (mt) cc_final: 0.7727 (tp) REVERT: B 439 ASN cc_start: 0.7038 (t0) cc_final: 0.6039 (p0) REVERT: B 457 ARG cc_start: 0.4792 (tpt90) cc_final: 0.4517 (ttp80) REVERT: B 480 CYS cc_start: 0.4412 (OUTLIER) cc_final: 0.3464 (t) REVERT: B 512 VAL cc_start: 0.7950 (t) cc_final: 0.7732 (m) REVERT: B 540 ASN cc_start: 0.7270 (t0) cc_final: 0.6953 (t0) REVERT: B 567 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.5382 (mmm160) REVERT: B 704 SER cc_start: 0.7206 (t) cc_final: 0.6926 (m) REVERT: B 748 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7320 (pm20) REVERT: B 776 LYS cc_start: 0.8424 (tmtt) cc_final: 0.8120 (ttpp) REVERT: B 873 TYR cc_start: 0.7976 (m-10) cc_final: 0.7677 (m-10) REVERT: B 900 MET cc_start: 0.7956 (mmp) cc_final: 0.7683 (mmt) REVERT: B 918 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7407 (tp30) REVERT: B 950 ASP cc_start: 0.7217 (m-30) cc_final: 0.6954 (m-30) REVERT: B 1007 TYR cc_start: 0.7806 (t80) cc_final: 0.7299 (t80) REVERT: B 1014 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7412 (mtt180) REVERT: B 1122 VAL cc_start: 0.8364 (t) cc_final: 0.8145 (m) REVERT: B 1123 SER cc_start: 0.7154 (m) cc_final: 0.6690 (m) REVERT: C 21 ARG cc_start: 0.5022 (ttt-90) cc_final: 0.4792 (mtt-85) REVERT: C 52 GLN cc_start: 0.6717 (tp-100) cc_final: 0.6436 (tp40) REVERT: C 121 ASN cc_start: 0.6005 (OUTLIER) cc_final: 0.5785 (t0) REVERT: C 204 TYR cc_start: 0.6503 (m-80) cc_final: 0.6143 (m-80) REVERT: C 242 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7326 (mp) REVERT: C 271 GLN cc_start: 0.7982 (mp10) cc_final: 0.7768 (mp10) REVERT: C 290 ASP cc_start: 0.7081 (t0) cc_final: 0.6879 (t0) REVERT: C 324 GLU cc_start: 0.6014 (pm20) cc_final: 0.5792 (pm20) REVERT: C 429 PHE cc_start: 0.6731 (t80) cc_final: 0.6346 (t80) REVERT: C 673 SER cc_start: 0.7074 (t) cc_final: 0.6402 (m) REVERT: C 825 LYS cc_start: 0.7153 (tppt) cc_final: 0.6758 (tppt) REVERT: C 919 ASN cc_start: 0.7951 (m-40) cc_final: 0.7608 (m110) outliers start: 122 outliers final: 78 residues processed: 667 average time/residue: 0.1700 time to fit residues: 181.9061 Evaluate side-chains 643 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 556 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 112 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 204 optimal weight: 2.9990 chunk 205 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 260 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 613 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1142 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 960 ASN C1058 HIS ** C1106 GLN ** 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 = 0.3640 r_free = 0.3640 target = 0.085252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069827 restraints weight = 106854.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071901 restraints weight = 59653.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073269 restraints weight = 39178.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074221 restraints weight = 28950.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.074840 restraints weight = 23224.663| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27539 Z= 0.165 Angle : 0.768 13.697 37641 Z= 0.371 Chirality : 0.048 0.489 4488 Planarity : 0.005 0.069 4690 Dihedral : 9.944 109.168 5479 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.36 % Allowed : 18.23 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 3223 helix: 0.61 (0.20), residues: 702 sheet: -0.55 (0.20), residues: 622 loop : -1.32 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1019 TYR 0.020 0.002 TYR A 365 PHE 0.036 0.002 PHE B 92 TRP 0.019 0.002 TRP A 353 HIS 0.026 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00360 (27404) covalent geometry : angle 0.72609 (37278) SS BOND : bond 0.00386 ( 42) SS BOND : angle 1.90007 ( 84) hydrogen bonds : bond 0.04233 ( 1034) hydrogen bonds : angle 6.29688 ( 2898) link_ALPHA1-4 : bond 0.01524 ( 6) link_ALPHA1-4 : angle 2.55931 ( 18) link_BETA1-4 : bond 0.00377 ( 29) link_BETA1-4 : angle 1.79408 ( 87) link_BETA1-6 : bond 0.01599 ( 3) link_BETA1-6 : angle 2.16843 ( 9) link_NAG-ASN : bond 0.00555 ( 55) link_NAG-ASN : angle 3.30629 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 