Starting phenix.real_space_refine on Mon Jul 6 15:26:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x08_32920/07_2026/7x08_32920.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x08_32920/07_2026/7x08_32920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x08_32920/07_2026/7x08_32920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x08_32920/07_2026/7x08_32920.map" model { file = "/net/cci-nas-00/data/ceres_data/7x08_32920/07_2026/7x08_32920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x08_32920/07_2026/7x08_32920.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7x08_32920/07_2026/7x08_32920.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x08_32920/07_2026/7x08_32920.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 159 5.16 5 C 23067 2.51 5 N 5970 2.21 5 O 7200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 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: 36396 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "B" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "H" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "L" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1550 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "I" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "M" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1550 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "J" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "N" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1550 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 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: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 180 Unusual residues: {'EIC': 2, 'NAG': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 8.38, per 1000 atoms: 0.23 Number of scatterers: 36396 At special positions: 0 Unit cell: (185.877, 197.834, 217.4, 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 159 16.00 O 7200 8.00 N 5970 7.00 C 23067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, 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=1.78 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=1.92 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.49 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.78 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.49 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=1.78 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=1.94 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=1.99 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.49 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 149 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS M 138 " - pdb=" SG CYS M 197 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 149 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 197 " 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 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 K 1 " - " NAG K 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 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1403 " - " ASN A 61 " " NAG A1404 " - " ASN A 122 " " NAG A1405 " - " ASN A 149 " " NAG A1406 " - " ASN A 165 " " NAG A1407 " - " ASN A 234 " " NAG A1408 " - " ASN A 282 " " NAG A1409 " - " ASN A 343 " " NAG A1410 " - " ASN A 603 " " NAG A1413 " - " ASN A 657 " " NAG A1414 " - " ASN A 709 " " NAG B1403 " - " ASN B 61 " " NAG B1404 " - " ASN B 122 " " NAG B1405 " - " ASN B 149 " " NAG B1406 " - " ASN B 165 " " NAG B1407 " - " ASN B 234 " " NAG B1408 " - " ASN B 282 " " NAG B1409 " - " ASN B 343 " " NAG B1410 " - " ASN B 603 " " NAG B1413 " - " ASN B 657 " " NAG B1414 " - " ASN B 709 " " NAG C1403 " - " ASN C 61 " " NAG C1404 " - " ASN C 122 " " NAG C1405 " - " ASN C 149 " " NAG C1406 " - " ASN C 165 " " NAG C1407 " - " ASN C 234 " " NAG C1408 " - " ASN C 282 " " NAG C1409 " - " ASN C 343 " " NAG C1410 " - " ASN C 603 " " NAG C1413 " - " ASN C 657 " " NAG C1414 " - " ASN C 709 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG K 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN C 331 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN A 17 " " NAG U 1 " - " ASN A 616 " " NAG V 1 " - " ASN A 801 " " NAG W 1 " - " ASN A1134 " " NAG X 1 " - " ASN B 17 " " NAG Y 1 " - " ASN B 616 " " NAG Z 1 " - " ASN B 801 " " NAG a 1 " - " ASN B1074 " " NAG b 1 " - " ASN B1134 " " NAG c 1 " - " ASN C 17 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1074 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8478 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 78 sheets defined 17.5% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.835A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.089A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.764A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.897A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.744A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 841 removed outlier: 4.059A pdb=" N LEU A 841 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.098A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.476A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.834A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.090A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.763A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.744A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 841 removed outlier: 4.058A pdb=" N LEU B 841 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.098A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.477A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.834A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.089A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.763A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.744A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 