Starting phenix.real_space_refine on Sun Jul 5 09:52:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n1x_24126/07_2026/7n1x_24126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n1x_24126/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7n1x_24126/07_2026/7n1x_24126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n1x_24126/07_2026/7n1x_24126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n1x_24126/07_2026/7n1x_24126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n1x_24126/07_2026/7n1x_24126.map" model { file = "/net/cci-nas-00/data/ceres_data/7n1x_24126/07_2026/7n1x_24126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n1x_24126/07_2026/7n1x_24126.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.22, per 1000 atoms: 0.27 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: 2.70 Conformation dependent library (CDL) restraints added in 1.1 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: 1.18 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: 6.94 Time building geometry restraints manager: 3.50 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 - 18.42: 14226 18.42 - 36.84: 1071 36.84 - 55.26: 170 55.26 - 73.69: 65 73.69 - 92.11: 34 Dihedral angle restraints: 15566 sinusoidal: 6081 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 15563 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: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.190 Find NCS groups from input model: 1.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 : 14.576 92.107 9338 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/Z covalent geometry : bond 0.01410 / 0.80 (27404) covalent geometry : angle 1.89450 / 1.24 (37278) SS BOND : bond 0.01282 / 0.73 ( 42) SS BOND : angle 2.41078 / 1.54 ( 84) hydrogen bonds : bond 0.17129 / 11.27 ( 1034) hydrogen bonds : angle 9.23249 / 6.20 ( 2898) link_ALPHA1-4 : bond 0.02746 / 1.39 ( 6) link_ALPHA1-4 : angle 3.79525 / 2.25 ( 18) link_BETA1-4 : bond 0.01872 / 1.18 ( 29) link_BETA1-4 : angle 3.53109 / 2.31 ( 87) link_BETA1-6 : bond 0.03503 / 1.75 ( 3) link_BETA1-6 : angle 3.35661 / 2.12 ( 9) link_NAG-ASN : bond 0.17293 / 10.54 ( 55) link_NAG-ASN : angle 11.42239 / 8.04 ( 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 : 1.209 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: 0.1900 time to fit residues: 246.1502 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 : 1.024 ------------------------------------------------------------------------------- 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... 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 = 0.085804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.070169 restraints weight = 107001.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072310 restraints weight = 59788.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.073707 restraints weight = 39168.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074673 restraints weight = 28829.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.075315 restraints weight = 23053.530| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27539 Z= 0.183 Angle : 0.909 19.492 37641 Z= 0.445 Chirality : 0.052 0.681 4488 Planarity : 0.005 0.099 4690 Dihedral : 7.869 71.949 3538 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.34 % Allowed : 11.63 % 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: -1.41 (0.14), residues: 3223 helix: -0.40 (0.19), residues: 714 sheet: -0.30 (0.20), residues: 620 loop : -1.39 (0.13), residues: 1889 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 0.024 0.002 TRP A 64 HIS 0.012 0.002 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (27404) covalent geometry : angle 0.83542 / 0.43 (37278) SS BOND : bond 0.00453 / 0.27 ( 42) SS BOND : angle 2.34452 / 1.69 ( 84) hydrogen bonds : bond 0.05178 / 3.38 ( 1034) hydrogen bonds : angle 6.95506 / 4.67 ( 2898) link_ALPHA1-4 : bond 0.00959 / 0.49 ( 6) link_ALPHA1-4 : angle 2.27977 / 1.39 ( 18) link_BETA1-4 : bond 0.00507 / 0.27 ( 29) link_BETA1-4 : angle 2.07350 / 1.34 ( 87) link_BETA1-6 : bond 0.00507 / 0.25 ( 3) link_BETA1-6 : angle 1.23474 / 0.76 ( 9) link_NAG-ASN : bond 0.00795 / 0.50 ( 55) link_NAG-ASN : angle 5.00222 / 3.29 ( 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 748 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 653 time to evaluate : 0.911 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: A 121 ASN cc_start: 0.5597 (t0) cc_final: 0.5236 (t0) REVERT: A 146 HIS cc_start: 0.5052 (p-80) cc_final: 0.3710 (m-70) REVERT: A 317 ASN cc_start: 0.5864 (OUTLIER) cc_final: 0.5326 (p0) REVERT: A 388 ASN cc_start: 0.5012 (m-40) cc_final: 0.4315 (t0) REVERT: A 466 ARG cc_start: 0.4846 (mtp85) cc_final: 0.4262 (ttt90) REVERT: A 551 VAL cc_start: 0.8157 (t) cc_final: 0.7809 (p) REVERT: A 565 PHE cc_start: 0.6757 (m-80) cc_final: 0.6552 (m-10) REVERT: A 661 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6684 (mm-30) REVERT: A 697 MET cc_start: 0.6946 (tpt) cc_final: 0.6698 (tpt) REVERT: A 740 MET cc_start: 0.7707 (mtm) cc_final: 0.7312 (mtt) REVERT: A 779 GLN cc_start: 0.7748 (tt0) cc_final: 0.7515 (tt0) REVERT: A 788 ILE cc_start: 0.7733 (mm) cc_final: 0.7530 (mp) REVERT: A 806 LEU cc_start: 0.8663 (mm) cc_final: 0.8396 (mm) REVERT: A 870 ILE cc_start: 0.8280 (mt) cc_final: 0.7921 (mp) REVERT: A 1146 ASP cc_start: 0.8054 (m-30) cc_final: 0.6710 (m-30) REVERT: A 1148 PHE cc_start: 0.5921 (m-80) cc_final: 0.5702 (m-80) REVERT: B 43 PHE cc_start: 0.7393 (t80) cc_final: 0.7040 (t80) REVERT: B 152 TRP cc_start: 0.2695 (m100) cc_final: 0.2114 (m100) REVERT: B 157 PHE cc_start: 0.5536 (t80) cc_final: 0.5138 (t80) REVERT: B 227 VAL cc_start: 0.7707 (p) cc_final: 0.7243 (t) REVERT: B 238 PHE cc_start: 0.6871 (p90) cc_final: 0.5886 (p90) REVERT: B 286 THR cc_start: 0.7789 (m) cc_final: 0.7476 (p) REVERT: B 293 LEU cc_start: 0.7754 (tt) cc_final: 0.7545 (tt) REVERT: B 409 GLN cc_start: 0.5984 (OUTLIER) cc_final: 0.5759 (tt0) REVERT: B 439 ASN cc_start: 0.6981 (t0) cc_final: 0.5851 (p0) REVERT: B 462 LYS cc_start: 0.6971 (tptt) cc_final: 0.6503 (tttp) REVERT: B 468 ILE cc_start: 0.7087 (pt) cc_final: 0.6833 (tp) REVERT: B 480 CYS cc_start: 0.4448 (OUTLIER) cc_final: 0.3377 (t) REVERT: B 540 ASN cc_start: 0.7363 (t0) cc_final: 0.7135 (t0) REVERT: B 565 PHE cc_start: 0.6593 (m-80) cc_final: 0.6140 (m-80) REVERT: B 567 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.5496 (mmm160) REVERT: B 611 LEU cc_start: 0.8686 (tp) cc_final: 0.8464 (tp) REVERT: B 693 ILE cc_start: 0.8083 (pt) cc_final: 0.7872 (pt) REVERT: B 748 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: B 776 LYS cc_start: 0.8393 (tmtt) cc_final: 0.8127 (tptp) REVERT: B 788 ILE cc_start: 0.7853 (mm) cc_final: 0.7649 (mm) REVERT: B 806 LEU cc_start: 0.8771 (mt) cc_final: 0.8561 (mt) REVERT: B 918 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7373 (tp30) REVERT: B 950 ASP cc_start: 0.7337 (m-30) cc_final: 0.6995 (m-30) REVERT: B 957 GLN cc_start: 0.8033 (tt0) cc_final: 0.7817 (tt0) REVERT: B 1037 SER cc_start: 0.8373 (t) cc_final: 0.8082 (p) REVERT: B 1041 ASP cc_start: 0.7497 (t0) cc_final: 0.7262 (t0) REVERT: C 21 ARG cc_start: 0.5713 (ttt180) cc_final: 0.5431 (mtt-85) REVERT: C 63 THR cc_start: 0.7301 (p) cc_final: 0.6979 (p) REVERT: C 170 TYR cc_start: 0.6284 (m-80) cc_final: 0.6073 (m-80) REVERT: C 190 ARG cc_start: 0.7070 (mmt180) cc_final: 0.6741 (mmm-85) REVERT: C 204 TYR cc_start: 0.6867 (m-80) cc_final: 0.6506 (m-80) REVERT: C 237 ARG cc_start: 0.6529 (ptt180) cc_final: 0.6173 (ptt-90) REVERT: C 274 THR cc_start: 0.7668 (m) cc_final: 0.7277 (t) REVERT: C 290 ASP cc_start: 0.6973 (t0) cc_final: 0.6593 (t0) REVERT: C 298 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7898 (mm-30) REVERT: C 324 GLU cc_start: 0.6139 (pm20) cc_final: 0.5869 (pm20) REVERT: C 355 ARG cc_start: 0.7002 (mtp85) cc_final: 0.6693 (mtp85) REVERT: C 466 ARG cc_start: 0.3957 (OUTLIER) cc_final: 0.3496 (ttp80) REVERT: C 510 VAL cc_start: 0.7212 (t) cc_final: 0.6974 (t) REVERT: C 517 LEU cc_start: 0.5266 (mp) cc_final: 0.4996 (mp) REVERT: C 541 PHE cc_start: 0.7820 (p90) cc_final: 0.7571 (p90) REVERT: C 576 VAL cc_start: 0.8045 (p) cc_final: 0.7827 (t) REVERT: C 588 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.7968 (p) REVERT: C 673 SER cc_start: 0.6964 (t) cc_final: 0.6273 (m) REVERT: C 779 GLN cc_start: 0.7976 (pp30) cc_final: 0.7668 (pp30) REVERT: C 825 LYS cc_start: 0.7141 (tppt) cc_final: 0.6747 (tppt) REVERT: C 919 ASN cc_start: 0.8018 (m-40) cc_final: 0.7618 (m110) REVERT: C 991 VAL cc_start: 0.8506 (t) cc_final: 0.7874 (t) REVERT: C 1058 HIS cc_start: 0.7569 (m-70) cc_final: 0.7328 (m170) outliers start: 95 outliers final: 41 residues processed: 707 average time/residue: 0.1830 time to fit residues: 203.5246 Evaluate side-chains 623 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 575 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 PHE 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: 2.9990 chunk 131 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 323 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 493 GLN A 580 GLN A 641 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 115 GLN B 317 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 603 ASN C 960 ASN C1054 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.085554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069856 restraints weight = 107646.