587 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6950 (p0) cc_final: 0.6254 (t0) REVERT: A 144 TYR cc_start: 0.7710 (m-80) cc_final: 0.7444 (m-10) REVERT: A 146 HIS cc_start: 0.4589 (p-80) cc_final: 0.3212 (m-70) REVERT: A 287 ASP cc_start: 0.7883 (t0) cc_final: 0.7668 (t70) REVERT: A 304 LYS cc_start: 0.7963 (tptt) cc_final: 0.7685 (tptt) REVERT: A 306 PHE cc_start: 0.6948 (m-10) cc_final: 0.6480 (m-10) REVERT: A 319 ARG cc_start: 0.6377 (mpp80) cc_final: 0.6137 (mpp80) REVERT: A 388 ASN cc_start: 0.5020 (m-40) cc_final: 0.4317 (t0) REVERT: A 586 ASP cc_start: 0.7865 (m-30) cc_final: 0.7644 (m-30) REVERT: A 697 MET cc_start: 0.6763 (tpt) cc_final: 0.6525 (tpt) REVERT: A 779 GLN cc_start: 0.7875 (tt0) cc_final: 0.7597 (tt0) REVERT: A 780 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: A 904 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.5116 (m-10) REVERT: A 1031 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: A 1071 GLN cc_start: 0.7417 (mp10) cc_final: 0.7215 (mp10) REVERT: A 1115 ILE cc_start: 0.8568 (mp) cc_final: 0.8107 (tp) REVERT: A 1142 GLN cc_start: 0.7991 (tp40) cc_final: 0.7667 (tp-100) REVERT: A 1146 ASP cc_start: 0.7628 (m-30) cc_final: 0.7020 (m-30) REVERT: B 43 PHE cc_start: 0.7146 (t80) cc_final: 0.6845 (t80) REVERT: B 92 PHE cc_start: 0.7345 (t80) cc_final: 0.7123 (t80) REVERT: B 104 TRP cc_start: 0.6898 (m-90) cc_final: 0.6329 (m-90) REVERT: B 119 ILE cc_start: 0.6469 (mp) cc_final: 0.6258 (mp) REVERT: B 141 LEU cc_start: 0.6867 (tp) cc_final: 0.6579 (tp) REVERT: B 152 TRP cc_start: 0.2936 (m100) cc_final: 0.2303 (m100) REVERT: B 157 PHE cc_start: 0.5628 (t80) cc_final: 0.5054 (t80) REVERT: B 206 LYS cc_start: 0.7630 (tptt) cc_final: 0.7314 (tppt) REVERT: B 293 LEU cc_start: 0.8132 (tt) cc_final: 0.7532 (tt) REVERT: B 297 SER cc_start: 0.8340 (m) cc_final: 0.8103 (p) REVERT: B 387 LEU cc_start: 0.8139 (mt) cc_final: 0.7730 (tp) REVERT: B 439 ASN cc_start: 0.7078 (t0) cc_final: 0.6050 (p0) REVERT: B 457 ARG cc_start: 0.4875 (tpt90) cc_final: 0.4542 (ttp80) REVERT: B 480 CYS cc_start: 0.4525 (OUTLIER) cc_final: 0.3578 (t) REVERT: B 512 VAL cc_start: 0.7940 (t) cc_final: 0.7738 (m) REVERT: B 540 ASN cc_start: 0.7281 (t0) cc_final: 0.6969 (t0) REVERT: B 567 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.5441 (mmm160) REVERT: B 704 SER cc_start: 0.7206 (t) cc_final: 0.6910 (m) REVERT: B 748 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: B 776 LYS cc_start: 0.8426 (tmtt) cc_final: 0.8122 (ttpp) REVERT: B 873 TYR cc_start: 0.8004 (m-10) cc_final: 0.7720 (m-10) REVERT: B 900 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7695 (mmt) REVERT: B 918 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7424 (tp30) REVERT: B 950 ASP cc_start: 0.7231 (m-30) cc_final: 0.6973 (m-30) REVERT: B 1007 TYR cc_start: 0.7808 (t80) cc_final: 0.7343 (t80) REVERT: B 1014 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7491 (mtt180) REVERT: B 1123 SER cc_start: 0.7262 (m) cc_final: 0.6829 (m) REVERT: C 21 ARG cc_start: 0.5306 (ttt-90) cc_final: 0.5008 (mtt-85) REVERT: C 83 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7423 (p) REVERT: C 204 TYR cc_start: 0.6461 (m-80) cc_final: 0.6073 (m-80) REVERT: C 242 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7369 (mp) REVERT: C 271 GLN cc_start: 0.7920 (mp10) cc_final: 0.7548 (mp10) REVERT: C 273 ARG cc_start: 0.5627 (mtp85) cc_final: 0.5227 (mtp85) REVERT: C 274 THR cc_start: 0.7607 (m) cc_final: 0.7240 (t) REVERT: C 290 ASP cc_start: 0.7122 (t0) cc_final: 0.6879 (t0) REVERT: C 298 GLU cc_start: 0.8568 (tp30) cc_final: 0.8134 (tp30) REVERT: C 319 ARG cc_start: 0.7566 (mpt-90) cc_final: 0.7161 (mmt90) REVERT: C 324 GLU cc_start: 0.6031 (pm20) cc_final: 0.5800 (pm20) REVERT: C 429 PHE cc_start: 0.6832 (t80) cc_final: 0.6483 (t80) REVERT: C 534 VAL cc_start: 0.7652 (p) cc_final: 0.7425 (t) REVERT: C 542 ASN cc_start: 0.7396 (t0) cc_final: 0.6211 (m110) REVERT: C 543 PHE cc_start: 0.7405 (m-10) cc_final: 0.7119 (m-10) REVERT: C 661 GLU cc_start: 0.6957 (tp30) cc_final: 0.6734 (tp30) REVERT: C 673 SER cc_start: 0.7117 (t) cc_final: 0.6432 (m) REVERT: C 825 LYS cc_start: 0.7166 (tppt) cc_final: 0.6776 (tppt) REVERT: C 919 ASN cc_start: 0.7945 (m-40) cc_final: 0.7620 (m110) outliers start: 124 outliers final: 86 residues processed: 663 average time/residue: 0.1756 time to fit residues: 185.9910 Evaluate side-chains 651 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 555 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 269 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 317 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 703 ASN B 755 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.085110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.069813 restraints weight = 106038.