841 removed outlier: 4.058A pdb=" N LEU C 841 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.099A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.477A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 192 Processing helix chain 'I' and resid 196 through 198 No H-bonds generated for 'chain 'I' and resid 196 through 198' Processing helix chain 'M' and resid 125 through 131 Processing helix chain 'M' and resid 185 through 192 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'N' and resid 125 through 131 Processing helix chain 'N' and resid 185 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.208A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.485A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.930A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.984A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.490A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.963A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.207A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.485A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.930A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.984A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.656A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.491A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 7.125A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.207A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.486A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.929A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.983A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.006A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.489A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'H' and resid 17 through 23 Processing sheet with id=AF2, first strand: chain 'H' and resid 56 through 59 removed outlier: 5.217A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.733A pdb=" N ARG H 97 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA H 108 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU H 99 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 159 through 163 Processing sheet with id=AF7, first strand: chain 'L' and resid 17 through 21 Processing sheet with id=AF8, first strand: chain 'L' and resid 47 through 50 removed outlier: 5.707A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER L 92 " --> pdb=" O VAL L 100 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 118 through 122 Processing sheet with id=AG1, first strand: chain 'L' and resid 118 through 122 Processing sheet with id=AG2, first strand: chain 'L' and resid 158 through 159 removed outlier: 4.440A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AG4, first strand: chain 'I' and resid 56 through 59 removed outlier: 5.217A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 97 through 101 removed outlier: 6.734A pdb=" N ARG I 97 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA I 108 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU I 99 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA I 146 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL I 193 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 148 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 191 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 150 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 189 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 152 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 187 " --> pdb=" O LYS I 152 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA I 146 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL I 193 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 148 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 191 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 150 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 189 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 152 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 187 " --> pdb=" O LYS I 152 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 159 through 163 Processing sheet with id=AG9, first strand: chain 'M' and resid 17 through 21 Processing sheet with id=AH1, first strand: chain 'M' and resid 47 through 50 removed outlier: 5.707A pdb=" N LEU M 48 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN M 39 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER M 92 " --> pdb=" O VAL M 100 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 118 through 122 Processing sheet with id=AH3, first strand: chain 'M' and resid 118 through 122 Processing sheet with id=AH4, first strand: chain 'M' and resid 158 through 159 removed outlier: 4.440A pdb=" N TRP M 152 " --> pdb=" O VAL M 159 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 17 through 23 Processing sheet with id=AH6, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.216A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 97 through 101 removed outlier: 6.734A pdb=" N ARG J 97 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA J 108 " --> pdb=" O ARG J 97 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU J 99 " --> pdb=" O THR J 106 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 129 through 133 removed outlier: 5.009A pdb=" N ALA J 146 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 193 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 148 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 191 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU J 150 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 189 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS J 