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.071971 restraints weight = 60351.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.073393 restraints weight = 39750.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074340 restraints weight = 29302.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.074992 restraints weight = 23531.215| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27539 Z= 0.167 Angle : 0.807 17.044 37641 Z= 0.393 Chirality : 0.049 0.571 4488 Planarity : 0.005 0.044 4690 Dihedral : 6.964 70.027 3514 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.30 % Allowed : 14.16 % Favored : 82.54 % 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: -1.20 (0.14), residues: 3223 helix: 0.14 (0.19), residues: 719 sheet: -0.48 (0.19), residues: 640 loop : -1.31 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 44 TYR 0.029 0.002 TYR A 365 PHE 0.025 0.002 PHE C 157 TRP 0.022 0.002 TRP A 353 HIS 0.010 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (27404) covalent geometry : angle 0.75680 / 0.38 (37278) SS BOND : bond 0.00631 / 0.44 ( 42) SS BOND : angle 1.76995 / 1.25 ( 84) hydrogen bonds : bond 0.04583 / 3.01 ( 1034) hydrogen bonds : angle 6.62141 / 4.42 ( 2898) link_ALPHA1-4 : bond 0.01059 / 0.54 ( 6) link_ALPHA1-4 : angle 1.85859 / 1.12 ( 18) link_BETA1-4 : bond 0.00436 / 0.25 ( 29) link_BETA1-4 : angle 1.78405 / 1.16 ( 87) link_BETA1-6 : bond 0.00599 / 0.30 ( 3) link_BETA1-6 : angle 1.15450 / 0.69 ( 9) link_NAG-ASN : bond 0.00584 / 0.37 ( 55) link_NAG-ASN : angle 3.94046 / 2.63 ( 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 705 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 611 time to evaluate : 1.008 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 146 HIS cc_start: 0.4929 (p-80) cc_final: 0.3507 (m-70) REVERT: A 153 MET cc_start: 0.7156 (tpt) cc_final: 0.6556 (tpp) REVERT: A 304 LYS cc_start: 0.7994 (tptt) cc_final: 0.7673 (tptt) REVERT: A 388 ASN cc_start: 0.5029 (m-40) cc_final: 0.4340 (t0) REVERT: A 396 TYR cc_start: 0.5868 (m-80) cc_final: 0.4599 (m-80) REVERT: A 551 VAL cc_start: 0.8144 (t) cc_final: 0.7939 (p) REVERT: A 779 GLN cc_start: 0.7881 (tt0) cc_final: 0.7569 (tt0) REVERT: A 780 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: A 870 ILE cc_start: 0.8279 (mt) cc_final: 0.7935 (mp) REVERT: A 896 ILE cc_start: 0.8854 (mt) cc_final: 0.8642 (mt) REVERT: A 1031 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: A 1034 LEU cc_start: 0.8342 (mp) cc_final: 0.8136 (mt) REVERT: B 43 PHE cc_start: 0.7281 (t80) cc_final: 0.6935 (t80) REVERT: B 152 TRP cc_start: 0.2745 (m100) cc_final: 0.2144 (m100) REVERT: B 157 PHE cc_start: 0.5549 (t80) cc_final: 0.5034 (t80) REVERT: B 286 THR cc_start: 0.7830 (m) cc_final: 0.7497 (p) REVERT: B 354 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.6996 (m-40) REVERT: B 387 LEU cc_start: 0.8144 (mt) cc_final: 0.7712 (tp) REVERT: B 468 ILE cc_start: 0.7010 (pt) cc_final: 0.6760 (tp) REVERT: B 480 CYS cc_start: 0.4521 (OUTLIER) cc_final: 0.3483 (t) REVERT: B 540 ASN cc_start: 0.7301 (t0) cc_final: 0.7031 (t0) REVERT: B 565 PHE cc_start: 0.6474 (m-80) cc_final: 0.6196 (m-80) REVERT: B 567 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5417 (mmm160) REVERT: B 664 ILE cc_start: 0.8160 (mm) cc_final: 0.7828 (mm) REVERT: B 693 ILE cc_start: 0.8074 (pt) cc_final: 0.7869 (pt) REVERT: B 704 SER cc_start: 0.7312 (t) cc_final: 0.6960 (m) REVERT: B 773 GLU cc_start: 0.7458 (tp30) cc_final: 0.7255 (tp30) REVERT: B 776 LYS cc_start: 0.8409 (tmtt) cc_final: 0.8053 (ttpp) REVERT: B 806 LEU cc_start: 0.8705 (mt) cc_final: 0.8499 (mt) REVERT: B 873 TYR cc_start: 0.7944 (m-10) cc_final: 0.7692 (m-10) REVERT: B 900 MET cc_start: 0.8111 (mmp) cc_final: 0.7842 (mmp) REVERT: B 916 LEU cc_start: 0.8622 (tt) cc_final: 0.8417 (tp) REVERT: B 918 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7334 (tp30) REVERT: B 950 ASP cc_start: 0.7277 (m-30) cc_final: 0.6963 (m-30) REVERT: B 1014 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7446 (mtt90) REVERT: B 1037 SER cc_start: 0.8389 (t) cc_final: 0.8083 (p) REVERT: B 1041 ASP cc_start: 0.7561 (t0) cc_final: 0.7325 (t0) REVERT: C 204 TYR cc_start: 0.6558 (m-80) cc_final: 0.6319 (m-80) REVERT: C 237 ARG cc_start: 0.6529 (ptt180) cc_final: 0.6326 (ptt-90) REVERT: C 242 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7608 (mp) REVERT: C 271 GLN cc_start: 0.7969 (mp10) cc_final: 0.7722 (mp10) REVERT: C 274 THR cc_start: 0.7719 (m) cc_final: 0.7338 (t) REVERT: C 290 ASP cc_start: 0.7081 (t0) cc_final: 0.6641 (t0) REVERT: C 298 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8035 (mm-30) REVERT: C 576 VAL cc_start: 0.8157 (p) cc_final: 0.7896 (t) REVERT: C 588 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7951 (p) REVERT: C 654 GLU cc_start: 0.7073 (mp0) cc_final: 0.6833 (mm-30) REVERT: C 673 SER cc_start: 0.6976 (t) cc_final: 0.6310 (m) REVERT: C 699 LEU cc_start: 0.7955 (mt) cc_final: 0.7601 (mp) REVERT: C 819 GLU cc_start: 0.8225 (mp0) cc_final: 0.7981 (mp0) REVERT: C 825 LYS cc_start: 0.7232 (tppt) cc_final: 0.6766 (tppt) REVERT: C 919 ASN cc_start: 0.8039 (m-40) cc_final: 0.7668 (m110) outliers start: 94 outliers final: 57 residues processed: 664 average time/residue: 0.1820 time to fit residues: 190.8141 Evaluate side-chains 621 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 556 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 188 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE 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 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 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 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 719 THR 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 805 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 856 ASN 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 1136 THR 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 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 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 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: 0.4980 chunk 34 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 275 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 180 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 183 optimal weight: 0.0670 chunk 300 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN A 613 GLN ** A 703 ASN ** 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 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 474 GLN C 960 ASN C1058 HIS ** 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 = 0.3661 r_free = 0.3661 target = 0.086283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070656 restraints weight = 106831.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.072797 restraints weight = 59925.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074202 restraints weight = 39322.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.075178 restraints weight = 29011.