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.071899 restraints weight = 59174.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073262 restraints weight = 38730.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074213 restraints weight = 28560.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.074839 restraints weight = 22845.776| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27539 Z= 0.166 Angle : 0.770 12.757 37641 Z= 0.372 Chirality : 0.048 0.470 4488 Planarity : 0.005 0.070 4690 Dihedral : 9.698 109.199 5479 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.67 % Allowed : 18.76 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3223 helix: 0.66 (0.20), residues: 699 sheet: -0.55 (0.20), residues: 636 loop : -1.38 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C1107 TYR 0.027 0.002 TYR A 904 PHE 0.052 0.002 PHE C 157 TRP 0.022 0.002 TRP A 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00363 (27404) covalent geometry : angle 0.73032 (37278) SS BOND : bond 0.00429 ( 42) SS BOND : angle 1.96597 ( 84) hydrogen bonds : bond 0.04177 ( 1034) hydrogen bonds : angle 6.28890 ( 2898) link_ALPHA1-4 : bond 0.01667 ( 6) link_ALPHA1-4 : angle 2.72708 ( 18) link_BETA1-4 : bond 0.00382 ( 29) link_BETA1-4 : angle 1.77945 ( 87) link_BETA1-6 : bond 0.01779 ( 3) link_BETA1-6 : angle 2.20005 ( 9) link_NAG-ASN : bond 0.00520 ( 55) link_NAG-ASN : angle 3.18955 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 584 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6975 (p0) cc_final: 0.6278 (t0) REVERT: A 133 PHE cc_start: 0.6197 (m-80) cc_final: 0.5891 (m-80) REVERT: A 146 HIS cc_start: 0.4657 (p-80) cc_final: 0.3183 (m-70) REVERT: A 270 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.7001 (tp) REVERT: A 287 ASP cc_start: 0.7887 (t0) cc_final: 0.7659 (t70) REVERT: A 304 LYS cc_start: 0.7979 (tptt) cc_final: 0.7672 (tptt) REVERT: A 306 PHE cc_start: 0.6978 (m-10) cc_final: 0.6534 (m-10) REVERT: A 319 ARG cc_start: 0.6437 (mpp80) cc_final: 0.6205 (mpp80) REVERT: A 326 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6630 (mm) REVERT: A 388 ASN cc_start: 0.4993 (m-40) cc_final: 0.4343 (t0) REVERT: A 586 ASP cc_start: 0.7906 (m-30) cc_final: 0.7694 (m-30) REVERT: A 697 MET cc_start: 0.6776 (tpt) cc_final: 0.6546 (tpt) REVERT: A 779 GLN cc_start: 0.7887 (tt0) cc_final: 0.7601 (tt0) REVERT: A 780 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: A 1031 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: A 1115 ILE cc_start: 0.8606 (mp) cc_final: 0.8160 (tp) REVERT: A 1142 GLN cc_start: 0.8041 (tp40) cc_final: 0.7727 (tp-100) REVERT: A 1146 ASP cc_start: 0.7795 (m-30) cc_final: 0.7112 (m-30) REVERT: B 43 PHE cc_start: 0.7135 (t80) cc_final: 0.6820 (t80) REVERT: B 104 TRP cc_start: 0.7066 (m-90) cc_final: 0.6616 (m-90) REVERT: B 119 ILE cc_start: 0.6422 (mp) cc_final: 0.6155 (mp) REVERT: B 141 LEU cc_start: 0.6791 (tp) cc_final: 0.6589 (tp) REVERT: B 152 TRP cc_start: 0.2933 (m100) cc_final: 0.2289 (m100) REVERT: B 157 PHE cc_start: 0.5628 (t80) cc_final: 0.5071 (t80) REVERT: B 206 LYS cc_start: 0.7649 (tptt) cc_final: 0.7346 (tppt) REVERT: B 266 TYR cc_start: 0.6861 (m-80) cc_final: 0.6610 (m-80) REVERT: B 293 LEU cc_start: 0.8142 (tt) cc_final: 0.7580 (tt) REVERT: B 297 SER cc_start: 0.8295 (m) cc_final: 0.8092 (p) REVERT: B 387 LEU cc_start: 0.8140 (mt) cc_final: 0.7735 (tp) REVERT: B 439 ASN cc_start: 0.7046 (t0) cc_final: 0.6001 (p0) REVERT: B 457 ARG cc_start: 0.4927 (tpt90) cc_final: 0.4469 (ttp80) REVERT: B 480 CYS cc_start: 0.4593 (OUTLIER) cc_final: 0.3621 (t) REVERT: B 540 ASN cc_start: 0.7281 (t0) cc_final: 0.6961 (t0) REVERT: B 567 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.5411 (mmm160) REVERT: B 704 SER cc_start: 0.7240 (t) cc_final: 0.6939 (m) REVERT: B 720 ILE cc_start: 0.8286 (mm) cc_final: 0.7917 (tt) REVERT: B 748 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: B 776 LYS cc_start: 0.8374 (tmtt) cc_final: 0.8081 (ttpp) REVERT: B 873 TYR cc_start: 0.8053 (m-10) cc_final: 0.7767 (m-10) REVERT: B 900 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7702 (mmt) REVERT: B 918 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7412 (tp30) REVERT: B 950 ASP cc_start: 0.7251 (m-30) cc_final: 0.6987 (m-30) REVERT: B 1007 TYR cc_start: 0.7791 (t80) cc_final: 0.7316 (t80) REVERT: B 1014 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7447 (mtt90) REVERT: C 18 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.5714 (mm) REVERT: C 21 ARG cc_start: 0.5323 (ttt-90) cc_final: 0.5045 (mtt-85) REVERT: C 38 TYR cc_start: 0.7863 (m-80) cc_final: 0.7409 (m-80) REVERT: C 83 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7437 (p) REVERT: C 204 TYR cc_start: 0.6453 (m-80) cc_final: 0.6142 (m-80) REVERT: C 242 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7429 (mp) REVERT: C 271 GLN cc_start: 0.7886 (mp10) cc_final: 0.7525 (mp10) REVERT: C 290 ASP cc_start: 0.7104 (t0) cc_final: 0.6881 (t0) REVERT: C 298 GLU cc_start: 0.8555 (tp30) cc_final: 0.8120 (tp30) REVERT: C 309 GLU cc_start: 0.7620 (mp0) cc_final: 0.7404 (mt-10) REVERT: C 324 GLU cc_start: 0.6064 (pm20) cc_final: 0.5814 (pm20) REVERT: C 429 PHE cc_start: 0.6974 (t80) cc_final: 0.6665 (t80) REVERT: C 534 VAL cc_start: 0.7764 (p) cc_final: 0.7542 (t) REVERT: C 542 ASN cc_start: 0.7408 (t0) cc_final: 0.6308 (m110) REVERT: C 543 PHE cc_start: 0.7428 (m-10) cc_final: 0.7154 (m-10) REVERT: C 661 GLU cc_start: 0.6996 (tp30) cc_final: 0.6772 (tp30) REVERT: C 673 SER cc_start: 0.7101 (t) cc_final: 0.6400 (m) REVERT: C 825 LYS cc_start: 0.7178 (tppt) cc_final: 0.6781 (tppt) REVERT: C 919 ASN cc_start: 0.7985 (m-40) cc_final: 0.7613 (m110) outliers start: 133 outliers final: 98 residues processed: 660 average time/residue: 0.1779 time to fit residues: 188.0332 Evaluate side-chains 666 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 556 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 134 optimal weight: 0.0980 chunk 252 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 703 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1011 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 703 ASN B 755 GLN B 764 ASN B 787 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 360 ASN C 487 ASN C 655 HIS C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068728 restraints weight = 106788.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070796 restraints weight = 59553.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072161 restraints weight = 38969.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.073099 restraints weight = 28665.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073725 restraints weight = 22943.200| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27539 Z= 0.233 Angle : 0.858 14.067 37641 Z= 0.417 Chirality : 0.051 0.466 4488 Planarity : 0.005 0.073 4690 Dihedral : 10.177 108.524 5478 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.64 % Allowed : 18.93 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3223 helix: 0.24 (0.19), residues: 716 sheet: -0.75 (0.20), residues: 621 loop : -1.61 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 237 TYR 0.027 0.002 TYR B 351 PHE 0.043 0.003 PHE C 157 TRP 0.024 0.002 TRP C 353 HIS 0.010 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00510 (27404) covalent geometry : angle 0.81768 (37278) SS BOND : bond 0.00498 ( 42) SS BOND : angle 2.02948 ( 84) hydrogen bonds : bond 0.04641 ( 1034) hydrogen bonds : angle 6.54165 ( 2898) link_ALPHA1-4 : bond 0.01584 ( 6) link_ALPHA1-4 : angle 2.95854 ( 18) link_BETA1-4 : bond 0.00528 ( 29) link_BETA1-4 : angle 2.08470 ( 87) link_BETA1-6 : bond 0.01777 ( 3) link_BETA1-6 : angle 2.13590 ( 9) link_NAG-ASN : bond 0.00616 ( 55) link_NAG-ASN : angle 3.35671 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 578 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6945 (p0) cc_final: 0.6246 (t0) REVERT: A 133 PHE cc_start: 0.6269 (m-80) cc_final: 0.5951 (m-80) REVERT: A 146 HIS cc_start: 0.4450 (p-80) cc_final: 0.3082 (m-70) REVERT: A 270 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6976 (tp) REVERT: A 304 LYS cc_start: 0.7967 (tptt) cc_final: 0.7647 (tptt) REVERT: A 319 ARG cc_start: 0.6359 (mpp80) cc_final: 0.6142 (mpp80) REVERT: A 388 ASN cc_start: 0.5120 (m-40) cc_final: 0.4373 (t0) REVERT: A 697 MET cc_start: 0.6794 (tpt) cc_final: 0.6519 (tpt) REVERT: A 740 MET cc_start: 0.7159 (mtm) cc_final: 0.6800 (ttp) REVERT: A 779 GLN cc_start: 0.7861 (tt0) cc_final: 0.7586 (tt0) REVERT: A 780 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7308 (tt0) REVERT: A 1031 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: A 1115 ILE cc_start: 0.8659 (mp) cc_final: 0.8234 (tp) REVERT: A 1142 GLN cc_start: 0.8059 (tp40) cc_final: 0.7666 (tp-100) REVERT: A 1146 ASP cc_start: 0.7781 (m-30) cc_final: 0.7087 (m-30) REVERT: B 41 LYS cc_start: 0.8352 (pttt) cc_final: 0.8093 (mtmt) REVERT: B 43 PHE cc_start: 0.7077 (t80) cc_final: 0.6836 (t80) REVERT: B 133 PHE cc_start: 0.5732 (m-80) cc_final: 0.5076 (m-80) REVERT: B 141 LEU cc_start: 0.6888 (tp) cc_final: 0.6550 (mm) REVERT: B 152 TRP cc_start: 0.3023 (m100) cc_final: 0.2379 (m100) REVERT: B 157 PHE cc_start: 0.5678 (t80) cc_final: 0.4957 (t80) REVERT: B 206 LYS cc_start: 0.7709 (tptt) cc_final: 0.7428 (tppt) REVERT: B 266 TYR cc_start: 0.7006 (m-80) cc_final: 0.6759 (m-80) REVERT: B 273 ARG cc_start: 0.7258 (ttm170) cc_final: 0.6959 (ttm170) REVERT: B 293 LEU cc_start: 0.8145 (tt) cc_final: 0.7811 (tt) REVERT: B 387 LEU cc_start: 0.8136 (mt) cc_final: 0.7745 (tp) REVERT: B 457 ARG cc_start: 0.5069 (tpt90) cc_final: 0.4557 (ttp80) REVERT: B 480 CYS cc_start: 0.4567 (OUTLIER) cc_final: 0.3717 (t) REVERT: B 540 ASN cc_start: 0.7276 (t0) cc_final: 0.6993 (t0) REVERT: B 567 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5414 (mmm-85) REVERT: B 748 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: B 776 LYS cc_start: 0.8396 (tmtt) cc_final: 0.8017 (ttpp) REVERT: B 869 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7114 (mtp) REVERT: B 873 TYR cc_start: 0.8111 (m-10) cc_final: 0.7877 (m-10) REVERT: B 900 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7741 (mmt) REVERT: B 918 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7405 (tp30) REVERT: B 950 ASP cc_start: 0.7252 (m-30) cc_final: 0.7040 (m-30) REVERT: C 21 ARG cc_start: 0.5281 (ttt-90) cc_final: 0.4878 (mtt-85) REVERT: C 83 VAL cc_start: 0.7802 (OUTLIER) cc_final: 0.7555 (p) REVERT: C 204 TYR cc_start: 0.6478 (m-80) cc_final: 0.6157 (m-80) REVERT: C 271 GLN cc_start: 0.7868 (mp10) cc_final: 0.7560 (mp10) REVERT: C 273 ARG cc_start: 0.5743 (mtp85) cc_final: 0.5459 (mtp85) REVERT: C 298 GLU cc_start: 0.8500 (tp30) cc_final: 0.8061 (tp30) REVERT: C 324 GLU cc_start: 0.6136 (pm20) cc_final: 0.5901 (pm20) REVERT: C 365 TYR cc_start: 0.6439 (m-80) cc_final: 0.6230 (m-80) REVERT: C 392 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6932 (m-80) REVERT: C 429 PHE cc_start: 0.7176 (t80) cc_final: 0.6936 (t80) REVERT: C 542 ASN cc_start: 0.7313 (t0) cc_final: 0.6241 (m110) REVERT: C 543 PHE cc_start: 0.7459 (m-10) cc_final: 0.7116 (m-10) REVERT: C 673 SER cc_start: 0.7151 (t) cc_final: 0.6464 (m) REVERT: C 919 ASN cc_start: 0.8012 (m-40) cc_final: 0.7623 (m110) outliers start: 132 outliers final: 103 residues processed: 648 average time/residue: 0.1723 time to fit residues: 179.0609 Evaluate side-chains 661 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 548 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 139 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 195 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 231 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 703 ASN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C1106 GLN ** 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 = 0.3621 r_free = 0.3621 target = 0.084341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.069063 restraints weight = 107450.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.071122 restraints weight = 60174.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072484 restraints weight = 39579.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073402 restraints weight = 29225.