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.075814 restraints weight = 23235.004| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27539 Z= 0.132 Angle : 0.746 15.082 37641 Z= 0.364 Chirality : 0.047 0.514 4488 Planarity : 0.004 0.057 4690 Dihedral : 6.407 69.039 3509 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.62 % Allowed : 15.77 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3223 helix: 0.59 (0.20), residues: 703 sheet: -0.40 (0.20), residues: 624 loop : -1.21 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 466 TYR 0.023 0.002 TYR A1067 PHE 0.031 0.002 PHE C 429 TRP 0.026 0.002 TRP A 353 HIS 0.007 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (27404) covalent geometry : angle 0.70111 / 0.35 (37278) SS BOND : bond 0.00376 / 0.23 ( 42) SS BOND : angle 2.23492 / 1.48 ( 84) hydrogen bonds : bond 0.04070 / 2.64 ( 1034) hydrogen bonds : angle 6.33275 / 4.20 ( 2898) link_ALPHA1-4 : bond 0.00854 / 0.44 ( 6) link_ALPHA1-4 : angle 1.61524 / 0.99 ( 18) link_BETA1-4 : bond 0.00377 / 0.23 ( 29) link_BETA1-4 : angle 1.51308 / 0.99 ( 87) link_BETA1-6 : bond 0.00571 / 0.29 ( 3) link_BETA1-6 : angle 1.05888 / 0.63 ( 9) link_NAG-ASN : bond 0.00518 / 0.34 ( 55) link_NAG-ASN : angle 3.41386 / 2.29 ( 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 705 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 602 time to evaluate : 1.141 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: 0.6908 (p0) cc_final: 0.6368 (t0) REVERT: A 146 HIS cc_start: 0.4618 (p-80) cc_final: 0.3339 (m-70) REVERT: A 237 ARG cc_start: 0.7304 (mtm180) cc_final: 0.6871 (mtp85) REVERT: A 304 LYS cc_start: 0.8012 (tptt) cc_final: 0.7629 (tptt) REVERT: A 326 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6664 (mm) REVERT: A 388 ASN cc_start: 0.5009 (m-40) cc_final: 0.4464 (t0) REVERT: A 551 VAL cc_start: 0.8110 (t) cc_final: 0.7746 (p) REVERT: A 740 MET cc_start: 0.7865 (mtm) cc_final: 0.7505 (mtp) REVERT: A 779 GLN cc_start: 0.7860 (tt0) cc_final: 0.7563 (tt0) REVERT: A 780 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: A 904 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7106 (m-10) REVERT: A 1034 LEU cc_start: 0.8320 (mp) cc_final: 0.8075 (mt) REVERT: B 43 PHE cc_start: 0.7219 (t80) cc_final: 0.6884 (t80) REVERT: B 152 TRP cc_start: 0.2477 (m100) cc_final: 0.2087 (m100) REVERT: B 157 PHE cc_start: 0.5553 (t80) cc_final: 0.5105 (t80) REVERT: B 286 THR cc_start: 0.7764 (m) cc_final: 0.7436 (p) REVERT: B 297 SER cc_start: 0.8317 (m) cc_final: 0.8001 (p) REVERT: B 354 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.6997 (m-40) REVERT: B 387 LEU cc_start: 0.8124 (mt) cc_final: 0.7658 (tp) REVERT: B 455 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6621 (mt) REVERT: B 457 ARG cc_start: 0.4697 (tpt90) cc_final: 0.4283 (tmt170) REVERT: B 462 LYS cc_start: 0.7448 (tppt) cc_final: 0.7137 (tttp) REVERT: B 468 ILE cc_start: 0.6986 (pt) cc_final: 0.6758 (tp) REVERT: B 540 ASN cc_start: 0.7297 (t0) cc_final: 0.6984 (t0) REVERT: B 567 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.5538 (mmm-85) REVERT: B 693 ILE cc_start: 0.8047 (pt) cc_final: 0.7815 (pt) REVERT: B 704 SER cc_start: 0.7210 (t) cc_final: 0.6946 (m) REVERT: B 725 GLU cc_start: 0.7329 (tt0) cc_final: 0.7093 (tt0) REVERT: B 748 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: B 773 GLU cc_start: 0.7429 (tp30) cc_final: 0.7212 (tp30) REVERT: B 776 LYS cc_start: 0.8393 (tmtt) cc_final: 0.7981 (ttpp) REVERT: B 873 TYR cc_start: 0.7962 (m-10) cc_final: 0.7677 (m-10) REVERT: B 900 MET cc_start: 0.7985 (mmp) cc_final: 0.7685 (mmt) REVERT: B 901 GLN cc_start: 0.8055 (tt0) cc_final: 0.7854 (tt0) REVERT: B 916 LEU cc_start: 0.8605 (tt) cc_final: 0.8309 (tp) REVERT: B 918 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7346 (tp30) REVERT: B 950 ASP cc_start: 0.7224 (m-30) cc_final: 0.6982 (m-30) REVERT: B 1014 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7422 (mtt180) REVERT: B 1037 SER cc_start: 0.8382 (t) cc_final: 0.8075 (p) REVERT: B 1041 ASP cc_start: 0.7648 (t0) cc_final: 0.7402 (t0) REVERT: C 41 LYS cc_start: 0.7662 (mttp) cc_final: 0.7253 (mtmm) REVERT: C 121 ASN cc_start: 0.5626 (OUTLIER) cc_final: 0.5275 (t0) REVERT: C 200 TYR cc_start: 0.5618 (m-80) cc_final: 0.5398 (m-80) REVERT: C 204 TYR cc_start: 0.6605 (m-80) cc_final: 0.6315 (m-80) REVERT: C 237 ARG cc_start: 0.6446 (ptt180) cc_final: 0.6235 (ptt-90) REVERT: C 242 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7429 (mp) REVERT: C 271 GLN cc_start: 0.8047 (mp10) cc_final: 0.7826 (mp10) REVERT: C 274 THR cc_start: 0.7801 (m) cc_final: 0.7264 (t) REVERT: C 290 ASP cc_start: 0.7131 (t0) cc_final: 0.6816 (t0) REVERT: C 298 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7959 (mm-30) REVERT: C 388 ASN cc_start: 0.6927 (OUTLIER) cc_final: 0.6723 (p0) REVERT: C 567 ARG cc_start: 0.5707 (mtt180) cc_final: 0.5410 (mtt180) REVERT: C 673 SER cc_start: 0.7023 (t) cc_final: 0.6349 (m) REVERT: C 825 LYS cc_start: 0.7162 (tppt) cc_final: 0.6733 (tppt) REVERT: C 919 ASN cc_start: 0.8007 (m-40) cc_final: 0.7644 (m110) outliers start: 103 outliers final: 62 residues processed: 666 average time/residue: 0.1766 time to fit residues: 186.5310 Evaluate side-chains 626 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 553 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 326 ILE 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 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 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 1136 THR Chi-restraints excluded: chain A residue 1145 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 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 455 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 724 THR 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 869 MET Chi-restraints excluded: chain B residue 896 ILE 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 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 388 ASN 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 662 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 229 optimal weight: 0.8980 chunk 134 optimal weight: 0.0020 chunk 225 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 182 optimal weight: 0.0060 chunk 309 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 77 optimal weight: 0.0670 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** A 703 ASN ** 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 B 955 ASN B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1058 HIS ** 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 = 0.3663 r_free = 0.3663 target = 0.086369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070843 restraints weight = 107213.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072954 restraints weight = 59769.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074358 restraints weight = 39250.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.075323 restraints weight = 28923.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.075953 restraints weight = 23175.800| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27539 Z= 0.127 Angle : 0.717 14.042 37641 Z= 0.348 Chirality : 0.047 0.481 4488 Planarity : 0.004 0.067 4690 Dihedral : 6.079 69.975 3507 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.30 % Allowed : 17.70 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3223 helix: 0.77 (0.20), residues: 703 sheet: -0.46 (0.20), residues: 628 loop : -1.16 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.025 0.001 TYR A1067 PHE 0.028 0.002 PHE C1121 TRP 0.019 0.001 TRP A 353 HIS 0.010 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (27404) covalent geometry : angle 0.67901 / 0.34 (37278) SS BOND : bond 0.00397 / 0.24 ( 42) SS BOND : angle 1.71966 / 1.13 ( 84) hydrogen bonds : bond 0.03957 / 2.57 ( 1034) hydrogen bonds : angle 6.17177 / 4.09 ( 2898) link_ALPHA1-4 : bond 0.00818 / 0.42 ( 6) link_ALPHA1-4 : angle 1.48704 / 0.92 ( 18) link_BETA1-4 : bond 0.00382 / 0.23 ( 29) link_BETA1-4 : angle 1.45959 / 0.96 ( 87) link_BETA1-6 : bond 0.00575 / 0.29 ( 3) link_BETA1-6 : angle 1.03571 / 0.60 ( 9) link_NAG-ASN : bond 0.00513 / 0.33 ( 55) link_NAG-ASN : angle 3.18764 / 2.15 ( 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 682 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 588 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: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6967 (p0) cc_final: 0.6410 (t0) REVERT: A 127 VAL cc_start: 0.6981 (OUTLIER) cc_final: 0.6737 (m) REVERT: A 128 ILE cc_start: 0.7187 (mm) cc_final: 0.6949 (mm) REVERT: A 146 HIS cc_start: 0.4572 (p-80) cc_final: 0.3411 (m-70) REVERT: A 287 ASP cc_start: 0.7878 (t0) cc_final: 0.7645 (t0) REVERT: A 306 PHE cc_start: 0.6867 (m-10) cc_final: 0.6438 (m-10) REVERT: A 388 ASN cc_start: 0.4965 (m-40) cc_final: 0.4470 (t0) REVERT: A 560 LEU cc_start: 0.7907 (mt) cc_final: 0.7625 (mp) REVERT: A 586 ASP cc_start: 0.7870 (m-30) cc_final: 0.7140 (m-30) REVERT: A 697 MET cc_start: 0.6788 (tpt) cc_final: 0.6557 (tpt) REVERT: A 779 GLN cc_start: 0.7887 (tt0) cc_final: 0.7625 (tt0) REVERT: A 780 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: A 800 PHE cc_start: 0.8058 (m-80) cc_final: 0.7837 (m-10) REVERT: A 904 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7041 (m-10) REVERT: A 1002 GLN cc_start: 0.7351 (mt0) cc_final: 0.7136 (mt0) REVERT: A 1034 LEU cc_start: 0.8363 (mp) cc_final: 0.8089 (mt) REVERT: A 1115 ILE cc_start: 0.8632 (mp) cc_final: 0.8212 (tp) REVERT: B 43 PHE cc_start: 0.7282 (t80) cc_final: 0.6830 (t80) REVERT: B 92 PHE cc_start: 0.7530 (t80) cc_final: 0.7209 (t80) REVERT: B 104 TRP cc_start: 0.6662 (m-90) cc_final: 0.6140 (m-90) REVERT: B 152 TRP cc_start: 0.2355 (m100) cc_final: 0.2026 (m100) REVERT: B 157 PHE cc_start: 0.5592 (t80) cc_final: 0.5070 (t80) REVERT: B 206 LYS cc_start: 0.7624 (tptt) cc_final: 0.7267 (tppt) REVERT: B 286 THR cc_start: 0.7678 (m) cc_final: 0.7377 (p) REVERT: B 297 SER cc_start: 0.8319 (m) cc_final: 0.8037 (p) REVERT: B 354 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7039 (m-40) REVERT: B 387 LEU cc_start: 0.8164 (mt) cc_final: 0.7714 (tp) REVERT: B 457 ARG cc_start: 0.4722 (tpt90) cc_final: 0.4330 (tmt170) REVERT: B 462 LYS cc_start: 0.7465 (tppt) cc_final: 0.7038 (tttp) REVERT: B 468 ILE cc_start: 0.7035 (pt) cc_final: 0.6799 (tp) REVERT: B 480 CYS cc_start: 0.4410 (OUTLIER) cc_final: 0.3440 (t) REVERT: B 540 ASN cc_start: 0.7315 (t0) cc_final: 0.6969 (t0) REVERT: B 565 PHE cc_start: 0.6560 (m-80) cc_final: 0.6256 (m-80) REVERT: B 567 ARG cc_start: 0.6425 (OUTLIER) cc_final: 0.5364 (mmm160) REVERT: B 693 ILE cc_start: 0.7996 (pt) cc_final: 0.7787 (pt) REVERT: B 725 GLU cc_start: 0.7356 (tt0) cc_final: 0.7069 (tt0) REVERT: B 748 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: B 776 LYS cc_start: 0.8407 (tmtt) cc_final: 0.8128 (ttpp) REVERT: B 873 TYR cc_start: 0.7934 (m-10) cc_final: 0.7676 (m-10) REVERT: B 900 MET cc_start: 0.7909 (mmp) cc_final: 0.7635 (mmt) REVERT: B 918 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7376 (tp30) REVERT: B 950 ASP cc_start: 0.7223 (m-30) cc_final: 0.7012 (m-30) REVERT: B 1007 TYR cc_start: 0.7834 (t80) cc_final: 0.7431 (t80) REVERT: B 1037 SER cc_start: 0.8353 (t) cc_final: 0.8077 (p) REVERT: B 1041 ASP cc_start: 0.7637 (t0) cc_final: 0.7319 (t0) REVERT: C 121 ASN cc_start: 0.5942 (OUTLIER) cc_final: 0.5376 (t0) REVERT: C 200 TYR cc_start: 0.5549 (m-80) cc_final: 0.5339 (m-80) REVERT: C 204 TYR cc_start: 0.6478 (m-80) cc_final: 0.6175 (m-80) REVERT: C 271 GLN cc_start: 0.8011 (mp10) cc_final: 0.7799 (mp10) REVERT: C 273 ARG cc_start: 0.5606 (mtp85) cc_final: 0.5330 (mtp85) REVERT: C 274 THR cc_start: 0.7675 (m) cc_final: 0.7273 (t) REVERT: C 290 ASP cc_start: 0.7042 (t0) cc_final: 0.6834 (t0) REVERT: C 298 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7918 (mm-30) REVERT: C 353 TRP cc_start: 0.3357 (p-90) cc_final: 0.3088 (p-90) REVERT: C 388 ASN cc_start: 0.6912 (p0) cc_final: 0.6648 (p0) REVERT: C 429 PHE cc_start: 0.6596 (t80) cc_final: 0.6227 (t80) REVERT: C 542 ASN cc_start: 0.7426 (t0) cc_final: 0.6359 (m110) REVERT: C 585 LEU cc_start: 0.7545 (mp) cc_final: 0.7343 (mt) REVERT: C 673 SER cc_start: 0.7037 (t) cc_final: 0.6331 (m) REVERT: C 825 LYS cc_start: 0.7116 (tppt) cc_final: 0.6715 (tppt) REVERT: C 919 ASN cc_start: 0.7971 (m-40) cc_final: 0.7634 (m110) REVERT: C 970 PHE cc_start: 0.7739 (m-10) cc_final: 0.7464 (m-10) outliers start: 94 outliers final: 58 residues processed: 641 average time/residue: 0.1746 time to fit residues: 178.9035 Evaluate side-chains 616 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 550 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 308 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 582 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 780 GLU 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 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 135 PHE 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 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 480 CYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 724 THR 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 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 90 VAL 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 515 PHE Chi-restraints excluded: chain C residue 519 HIS 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 786 LYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 952 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 112 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 260 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 613 GLN A 703 ASN A 955 ASN A1011 GLN B 164 ASN B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 787 GLN B 954 GLN B 965 GLN B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 935 GLN C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.084535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069137 restraints weight = 108071.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071204 restraints weight = 60670.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.072576 restraints weight = 39894.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.073522 restraints weight = 29502.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074155 restraints weight = 23688.311| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 27539 Z= 0.213 Angle : 0.798 13.137 37641 Z= 0.391 Chirality : 0.049 0.473 4488 Planarity : 0.005 0.071 4690 Dihedral : 6.370 66.699 3503 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.43 % Allowed : 17.77 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3223 helix: 0.54 (0.20), residues: 704 sheet: -0.56 (0.20), residues: 621 loop : -1.35 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 237 TYR 0.024 0.002 TYR A 365 PHE 0.044 0.003 PHE C 157 TRP 0.021 0.002 TRP B 436 HIS 0.008 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (27404) covalent geometry : angle 0.76087 / 0.38 (37278) SS BOND : bond 0.00464 / 0.28 ( 42) SS BOND : angle 1.95999 / 1.34 ( 84) hydrogen bonds : bond 0.04456 / 2.91 ( 1034) hydrogen bonds : angle 6.38991 / 4.24 ( 2898) link_ALPHA1-4 : bond 0.00743 / 0.37 ( 6) link_ALPHA1-4 : angle 1.53004 / 0.95 ( 18) link_BETA1-4 : bond 0.00508 / 0.32 ( 29) link_BETA1-4 : angle 1.81758 / 1.18 ( 87) link_BETA1-6 : bond 0.00566 / 0.29 ( 3) link_BETA1-6 : angle 1.08501 / 0.65 ( 9) link_NAG-ASN : bond 0.00584 / 0.38 ( 55) link_NAG-ASN : angle 3.20849 / 2.13 ( 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 692 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 566 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: A 121 ASN cc_start: 0.6960 (p0) cc_final: 0.6292 (t0) REVERT: A 144 TYR cc_start: 0.7562 (m-10) cc_final: 0.6484 (m-10) REVERT: A 146 HIS cc_start: 0.4665 (p-80) cc_final: 0.3395 (m-70) REVERT: A 304 LYS cc_start: 0.7956 (tptt) cc_final: 0.7683 (tptt) REVERT: A 388 ASN cc_start: 0.4899 (m-40) cc_final: 0.4309 (t0) REVERT: A 697 MET cc_start: 0.6809 (tpt) cc_final: 0.6491 (tpp) REVERT: A 740 MET cc_start: 0.7606 (mtm) cc_final: 0.6800 (mtt) REVERT: A 779 GLN cc_start: 0.7886 (tt0) cc_final: 0.7595 (tt0) REVERT: A 780 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: A 904 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7185 (m-10) REVERT: A 1031 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: A 1115 ILE cc_start: 0.8624 (mp) cc_final: 0.8189 (tp) REVERT: A 1126 CYS cc_start: 0.5055 (p) cc_final: 0.4855 (p) REVERT: B 43 PHE cc_start: 0.7260 (t80) cc_final: 0.6909 (t80) REVERT: B 141 LEU cc_start: 