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073954 restraints weight = 23500.003| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27539 Z= 0.202 Angle : 0.828 14.557 37641 Z= 0.402 Chirality : 0.050 0.458 4488 Planarity : 0.005 0.075 4690 Dihedral : 9.888 108.093 5478 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.46 % Allowed : 20.02 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.14), residues: 3223 helix: 0.30 (0.19), residues: 708 sheet: -0.74 (0.20), residues: 622 loop : -1.61 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1107 TYR 0.027 0.002 TYR A 266 PHE 0.046 0.002 PHE C 157 TRP 0.021 0.002 TRP C 353 HIS 0.007 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00443 (27404) covalent geometry : angle 0.78955 (37278) SS BOND : bond 0.00461 ( 42) SS BOND : angle 1.94077 ( 84) hydrogen bonds : bond 0.04417 ( 1034) hydrogen bonds : angle 6.50439 ( 2898) link_ALPHA1-4 : bond 0.01844 ( 6) link_ALPHA1-4 : angle 3.03447 ( 18) link_BETA1-4 : bond 0.00437 ( 29) link_BETA1-4 : angle 1.93483 ( 87) link_BETA1-6 : bond 0.01768 ( 3) link_BETA1-6 : angle 2.04497 ( 9) link_NAG-ASN : bond 0.00571 ( 55) link_NAG-ASN : angle 3.23693 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 581 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6976 (p0) cc_final: 0.6202 (t0) REVERT: A 144 TYR cc_start: 0.7813 (m-10) cc_final: 0.6769 (m-10) REVERT: A 146 HIS cc_start: 0.4098 (p-80) cc_final: 0.2800 (m90) REVERT: A 270 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6915 (tp) REVERT: A 287 ASP cc_start: 0.7902 (t0) cc_final: 0.7645 (t70) REVERT: A 304 LYS cc_start: 0.7952 (tptt) cc_final: 0.7627 (tptt) REVERT: A 424 LYS cc_start: 0.5552 (tppt) cc_final: 0.5109 (tppt) REVERT: A 697 MET cc_start: 0.6812 (tpt) cc_final: 0.6582 (tpt) REVERT: A 779 GLN cc_start: 0.7848 (tt0) cc_final: 0.7593 (tt0) REVERT: A 780 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: A 940 SER cc_start: 0.6699 (m) cc_final: 0.6230 (p) REVERT: A 1031 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: A 1115 ILE cc_start: 0.8690 (mp) cc_final: 0.8308 (tp) REVERT: A 1142 GLN cc_start: 0.8140 (tp40) cc_final: 0.7818 (tp-100) REVERT: A 1146 ASP cc_start: 0.7876 (m-30) cc_final: 0.7192 (m-30) REVERT: B 41 LYS cc_start: 0.8334 (pttt) cc_final: 0.8058 (mtmt) REVERT: B 43 PHE cc_start: 0.7073 (t80) cc_final: 0.6803 (t80) REVERT: B 141 LEU cc_start: 0.6573 (tp) cc_final: 0.6232 (mm) REVERT: B 152 TRP cc_start: 0.3020 (m100) cc_final: 0.2395 (m100) REVERT: B 157 PHE cc_start: 0.5662 (t80) cc_final: 0.4967 (t80) REVERT: B 206 LYS cc_start: 0.7745 (tptt) cc_final: 0.7466 (tppt) REVERT: B 266 TYR cc_start: 0.6990 (m-80) cc_final: 0.6766 (m-80) REVERT: B 293 LEU cc_start: 0.8199 (tt) cc_final: 0.7669 (tt) REVERT: B 304 LYS cc_start: 0.7379 (tmmt) cc_final: 0.7162 (tmmt) REVERT: B 387 LEU cc_start: 0.8108 (mt) cc_final: 0.7746 (tp) REVERT: B 457 ARG cc_start: 0.5049 (tpt90) cc_final: 0.4536 (ttp80) REVERT: B 480 CYS cc_start: 0.4573 (OUTLIER) cc_final: 0.3778 (t) REVERT: B 540 ASN cc_start: 0.7283 (t0) cc_final: 0.6999 (t0) REVERT: B 567 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.5393 (mmm-85) REVERT: B 776 LYS cc_start: 0.8389 (tmtt) cc_final: 0.8002 (ttpp) REVERT: B 869 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7154 (mtp) REVERT: B 900 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7768 (mmt) REVERT: B 918 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7365 (tp30) REVERT: B 950 ASP cc_start: 0.7256 (m-30) cc_final: 0.7023 (m-30) REVERT: C 21 ARG cc_start: 0.5187 (ttt-90) cc_final: 0.4831 (mtt-85) REVERT: C 38 TYR cc_start: 0.7832 (m-80) cc_final: 0.7433 (m-80) REVERT: C 83 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7633 (p) REVERT: C 204 TYR cc_start: 0.6394 (m-80) cc_final: 0.6095 (m-80) REVERT: C 298 GLU cc_start: 0.8468 (tp30) cc_final: 0.8045 (tp30) REVERT: C 309 GLU cc_start: 0.7631 (mp0) cc_final: 0.7395 (mt-10) REVERT: C 319 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7322 (mmt90) REVERT: C 324 GLU cc_start: 0.6116 (pm20) cc_final: 0.5877 (pm20) REVERT: C 365 TYR cc_start: 0.6260 (m-80) cc_final: 0.6044 (m-80) REVERT: C 542 ASN cc_start: 0.7359 (t0) cc_final: 0.6341 (m110) REVERT: C 588 