0.6879 (tp) cc_final: 0.6548 (mm) REVERT: B 152 TRP cc_start: 0.2931 (m100) cc_final: 0.2271 (m100) REVERT: B 157 PHE cc_start: 0.5609 (t80) cc_final: 0.4798 (t80) REVERT: B 206 LYS cc_start: 0.7686 (tptt) cc_final: 0.7368 (tppt) REVERT: B 293 LEU cc_start: 0.8022 (tt) cc_final: 0.7730 (tt) REVERT: B 387 LEU cc_start: 0.8166 (mt) cc_final: 0.7733 (tp) REVERT: B 457 ARG cc_start: 0.4850 (tpt90) cc_final: 0.4421 (ttp80) REVERT: B 480 CYS cc_start: 0.4532 (OUTLIER) cc_final: 0.3609 (t) REVERT: B 540 ASN cc_start: 0.7333 (t0) cc_final: 0.7001 (t0) REVERT: B 567 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.5433 (mmm160) REVERT: B 693 ILE cc_start: 0.7957 (pt) cc_final: 0.7744 (pt) REVERT: B 704 SER cc_start: 0.7233 (t) cc_final: 0.6920 (m) REVERT: B 725 GLU cc_start: 0.7423 (tt0) cc_final: 0.7124 (tt0) REVERT: B 748 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: B 776 LYS cc_start: 0.8431 (tmtt) cc_final: 0.8130 (ttpp) REVERT: B 873 TYR cc_start: 0.7998 (m-10) cc_final: 0.7736 (m-10) REVERT: B 900 MET cc_start: 0.7975 (mmp) cc_final: 0.7722 (mmt) REVERT: B 901 GLN cc_start: 0.8200 (tt0) cc_final: 0.7935 (tp40) REVERT: B 918 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7413 (tp30) REVERT: B 950 ASP cc_start: 0.7194 (m-30) cc_final: 0.6946 (m-30) REVERT: B 1007 TYR cc_start: 0.7830 (t80) cc_final: 0.7337 (t80) REVERT: B 1037 SER cc_start: 0.8331 (t) cc_final: 0.8078 (p) REVERT: B 1122 VAL cc_start: 0.8399 (t) cc_final: 0.8188 (m) REVERT: B 1123 SER cc_start: 0.7275 (m) cc_final: 0.6842 (m) REVERT: C 204 TYR cc_start: 0.6493 (m-80) cc_final: 0.6224 (m-80) REVERT: C 271 GLN cc_start: 0.7913 (mp10) cc_final: 0.7691 (mp10) REVERT: C 274 THR cc_start: 0.7573 (m) cc_final: 0.7188 (t) REVERT: C 429 PHE cc_start: 0.6923 (t80) cc_final: 0.6530 (t80) REVERT: C 537 LYS cc_start: 0.6963 (mppt) cc_final: 0.6725 (mppt) REVERT: C 542 ASN cc_start: 0.7291 (t0) cc_final: 0.6261 (m110) REVERT: C 576 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7879 (t) REVERT: C 588 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7857 (p) REVERT: C 673 SER cc_start: 0.7139 (t) cc_final: 0.6470 (m) REVERT: C 825 LYS cc_start: 0.7199 (tppt) cc_final: 0.6814 (tppt) REVERT: C 919 ASN cc_start: 0.7966 (m-40) cc_final: 0.7621 (m110) REVERT: C 970 PHE cc_start: 0.7694 (m-10) cc_final: 0.7367 (m-80) outliers start: 126 outliers final: 86 residues processed: 646 average time/residue: 0.1714 time to fit residues: 178.7920 Evaluate side-chains 640 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 546 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 904 TYR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU 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 235 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL 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 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 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 724 THR 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 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1152 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 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 401 VAL 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 576 VAL 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 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 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 1058 HIS 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: 2.9990 chunk 238 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 210 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 965 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.084834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069386 restraints weight = 107061.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.071460 restraints weight = 60050.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.072844 restraints weight = 39495.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.073791 restraints weight = 29168.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.074434 restraints weight = 23409.997| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3948 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= 0.167 Angle : 0.763 12.663 37641 Z= 0.372 Chirality : 0.048 0.452 4488 Planarity : 0.005 0.069 4690 Dihedral : 6.227 67.084 3503 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.14 % Allowed : 18.86 % Favored : 76.99 % 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: -1.14 (0.14), residues: 3223 helix: 0.65 (0.20), residues: 696 sheet: -0.64 (0.20), residues: 620 loop : -1.36 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 237 TYR 0.022 0.002 TYR A 365 PHE 0.029 0.002 PHE B 92 TRP 0.021 0.002 TRP A 152 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (27404) covalent geometry : angle 0.72778 / 0.36 (37278) SS BOND : bond 0.00416 / 0.25 ( 42) SS BOND : angle 1.86214 / 1.23 ( 84) hydrogen bonds : bond 0.04224 / 2.75 ( 1034) hydrogen bonds : angle 6.30533 / 4.18 ( 2898) link_ALPHA1-4 : bond 0.00790 / 0.40 ( 6) link_ALPHA1-4 : angle 1.50572 / 0.93 ( 18) link_BETA1-4 : bond 0.00400 / 0.24 ( 29) link_BETA1-4 : angle 1.57988 / 1.02 ( 87) link_BETA1-6 : bond 0.00575 / 0.29 ( 3) link_BETA1-6 : angle 1.01737 / 0.60 ( 9) link_NAG-ASN : bond 0.00517 / 0.34 ( 55) link_NAG-ASN : angle 3.09673 / 2.07 ( 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 692 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 574 time to evaluate : 0.992 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: 0.6966 (p0) cc_final: 0.6289 (t0) REVERT: A 146 HIS cc_start: 0.4455 (p-80) cc_final: 0.3019 (m-70) REVERT: A 270 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6981 (tp) REVERT: A 287 ASP cc_start: 0.7892 (t0) cc_final: 0.7655 (t70) REVERT: A 304 LYS cc_start: 0.7972 (tptt) cc_final: 0.7678 (tptt) REVERT: A 357 ARG cc_start: 0.7032 (tpt170) cc_final: 0.6831 (tpt170) REVERT: A 388 ASN cc_start: 0.4906 (m-40) cc_final: 0.4312 (t0) REVERT: A 697 MET cc_start: 0.6780 (tpt) cc_final: 0.6499 (tpp) REVERT: A 779 GLN cc_start: 0.7901 (tt0) cc_final: 0.7608 (tt0) REVERT: A 780 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: A 904 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7092 (m-10) REVERT: A 1031 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6561 (mp0) REVERT: A 1115 ILE cc_start: 0.8630 (mp) cc_final: 0.8212 (tp) REVERT: B 43 PHE cc_start: 0.7227 (t80) cc_final: 0.6859 (t80) REVERT: B 141 LEU cc_start: 0.6893 (tp) cc_final: 0.6561 (mm) REVERT: B 152 TRP cc_start: 0.2967 (m100) cc_final: 0.2308 (m100) REVERT: B 157 PHE cc_start: 0.5576 (t80) cc_final: 0.4801 (t80) REVERT: B 206 LYS cc_start: 0.7588 (tptt) cc_final: 0.7253 (tppt) REVERT: B 266 TYR cc_start: 0.6736 (m-80) cc_final: 0.6521 (m-80) REVERT: B 293 LEU cc_start: 0.8067 (tt) cc_final: 0.7808 (tt) REVERT: B 387 LEU cc_start: 0.8150 (mt) cc_final: 0.7740 (tp) REVERT: B 457 ARG cc_start: 0.4951 (tpt90) cc_final: 0.4512 (ttp80) REVERT: B 462 LYS cc_start: 0.7487 (tppt) cc_final: 0.6911 (tttp) REVERT: B 480 CYS cc_start: 0.4611 (OUTLIER) cc_final: 0.3652 (t) REVERT: B 540 ASN cc_start: 0.7333 (t0) cc_final: 0.7020 (t0) REVERT: B 567 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.5406 (mmm160) REVERT: B 704 SER cc_start: 0.7228 (t) cc_final: 0.6928 (m) REVERT: B 725 GLU cc_start: 0.7457 (tt0) cc_final: 0.7139 (tt0) REVERT: B 748 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7319 (pm20) REVERT: B 776 LYS cc_start: 0.8385 (tmtt) cc_final: 0.7999 (ttpp) REVERT: B 873 TYR cc_start: 0.8029 (m-10) cc_final: 0.7777 (m-10) REVERT: B 900 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7718 (mmt) REVERT: B 918 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7411 (tp30) REVERT: B 950 ASP cc_start: 0.7221 (m-30) cc_final: 0.6996 (m-30) REVERT: B 994 ASP cc_start: 0.7490 (t70) cc_final: 0.7248 (t0) REVERT: B 1007 TYR cc_start: 0.7828 (t80) cc_final: 0.7345 (t80) REVERT: B 1123 SER cc_start: 0.7214 (m) cc_final: 0.6764 (m) REVERT: C 38 TYR cc_start: 0.7836 (m-80) cc_final: 0.7395 (m-80) REVERT: C 83 VAL cc_start: 0.7740 (OUTLIER) cc_final: 0.7443 (p) REVERT: C 200 TYR cc_start: 0.5747 (m-80) cc_final: 0.5483 (m-80) REVERT: C 204 TYR cc_start: 0.6372 (m-80) cc_final: 0.6090 (m-80) REVERT: C 271 GLN cc_start: 0.7934 (mp10) cc_final: 0.7555 (mp10) REVERT: C 298 GLU cc_start: 0.8584 (tp30) cc_final: 0.8130 (tp30) REVERT: C 319 ARG cc_start: 0.7395 (mmt90) cc_final: 0.6750 (tpp-160) REVERT: C 351 TYR cc_start: 0.4753 (p90) cc_final: 0.4418 (p90) REVERT: C 429 PHE cc_start: 0.6992 (t80) cc_final: 0.6663 (t80) REVERT: C 542 ASN cc_start: 0.7324 (t0) cc_final: 0.6368 (m110) REVERT: C 552 LEU cc_start: 0.8366 (tp) cc_final: 0.8156 (tt) REVERT: C 574 ASP cc_start: 0.5280 (p0) cc_final: 0.5071 (p0) REVERT: C 576 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7896 (t) REVERT: C 673 SER cc_start: 0.7130 (t) cc_final: 0.6419 (m) REVERT: C 825 LYS cc_start: 0.7169 (tppt) cc_final: 0.6778 (tppt) REVERT: C 902 MET cc_start: 0.8336 (mmm) cc_final: 0.8109 (mmm) REVERT: C 919 ASN cc_start: 0.7961 (m-40) cc_final: 0.7624 (m110) REVERT: C 970 PHE cc_start: 0.7735 (m-10) cc_final: 0.7437 (m-80) outliers start: 118 outliers final: 85 residues processed: 642 average time/residue: 0.1709 time to fit residues: 177.6181 Evaluate side-chains 643 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 548 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 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 696 THR 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 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU 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 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LEU 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 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 488 CYS 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 585 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 724 THR 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 1012 LEU Chi-restraints excluded: chain B residue 1136 THR 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 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 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 576 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN B 422 ASN B 703 ASN B 955 ASN B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1106 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.085052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069661 restraints weight = 107220.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.071757 restraints weight = 60204.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.073163 restraints weight = 39552.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074101 restraints weight = 29071.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074752 restraints weight = 23284.028| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 27539 Z= 0.162 Angle : 0.768 12.471 37641 Z= 0.374 Chirality : 0.048 0.436 4488 Planarity : 0.005 0.115 4690 Dihedral : 6.179 69.179 3502 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.07 % Allowed : 19.70 % Favored : 76.22 % 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: -1.13 (0.14), residues: 3223 helix: 0.70 (0.20), residues: 691 sheet: -0.69 (0.20), residues: 632 loop : -1.36 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 273 TYR 0.023 0.002 TYR A 365 PHE 0.053 0.002 PHE B 92 TRP 0.022 0.002 TRP C 353 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (27404) covalent geometry : angle 0.73373 / 0.37 (37278) SS BOND : bond 0.00432 / 0.26 ( 42) SS BOND : angle 2.13763 / 1.31 ( 84) hydrogen bonds : bond 0.04192 / 2.73 ( 1034) hydrogen bonds : angle 6.28181 / 4.15 ( 2898) link_ALPHA1-4 : bond 0.00784 / 0.39 ( 6) link_ALPHA1-4 : angle 1.45858 / 0.91 ( 18) link_BETA1-4 : bond 0.00377 / 0.22 ( 29) link_BETA1-4 : angle 1.56179 / 1.01 ( 87) link_BETA1-6 : bond 0.00574 / 0.29 ( 3) link_BETA1-6 : angle 1.00670 / 0.60 ( 9) link_NAG-ASN : bond 0.00533 / 0.34 ( 55) link_NAG-ASN : angle 2.99887 / 2.00 ( 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 685 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 569 time to evaluate : 1.029 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 81 ASN cc_start: 0.7729 (p0) cc_final: 0.7350 (p0) REVERT: A 121 ASN cc_start: 0.6949 (p0) cc_final: 0.6251 (t0) REVERT: A 146 HIS cc_start: 0.4084 (p-80) cc_final: 0.2723 (m-70) REVERT: A 188 ASN cc_start: 0.5745 (OUTLIER) cc_final: 0.5034 (p0) REVERT: A 269 TYR cc_start: 0.6573 (m-80) cc_final: 0.5606 (m-80) REVERT: A 270 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6967 (tp) REVERT: A 287 ASP cc_start: 0.7891 (t0) cc_final: 0.7651 (t70) REVERT: A 304 LYS cc_start: 0.7985 (tptt) cc_final: 0.7676 (tptt) REVERT: A 388 ASN cc_start: 0.4940 (m-40) cc_final: 0.4338 (t0) REVERT: A 543 PHE cc_start: 0.7504 (m-80) cc_final: 0.7297 (m-80) REVERT: A 779 GLN cc_start: 0.7892 (tt0) cc_final: 0.7608 (tt0) REVERT: A 780 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: A 904 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.5398 (m-10) REVERT: A 1031 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: A 1115 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8234 (tp) REVERT: B 43 PHE cc_start: 0.7159 (t80) cc_final: 0.6831 (t80) REVERT: B 92 PHE cc_start: 0.7399 (t80) cc_final: 0.7172 (t80) REVERT: B 141 LEU cc_start: 0.6851 (tp) cc_final: 0.6549 (mm) REVERT: B 152 TRP cc_start: 0.2894 (m100) cc_final: 0.2299 (m100) REVERT: B 157 PHE cc_start: 0.5598 (t80) cc_final: 0.4878 (t80) REVERT: B 206 LYS cc_start: 0.7592 (tptt) cc_final: 0.7275 (tppt) REVERT: B 273 ARG cc_start: 0.7502 (tpp80) cc_final: 0.6991 (ttm170) REVERT: B 293 LEU cc_start: 0.8109 (tt) cc_final: 0.7885 (tt) REVERT: B 387 LEU cc_start: 0.8148 (mt) cc_final: 0.7732 (tp) REVERT: B 422 ASN cc_start: 0.4739 (m-40) cc_final: 0.4508 (m110) REVERT: B 457 ARG cc_start: 0.4956 (tpt90) cc_final: 0.4523 (ttp80) REVERT: B 462 LYS cc_start: 0.7469 (tppt) cc_final: 0.6923 (tttp) REVERT: B 480 CYS cc_start: 0.4490 (OUTLIER) cc_final: 0.3595 (t) REVERT: B 540 ASN cc_start: 0.7303 (t0) cc_final: 0.6962 (t0) REVERT: B 567 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.5435 (mmm160) REVERT: B 704 SER cc_start: 0.7230 (t) cc_final: 0.6933 (m) REVERT: B 725 GLU cc_start: 0.7481 (tt0) cc_final: 0.7167 (tt0) REVERT: B 748 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: B 776 LYS cc_start: 0.8384 (tmtt) cc_final: 0.7997 (ttpp) REVERT: B 873 TYR cc_start: 0.8047 (m-10) cc_final: 0.7780 (m-10) REVERT: B 900 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7693 (mmt) REVERT: B 918 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7336 (tp30) REVERT: B 950 ASP cc_start: 0.7210 (m-30) cc_final: 0.6980 (m-30) REVERT: B 994 ASP cc_start: 0.7457 (t70) cc_final: 0.7214 (t0) REVERT: B 1007 TYR cc_start: 0.7828 (t80) cc_final: 0.7346 (t80) REVERT: C 38 TYR cc_start: 0.7859 (m-80) cc_final: 0.7414 (m-80) REVERT: C 83 VAL cc_start: 0.7744 (OUTLIER) cc_final: 0.7437 (p) REVERT: C 200 TYR cc_start: 0.5752 (m-80) cc_final: 0.5481 (m-80) REVERT: C 204 TYR cc_start: 0.6363 (m-80) cc_final: 0.6091 (m-80) REVERT: C 271 GLN cc_start: 0.7916 (mp10) cc_final: 0.7576 (mp10) REVERT: C 274 THR cc_start: 0.7652 (m) cc_final: 0.7344 (t) REVERT: C 298 GLU cc_start: 0.8574 (tp30) cc_final: 0.8143 (tp30) REVERT: C 319 ARG cc_start: 0.7305 (mmt90) cc_final: 0.6694 (tpp-160) REVERT: C 351 TYR cc_start: 0.4755 (p90) cc_final: 0.4433 (p90) REVERT: C 429 PHE cc_start: 0.7021 (t80) cc_final: 0.6671 (t80) REVERT: C 542 ASN cc_start: 0.7348 (t0) cc_final: 0.6439 (m110) REVERT: C 552 LEU cc_start: 0.8376 (tp) cc_final: 0.8055 (tt) REVERT: C 576 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7939 (t) REVERT: C 673 SER cc_start: 0.7174 (t) cc_final: 0.6472 (m) REVERT: C 902 MET cc_start: 0.8356 (mmm) cc_final: 0.8126 (mmm) REVERT: C 919 ASN cc_start: 0.7986 (m-40) cc_final: 0.7687 (m110) REVERT: C 970 PHE cc_start: 0.7757 (m-10) cc_final: 0.7465 (m-80) outliers start: 116 outliers final: 88 residues processed: 632 average time/residue: 0.1630 time to fit residues: 164.6936 Evaluate side-chains 645 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 545 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 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 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 874 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 926 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1115 ILE 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 241 LEU 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 347 PHE 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 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 724 THR 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 1012 LEU Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL 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 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 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 693 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 139 optimal weight: 2.9990 chunk 307 optimal weight: 0.9980 chunk 195 optimal weight: 0.0030 chunk 50 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 231 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 955 ASN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 487 ASN C 960 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.083965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068757 restraints weight = 107142.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070818 restraints weight = 60176.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072178 restraints weight = 39493.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.073117 restraints weight = 29109.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073760 restraints weight = 23301.405| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 27539 Z= 0.231 Angle : 0.857 12.536 37641 Z= 0.419 Chirality : 0.051 0.445 4488 Planarity : 0.006 0.099 4690 Dihedral : 6.523 67.246 3502 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.29 % Allowed : 19.95 % Favored : 75.76 % 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: -1.52 (0.14), residues: 3223 helix: 0.17 (0.19), residues: 716 sheet: -0.82 (0.20), residues: 618 loop : -1.59 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 273 TYR 0.049 0.002 TYR A 265 PHE 0.046 0.003 PHE B 92 TRP 0.032 0.003 TRP B 436 HIS 0.009 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (27404) covalent geometry : angle 0.82236 / 0.41 (37278) SS BOND : bond 0.00558 / 0.33 ( 42) SS BOND : angle 2.28974 / 1.41 ( 84) hydrogen bonds : bond 0.04659 / 3.03 ( 1034) hydrogen bonds : angle 6.55598 / 4.34 ( 2898) link_ALPHA1-4 : bond 0.00751 / 0.37 ( 6) link_ALPHA1-4 : angle 1.49452 / 0.93 ( 18) link_BETA1-4 : bond 0.00494 / 0.30 ( 29) link_BETA1-4 : angle 1.88633 / 1.21 ( 87) link_BETA1-6 : bond 0.00554 / 0.28 ( 3) link_BETA1-6 : angle 1.00743 / 0.61 ( 9) link_NAG-ASN : bond 0.00606 / 0.39 ( 55) link_NAG-ASN : angle 3.15122 / 2.09 ( 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 692 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 570 time to evaluate : 0.982 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: A 81 ASN cc_start: 0.7585 (p0) cc_final: 0.7251 (p0) REVERT: A 121 ASN cc_start: 0.6978 (p0) cc_final: 0.6291 (t0) REVERT: A 133 PHE cc_start: 0.6202 (m-80) cc_final: 0.5987 (m-80) REVERT: A 146 HIS cc_start: 0.4169 (p-80) cc_final: 0.2699 (m90) REVERT: A 237 ARG cc_start: 0.7489 (mtm180) cc_final: 0.7108 (mtp85) REVERT: A 270 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6931 (tp) REVERT: A 304 LYS cc_start: 0.7973 (tptt) cc_final: 0.7660 (tptt) REVERT: A 357 ARG cc_start: 0.7059 (tpt170) cc_final: 0.6832 (tpt170) REVERT: A 388 ASN cc_start: 0.5015 (m-40) cc_final: 0.4356 (t0) REVERT: A 779 GLN cc_start: 0.7869 (tt0) cc_final: 0.7608 (tt0) REVERT: A 780 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: A 1031 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: A 1115 ILE cc_start: 0.8654 (mp) cc_final: 0.8240 (tp) REVERT: B 41 LYS cc_start: 0.8358 (pttt) cc_final: 0.8071 (mtmt) REVERT: B 92 PHE cc_start: 0.7494 (t80) cc_final: 0.7280 (t80) REVERT: B 141 LEU cc_start: 0.6682 (tp) cc_final: 0.6346 (mm) REVERT: B 152 TRP cc_start: 0.2982 (m100) cc_final: 0.2367 (m100) REVERT: B 157 PHE cc_start: 0.5635 (t80) cc_final: 0.4877 (t80) REVERT: B 206 LYS cc_start: 0.7677 (tptt) cc_final: 0.7360 (tppt) REVERT: B 293 LEU cc_start: 0.8125 (tt) cc_final: 0.7874 (tt) REVERT: B 387 LEU cc_start: 0.8120 (mt) cc_final: 0.7723 (tp) REVERT: B 457 ARG cc_start: 0.5072 (tpt90) cc_final: 0.4595 (ttp80) REVERT: B 462 LYS cc_start: 0.7561 (tppt) cc_final: 0.7219 (tptt) REVERT: B 480 CYS cc_start: 0.4515 (OUTLIER) cc_final: 0.3755 (t) REVERT: B 540 ASN cc_start: 0.7307 (t0) cc_final: 0.7003 (t0) REVERT: B 567 ARG cc_start: 0.6445 (OUTLIER) cc_final: 0.5441 (mmm-85) REVERT: B 748 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: B 776 LYS cc_start: 0.8410 (tmtt) cc_final: 0.8042 (ttpp) REVERT: B 869 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7136 (mtp) REVERT: B 900 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7750 (mmt) REVERT: B 918 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7377 (tp30) REVERT: B 950 ASP cc_start: 0.7231 (m-30) cc_final: 0.6954 (m-30) REVERT: B 1028 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7294 (mtpp) REVERT: B 1034 LEU cc_start: 0.8515 (mp) cc_final: 0.8308 (mt) REVERT: C 83 VAL cc_start: 0.7830 (OUTLIER) cc_final: 0.7566 (p) REVERT: C 200 TYR cc_start: 0.5851 (m-80) cc_final: 0.5514 (m-80) REVERT: C 204 TYR cc_start: 0.6384 (m-80) cc_final: 0.6091 (m-80) REVERT: C 242 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7327 (mp) REVERT: C 271 GLN cc_start: 0.7875 (mp10) cc_final: 0.7582 (mp10) REVERT: C 274 THR cc_start: 0.7594 (m) cc_final: 0.7299 (t) REVERT: C 298 GLU cc_start: 0.8574 (tp30) cc_final: 0.8164 (tp30) REVERT: C 319 ARG cc_start: 0.7308 (mmt90) cc_final: 0.6757 (tpp-160) REVERT: C 392 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: C 429 PHE cc_start: 0.7197 (t80) cc_final: 0.6982 (t80) REVERT: C 534 VAL cc_start: 0.7687 (p) cc_final: 0.7407 (t) REVERT: C 542 ASN cc_start: 0.7253 (t0) cc_final: 0.6379 (m110) REVERT: C 552 LEU cc_start: 0.8386 (tp) cc_final: 0.8050 (tt) REVERT: C 576 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7934 (t) REVERT: C 673 SER cc_start: 0.7198 (t) cc_final: 0.6476 (m) REVERT: C 902 MET cc_start: 0.8327 (mmm) cc_final: 0.8090 (mmm) REVERT: C 919 ASN cc_start: 0.8031 (m-40) cc_final: 0.7675 (m110) REVERT: C 969 ASN cc_start: 0.7989 (m-40) cc_final: 0.7222 (t0) REVERT: C 970 PHE cc_start: 0.7766 (m-10) cc_final: 0.7370 (m-80) outliers start: 122 outliers final: 95 residues processed: 633 average time/residue: 0.1743 time to fit residues: 177.7132 Evaluate side-chains 662 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 555 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 696 THR 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 1050 MET Chi-restraints excluded: chain A residue 1096 VAL 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 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 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 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 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 720 ILE Chi-restraints excluded: chain B residue 724 THR 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 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 1012 LEU Chi-restraints excluded: chain B residue 1126 CYS 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 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 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 693 ILE 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 952 VAL Chi-restraints excluded: chain C residue 957 GLN 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 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: 0.9980 chunk 209 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 chunk 272 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 703 ASN B 955 ASN B1036 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.085054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.069805 restraints weight = 106353.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071861 restraints weight = 59451.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073234 restraints weight = 39101.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.074177 restraints weight = 28850.