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7909 (p) REVERT: C 673 SER cc_start: 0.7124 (t) cc_final: 0.6418 (m) REVERT: C 919 ASN cc_start: 0.8018 (m-40) cc_final: 0.7634 (m110) outliers start: 127 outliers final: 96 residues processed: 646 average time/residue: 0.1774 time to fit residues: 183.4979 Evaluate side-chains 665 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 560 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 235 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 285 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 181 optimal weight: 0.0270 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 236 optimal weight: 0.7980 chunk 273 optimal weight: 0.7980 chunk 272 optimal weight: 0.1980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 703 ASN B 787 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 928 ASN C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.085758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.070454 restraints weight = 106447.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072526 restraints weight = 59371.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073888 restraints weight = 39000.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.074821 restraints weight = 28809.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.075463 restraints weight = 23114.215| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27539 Z= 0.145 Angle : 0.792 18.700 37641 Z= 0.379 Chirality : 0.048 0.429 4488 Planarity : 0.005 0.072 4690 Dihedral : 9.041 108.683 5475 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.55 % Allowed : 20.97 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3223 helix: 0.73 (0.20), residues: 688 sheet: -0.58 (0.20), residues: 655 loop : -1.44 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 237 TYR 0.022 0.002 TYR A 674 PHE 0.046 0.002 PHE C 157 TRP 0.025 0.002 TRP C 353 HIS 0.007 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00319 (27404) covalent geometry : angle 0.75651 (37278) SS BOND : bond 0.00464 ( 42) SS BOND : angle 1.81730 ( 84) hydrogen bonds : bond 0.04002 ( 1034) hydrogen bonds : angle 6.27059 ( 2898) link_ALPHA1-4 : bond 0.01846 ( 6) link_ALPHA1-4 : angle 2.96903 ( 18) link_BETA1-4 : bond 0.00358 ( 29) link_BETA1-4 : angle 1.67784 ( 87) link_BETA1-6 : bond 0.01658 ( 3) link_BETA1-6 : angle 2.02054 ( 9) link_NAG-ASN : bond 0.00531 ( 55) link_NAG-ASN : angle 3.05320 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 586 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7675 (p0) cc_final: 0.7377 (p0) REVERT: A 121 ASN cc_start: 0.6964 (p0) cc_final: 0.6179 (t0) REVERT: A 146 HIS cc_start: 0.4191 (p-80) cc_final: 0.2744 (m-70) REVERT: A 188 ASN cc_start: 0.5764 (OUTLIER) cc_final: 0.5019 (p0) REVERT: A 270 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6934 (tp) REVERT: A 287 ASP cc_start: 0.7886 (t0) cc_final: 0.7630 (t70) REVERT: A 304 LYS cc_start: 0.7992 (tptt) cc_final: 0.7669 (tptt) REVERT: A 424 LYS cc_start: 0.5473 (tppt) cc_final: 0.4881 (tppt) REVERT: A 567 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.6937 (mtt90) REVERT: A 697 MET cc_start: 0.6764 (tpt) cc_final: 0.6482 (tpt) REVERT: A 779 GLN cc_start: 0.7821 (tt0) cc_final: 0.7582 (tt0) REVERT: A 780 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: A 940 SER cc_start: 0.6768 (m) cc_final: 0.6276 (p) REVERT: A 1050 MET cc_start: 0.6556 (pmm) cc_final: 0.6322 (pmm) REVERT: A 1107 ARG cc_start: 0.7181 (mtp180) cc_final: 0.6806 (mtt90) REVERT: A 1142 GLN cc_start: 0.8179 (tp40) cc_final: 0.7862 (tp-100) REVERT: A 1146 ASP cc_start: 0.7948 (m-30) cc_final: 0.7235 (m-30) REVERT: B 152 TRP cc_start: 0.2821 (m100) cc_final: 0.2367 (m100) REVERT: B 157 PHE cc_start: 0.5699 (t80) cc_final: 0.5386 (t80) REVERT: B 206 LYS cc_start: 0.7636 (tptt) cc_final: 0.7366 (tppt) REVERT: B 293 LEU cc_start: 0.8063 (tt) cc_final: 0.7768 (tt) REVERT: B 387 LEU cc_start: 0.8102 (mt) cc_final: 0.7696 (tp) REVERT: B 457 ARG cc_start: 0.4958 (tpt90) cc_final: 0.4578 (ttp80) REVERT: B 480 CYS cc_start: 0.4597 (OUTLIER) cc_final: 0.3776 (t) REVERT: B 540 ASN cc_start: 0.7273 (t0) cc_final: 0.6979 (t0) REVERT: B 567 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.5480 (mmm-85) REVERT: B 720 ILE cc_start: 0.8317 (mm) cc_final: 0.7905 (tt) REVERT: B 776 LYS cc_start: 0.8392 (tmtt) cc_final: 0.7982 (ttpp) REVERT: B 869 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7263 (mtp) REVERT: B 895 GLN cc_start: 0.7431 (pm20) cc_final: 0.7091 (pm20) REVERT: B 900 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7662 (mmt) REVERT: B 918 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7306 (tp30) REVERT: B 950 ASP cc_start: 0.7247 (m-30) cc_final: 0.6938 (m-30) REVERT: B 1007 TYR cc_start: 0.7788 (t80) cc_final: 0.7414 (t80) REVERT: C 18 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.5255 (mt) REVERT: C 21 ARG cc_start: 0.5456 (ttt-90) cc_final: 0.4964 (mtt-85) REVERT: C 38 TYR cc_start: 0.7799 (m-80) cc_final: 0.7421 (m-80) REVERT: C 41 LYS cc_start: 0.7601 (mttp) cc_final: 0.7284 (mttp) REVERT: C 83 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7522 (p) REVERT: C 134 GLN cc_start: 0.6441 (mm110) cc_final: 0.6221 (mm110) REVERT: C 177 MET cc_start: 0.6049 (ppp) cc_final: 0.5506 (ppp) REVERT: C 204 TYR cc_start: 0.6339 (m-80) cc_final: 0.6053 (m-80) REVERT: C 220 PHE cc_start: 0.5999 (OUTLIER) cc_final: 0.5722 (t80) REVERT: C 242 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7144 (mp) REVERT: C 298 GLU cc_start: 0.8459 (tp30) cc_final: 0.8034 (tp30) REVERT: C 324 GLU cc_start: 0.6054 (pm20) cc_final: 0.5806 (pm20) REVERT: C 542 ASN cc_start: 0.7464 (t0) cc_final: 0.6588 (m110) REVERT: C 588 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7948 (p) REVERT: C 661 GLU cc_start: 0.7035 (tp30) cc_final: 0.6798 (tp30) REVERT: C 673 SER cc_start: 0.7164 (t) cc_final: 0.6439 (m) REVERT: C 674 TYR cc_start: 0.6845 (t80) cc_final: 0.6401 (t80) REVERT: C 919 ASN cc_start: 0.8007 (m-40) cc_final: 0.7711 (m110) REVERT: C 954 GLN cc_start: 0.7269 (mt0) cc_final: 0.6945 (mt0) REVERT: C 969 ASN cc_start: 0.8047 (m-40) cc_final: 0.7291 (t0) outliers start: 101 outliers final: 79 residues processed: 637 average time/residue: 0.1812 time to fit residues: 184.8021 Evaluate side-chains 652 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 561 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 95 optimal weight: 0.0470 chunk 270 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 271 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 295 optimal weight: 0.0970 chunk 196 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 305 optimal weight: 0.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** 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 = 0.3647 r_free = 0.3647 target = 0.085588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070588 restraints weight = 105681.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.072595 restraints weight = 59670.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073935 restraints weight = 39457.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.074839 restraints weight = 29230.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.075457 restraints weight = 23532.828| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 27539 Z= 0.209 Angle : 0.891 59.175 37641 Z= 0.457 Chirality : 0.051 1.140 4488 Planarity : 0.005 0.092 4690 Dihedral : 9.000 108.686 5471 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.48 % Allowed : 21.57 % Favored : 74.96 % 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: -1.14 (0.14), residues: 3223 helix: 0.73 (0.20), residues: 688 sheet: -0.58 (0.20), residues: 653 loop : -1.43 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG C 319 TYR 0.047 0.002 TYR A 501 PHE 0.044 0.002 PHE C 157 TRP 0.023 0.002 TRP A 152 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00452 (27404) covalent geometry : angle 0.86106 (37278) SS BOND : bond 0.00382 ( 42) SS BOND : angle 1.84055 ( 84) hydrogen bonds : bond 0.04007 ( 1034) hydrogen bonds : angle 6.26881 ( 2898) link_ALPHA1-4 : bond 0.01841 ( 6) link_ALPHA1-4 : angle 3.00026 ( 18) link_BETA1-4 : bond 0.00356 ( 29) link_BETA1-4 : angle 1.67937 ( 87) link_BETA1-6 : bond 0.01652 ( 3) link_BETA1-6 : angle 2.02604 ( 9) link_NAG-ASN : bond 0.00534 ( 55) link_NAG-ASN : angle 3.04970 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5572.84 seconds wall clock time: 97 minutes 5.34 seconds (5825.34 seconds total)