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.074820 restraints weight = 23113.658| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 27539 Z= 0.156 Angle : 0.792 16.467 37641 Z= 0.382 Chirality : 0.048 0.419 4488 Planarity : 0.005 0.066 4690 Dihedral : 6.241 71.377 3502 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.44 % Allowed : 20.93 % Favored : 75.62 % 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: -1.25 (0.14), residues: 3223 helix: 0.62 (0.20), residues: 686 sheet: -0.81 (0.20), residues: 629 loop : -1.42 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 273 TYR 0.023 0.002 TYR A 365 PHE 0.047 0.002 PHE C 157 TRP 0.024 0.002 TRP B 104 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (27404) covalent geometry : angle 0.76108 / 0.37 (37278) SS BOND : bond 0.00412 / 0.25 ( 42) SS BOND : angle 1.99354 / 1.24 ( 84) hydrogen bonds : bond 0.04167 / 2.69 ( 1034) hydrogen bonds : angle 6.34108 / 4.20 ( 2898) link_ALPHA1-4 : bond 0.00790 / 0.40 ( 6) link_ALPHA1-4 : angle 1.41844 / 0.90 ( 18) link_BETA1-4 : bond 0.00377 / 0.23 ( 29) link_BETA1-4 : angle 1.50438 / 0.97 ( 87) link_BETA1-6 : bond 0.00570 / 0.29 ( 3) link_BETA1-6 : angle 1.01669 / 0.61 ( 9) link_NAG-ASN : bond 0.00531 / 0.34 ( 55) link_NAG-ASN : angle 2.94292 / 1.96 ( 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 669 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 571 time to evaluate : 1.255 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 34 ARG cc_start: 0.6884 (mmp80) cc_final: 0.6381 (mmp80) REVERT: A 81 ASN cc_start: 0.7603 (p0) cc_final: 0.7299 (p0) REVERT: A 121 ASN cc_start: 0.6988 (p0) cc_final: 0.6253 (t0) REVERT: A 146 HIS cc_start: 0.4001 (p-80) cc_final: 0.2649 (m90) REVERT: A 237 ARG cc_start: 0.7410 (mtm180) cc_final: 0.7058 (mtp85) REVERT: A 270 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6911 (tp) REVERT: A 287 ASP cc_start: 0.7889 (t0) cc_final: 0.7622 (t70) REVERT: A 304 LYS cc_start: 0.7996 (tptt) cc_final: 0.7669 (tptt) REVERT: A 388 ASN cc_start: 0.5029 (m-40) cc_final: 0.4376 (t0) REVERT: A 697 MET cc_start: 0.6514 (tpt) cc_final: 0.6265 (tpt) REVERT: A 779 GLN cc_start: 0.7873 (tt0) cc_final: 0.7599 (tt0) REVERT: A 780 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: A 1115 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8326 (tp) REVERT: B 92 PHE cc_start: 0.7470 (t80) cc_final: 0.7209 (t80) REVERT: B 141 LEU cc_start: 0.6743 (tp) cc_final: 0.6361 (mm) REVERT: B 152 TRP cc_start: 0.2879 (m100) cc_final: 0.2329 (m100) REVERT: B 157 PHE cc_start: 0.5728 (t80) cc_final: 0.4966 (t80) REVERT: B 206 LYS cc_start: 0.7599 (tptt) cc_final: 0.7292 (tppt) REVERT: B 293 LEU cc_start: 0.8202 (tt) cc_final: 0.7772 (tt) REVERT: B 387 LEU cc_start: 0.8120 (mt) cc_final: 0.7711 (tp) REVERT: B 457 ARG cc_start: 0.4924 (tpt90) cc_final: 0.4464 (ttp80) REVERT: B 462 LYS cc_start: 0.7580 (tppt) cc_final: 0.7006 (tttp) REVERT: B 540 ASN cc_start: 0.7325 (t0) cc_final: 0.7029 (t0) REVERT: B 567 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.5435 (mmm-85) REVERT: B 697 MET cc_start: 0.7828 (ptm) cc_final: 0.7520 (ptm) REVERT: B 704 SER cc_start: 0.7223 (t) cc_final: 0.6908 (m) REVERT: B 776 LYS cc_start: 0.8397 (tmtt) cc_final: 0.7973 (ttpp) REVERT: B 869 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7113 (mtp) REVERT: B 900 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7697 (mmt) REVERT: B 918 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7307 (tp30) REVERT: B 950 ASP cc_start: 0.7205 (m-30) cc_final: 0.6981 (m-30) REVERT: B 1007 TYR cc_start: 0.7825 (t80) cc_final: 0.7322 (t80) REVERT: C 38 TYR cc_start: 0.7825 (m-80) cc_final: 0.7406 (m-80) REVERT: C 41 LYS cc_start: 0.7611 (mttp) cc_final: 0.7300 (mttp) REVERT: C 134 GLN cc_start: 0.6442 (mm110) cc_final: 0.6211 (mm110) REVERT: C 177 MET cc_start: 0.6205 (ppp) cc_final: 0.5710 (ppp) REVERT: C 200 TYR cc_start: 0.5609 (m-80) cc_final: 0.5359 (m-80) REVERT: C 204 TYR cc_start: 0.6343 (m-80) cc_final: 0.6045 (m-80) REVERT: C 274 THR cc_start: 0.7636 (m) cc_final: 0.7349 (t) REVERT: C 298 GLU cc_start: 0.8549 (tp30) cc_final: 0.8145 (tp30) REVERT: C 392 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6955 (m-80) REVERT: C 429 PHE cc_start: 0.7125 (t80) cc_final: 0.6900 (t80) REVERT: C 534 VAL cc_start: 0.7693 (p) cc_final: 0.7391 (t) REVERT: C 542 ASN cc_start: 0.7306 (t0) cc_final: 0.6528 (m110) REVERT: C 543 PHE cc_start: 0.7058 (m-10) cc_final: 0.6829 (m-10) REVERT: C 552 LEU cc_start: 0.8365 (tp) cc_final: 0.8047 (tt) REVERT: C 576 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7945 (t) REVERT: C 588 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7874 (p) REVERT: C 673 SER cc_start: 0.7167 (t) cc_final: 0.6442 (m) REVERT: C 869 MET cc_start: 0.7906 (mtm) cc_final: 0.7566 (mtm) REVERT: C 902 MET cc_start: 0.8334 (mmm) cc_final: 0.8120 (mmm) REVERT: C 919 ASN cc_start: 0.8030 (m-40) cc_final: 0.7687 (m110) REVERT: C 954 GLN cc_start: 0.7308 (mt0) cc_final: 0.6993 (mt0) REVERT: C 960 ASN cc_start: 0.8169 (m-40) cc_final: 0.7949 (m110) REVERT: C 969 ASN cc_start: 0.8024 (m-40) cc_final: 0.7252 (t0) REVERT: C 970 PHE cc_start: 0.7771 (m-10) cc_final: 0.7405 (m-80) outliers start: 98 outliers final: 80 residues processed: 622 average time/residue: 0.1695 time to fit residues: 170.7430 Evaluate side-chains 633 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 544 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 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 696 THR 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 926 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1115 ILE 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 286 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 307 THR 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 347 PHE 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 720 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU 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 900 MET Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 PHE 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 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 392 PHE Chi-restraints excluded: chain C residue 453 TYR 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 588 THR Chi-restraints excluded: chain C residue 617 CYS 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 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 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 95 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 271 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 519 HIS B 703 ASN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.069649 restraints weight = 106808.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071699 restraints weight = 59823.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073066 restraints weight = 39333.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.074001 restraints weight = 28989.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074633 restraints weight = 23310.425| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 27539 Z= 0.171 Angle : 0.797 14.689 37641 Z= 0.386 Chirality : 0.048 0.409 4488 Planarity : 0.005 0.074 4690 Dihedral : 6.070 52.067 3499 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.76 % Allowed : 20.51 % Favored : 75.73 % 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: 0.58 (0.20), residues: 686 sheet: -0.85 (0.20), residues: 628 loop : -1.42 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 273 TYR 0.023 0.002 TYR A 365 PHE 0.045 0.002 PHE C 157 TRP 0.026 0.002 TRP B 104 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (27404) covalent geometry : angle 0.76699 / 0.38 (37278) SS BOND : bond 0.00411 / 0.24 ( 42) SS BOND : angle 1.91437 / 1.20 ( 84) hydrogen bonds : bond 0.04222 / 2.74 ( 1034) hydrogen bonds : angle 6.30661 / 4.18 ( 2898) link_ALPHA1-4 : bond 0.00759 / 0.37 ( 6) link_ALPHA1-4 : angle 1.37009 / 0.87 ( 18) link_BETA1-4 : bond 0.00363 / 0.23 ( 29) link_BETA1-4 : angle 1.61112 / 1.04 ( 87) link_BETA1-6 : bond 0.00564 / 0.29 ( 3) link_BETA1-6 : angle 1.00733 / 0.60 ( 9) link_NAG-ASN : bond 0.00530 / 0.34 ( 55) link_NAG-ASN : angle 2.93643 / 1.96 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5657.12 seconds wall clock time: 98 minutes 35.09 seconds (5915.09 seconds total)