152 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 187 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 129 through 133 removed outlier: 5.009A pdb=" N ALA J 146 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 193 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 148 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 191 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU J 150 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 189 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS J 152 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 187 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 159 through 163 Processing sheet with id=AI2, first strand: chain 'N' and resid 17 through 21 Processing sheet with id=AI3, first strand: chain 'N' and resid 47 through 50 removed outlier: 5.707A pdb=" N LEU N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN N 39 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER N 92 " --> pdb=" O VAL N 100 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 118 through 122 Processing sheet with id=AI5, first strand: chain 'N' and resid 118 through 122 Processing sheet with id=AI6, first strand: chain 'N' and resid 158 through 159 removed outlier: 4.440A pdb=" N TRP N 152 " --> pdb=" O VAL N 159 " (cutoff:3.500A) 1432 hydrogen bonds defined for protein. 3855 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: 9.94 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11335 1.34 - 1.46: 9285 1.46 - 1.59: 16406 1.59 - 1.71: 0 1.71 - 1.84: 204 Bond restraints: 37230 Sorted by residual: bond pdb=" C GLY A 891 " pdb=" N PRO A 892 " ideal model delta sigma weight residual 1.329 1.390 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.26e-02 6.30e+03 2.21e+01 bond pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 1.332 1.390 -0.058 1.32e-02 5.74e+03 1.96e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.318 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.318 0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 37225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 49552 2.77 - 5.54: 978 5.54 - 8.31: 114 8.31 - 11.08: 7 11.08 - 13.85: 7 Bond angle restraints: 50658 Sorted by residual: angle pdb=" N VAL J 63 " pdb=" CA VAL J 63 " pdb=" C VAL J 63 " ideal model delta sigma weight residual 113.71 106.15 7.56 9.50e-01 1.11e+00 6.33e+01 angle pdb=" N VAL I 63 " pdb=" CA VAL I 63 " pdb=" C VAL I 63 " ideal model delta sigma weight residual 113.71 106.17 7.54 9.50e-01 1.11e+00 6.31e+01 angle pdb=" N VAL H 63 " pdb=" CA VAL H 63 " pdb=" C VAL H 63 " ideal model delta sigma weight residual 113.71 106.18 7.53 9.50e-01 1.11e+00 6.28e+01 angle pdb=" C GLY A 891 " pdb=" N PRO A 892 " pdb=" CA PRO A 892 " ideal model delta sigma weight residual 120.14 114.12 6.02 1.06e+00 8.90e-01 3.22e+01 angle pdb=" N LEU C 517 " pdb=" CA LEU C 517 " pdb=" C LEU C 517 " ideal model delta sigma weight residual 109.24 117.77 -8.53 1.51e+00 4.39e-01 3.19e+01 ... (remaining 50653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 18713 17.56 - 35.11: 1973 35.11 - 52.67: 636 52.67 - 70.22: 213 70.22 - 87.78: 44 Dihedral angle restraints: 21579 sinusoidal: 8349 harmonic: 13230 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.57 80.57 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.56 80.56 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.56 80.56 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 21576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 5892 0.305 - 0.609: 11 0.609 - 0.914: 13 0.914 - 1.218: 9 1.218 - 1.523: 9 Chirality restraints: 5934 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.50e+03 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.49e+03 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.49e+03 ... (remaining 5931 not shown) Planarity restraints: 6495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN B 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG B1413 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN C 657 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.577 2.00e-02 2.50e+03 pdb=" C1 NAG C1413 " -0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN A 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG A1413 " 0.391 2.00e-02 2.50e+03 ... (remaining 6492 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 262 2.51 - 3.11: 25839 3.11 - 3.70: 52308 3.70 - 4.30: 78566 4.30 - 4.90: 133029 Nonbonded interactions: 290004 Sorted by model distance: nonbonded pdb=" O SER B 940 " pdb=" OG1 THR B 941 " model vdw 1.910 3.040 nonbonded pdb=" O SER C 940 " pdb=" OG1 THR C 941 " model vdw 1.910 3.040 nonbonded pdb=" O SER A 940 " pdb=" OG1 THR A 941 " model vdw 1.911 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.195 3.040 ... (remaining 289999 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 1414) selection = (chain 'B' and resid 14 through 1414) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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 individual isotropic 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.650 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.120 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.012 0.457 37365 Z= 0.566 Angle : 1.584 58.496 51006 Z= 0.713 Chirality : 0.098 1.523 5934 Planarity : 0.010 0.279 6441 Dihedral : 17.172 87.781 12930 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.95 % Allowed : 8.41 % Favored : 90.64 % Rotamer: Outliers : 10.68 % Allowed : 15.40 % Favored : 73.92 % 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: -2.76 (0.11), residues: 4530 helix: -0.87 (0.18), residues: 741 sheet: -0.82 (0.13), residues: 1317 loop : -2.84 (0.10), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 408 TYR 0.022 0.002 TYR B 756 PHE 0.016 0.002 PHE A 133 TRP 0.012 0.002 TRP B 436 HIS 0.006 0.001 HIS I 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00876 / 0.42 (37230) covalent geometry : angle 0.96496 / 0.55 (50658) SS BOND : bond 0.12111 / 8.05 ( 57) SS BOND : angle 11.54578 / 6.89 ( 114) hydrogen bonds : bond 0.13318 / 8.78 ( 1324) hydrogen bonds : angle 7.34911 / 5.02 ( 3855) link_BETA1-4 : bond 0.21341 / 14.04 ( 24) link_BETA1-4 : angle 15.65353 / 11.07 ( 72) link_NAG-ASN : bond 0.07283 / 4.87 ( 54) link_NAG-ASN : angle 17.21285 / 11.77 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 421 poor density : 507 time to evaluate : 1.218 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: A 162 SER cc_start: 0.7888 (OUTLIER) cc_final: 0.7676 (p) REVERT: A 357 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7634 (tpt170) REVERT: A 389 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6695 (m-30) REVERT: A 661 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7051 (mm-30) REVERT: A 745 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: A 796 ASP cc_start: 0.6575 (t70) cc_final: 0.6075 (p0) REVERT: A 823 PHE cc_start: 0.7445 (t80) cc_final: 0.7217 (t80) REVERT: A 913 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: A 957 GLN cc_start: 0.7786 (tt0) cc_final: 0.7436 (tm-30) REVERT: A 1010 GLN cc_start: 0.8196 (mt0) cc_final: 0.7989 (mt0) REVERT: B 66 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6019 (p-80) REVERT: B 249 LEU cc_start: 0.7043 (mt) cc_final: 0.6780 (mp) REVERT: B 305 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8177 (t) REVERT: B 373 SER cc_start: 0.8345 (OUTLIER) cc_final: 0.8043 (m) REVERT: B 505 TYR cc_start: 0.6472 (m-80) cc_final: 0.5480 (t80) REVERT: B 645 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 646 ARG cc_start: 0.7973 (mtm180) cc_final: 0.7755 (mtp180) REVERT: B 740 MET cc_start: 0.8718 (ttt) cc_final: 0.8408 (ttm) REVERT: B 809 PRO cc_start: 0.6661 (Cg_endo) cc_final: 0.6443 (Cg_exo) REVERT: B 854 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8236 (mtpp) REVERT: B 869 MET cc_start: 0.8758 (mtt) cc_final: 0.8545 (mtt) REVERT: B 878 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8806 (mp) REVERT: B 1050 MET cc_start: 0.8702 (ptm) cc_final: 0.8449 (ptm) REVERT: C 66 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6530 (p-80) REVERT: C 188 ASN cc_start: 0.8203 (m110) cc_final: 0.7959 (m110) REVERT: C 389 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.6956 (t0) REVERT: C 444 LYS cc_start: 0.7745 (pttt) cc_final: 0.7373 (ptmm) REVERT: C 469 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8206 (p) REVERT: C 516 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5685 (tm-30) REVERT: C 847 ARG cc_start: 0.5650 (ttp-110) cc_final: 0.4883 (mmt180) REVERT: H 82 MET cc_start: 0.4931 (mtm) cc_final: 0.4426 (pmm) REVERT: H 151 VAL cc_start: -0.0697 (OUTLIER) cc_final: -0.0906 (t) REVERT: H 206 ASN cc_start: -0.0037 (OUTLIER) cc_final: -0.0773 (t0) REVERT: L 18 VAL cc_start: 0.1830 (t) cc_final: 0.1351 (m) REVERT: L 169 SER cc_start: 0.2648 (OUTLIER) cc_final: 0.2331 (m) REVERT: M 46 PRO cc_start: 0.3217 (Cg_exo) cc_final: 0.2998 (Cg_endo) REVERT: M 51 SER cc_start: 0.5724 (t) cc_final: 0.5464 (p) REVERT: M 114 LYS cc_start: 0.1495 (OUTLIER) cc_final: 0.1202 (mtmt) REVERT: M 169 SER cc_start: 0.2342 (OUTLIER) cc_final: 0.1655 (m) REVERT: M 184 LEU cc_start: -0.0066 (OUTLIER) cc_final: -0.0322 (mp) REVERT: J 116 THR cc_start: 0.3755 (m) cc_final: 0.3508 (p) REVERT: N 97 ASN cc_start: 0.4793 (OUTLIER) cc_final: 0.4435 (m110) REVERT: N 99 TRP cc_start: 0.4601 (m100) cc_final: 0.4217 (m100) outliers start: 421 outliers final: 50 residues processed: 824 average time/residue: 0.5352 time to fit residues: 554.7120 Evaluate side-chains 341 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 269 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain M residue 97 ASN Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 114 LYS Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 97 ASN Chi-restraints excluded: chain N residue 169 SER Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 239 GLN A 314 GLN A 317 ASN A 422 ASN A 450 ASN A 474 GLN A 501 ASN A 544 ASN A 564 GLN A 613 GLN A 644 GLN A 751 ASN A 804 GLN A 919 ASN A 925 ASN A 935 GLN A 955 ASN A1023 ASN A1036 GLN A1054 GLN A1064 HIS A1142 GLN B 183 GLN B 239 GLN B 314 GLN B 317 ASN B 422 ASN B 450 ASN B 474 GLN B 544 ASN B 564 GLN B 613 GLN B 751 ASN B 804 GLN B 913 GLN B 919 ASN B 925 ASN B 935 GLN B1023 ASN B1036 GLN B1054 GLN B1064 HIS B1142 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 173 GLN C 185 ASN C 207 HIS C 239 GLN C 314 GLN C 317 ASN C 334 ASN C 422 ASN C 450 ASN C 532 ASN C 544 ASN C 564 GLN C 613 GLN C 751 ASN C 919 ASN C 925 ASN C 957 GLN C1023 ASN C1036 GLN C1054 GLN C1064 HIS C1142 GLN H 81 GLN H 173 HIS L 6 GLN L 40 GLN L 41 HIS L 97 ASN L 98 ASN L 192 HIS ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN M 6 GLN M 40 GLN M 98 ASN M 192 HIS M 198 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN N 6 GLN N 40 GLN N 41 HIS N 192 HIS N 198 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.194721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142516 restraints weight = 45101.601| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 7.28 r_work: 0.3225 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37365 Z= 0.144 Angle : 0.785 17.191 51006 Z= 0.370 Chirality : 0.052 0.744 5934 Planarity : 0.005 0.074 6441 Dihedral : 7.607 89.375 5056 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.23 % Favored : 93.64 % Rotamer: Outliers : 4.31 % Allowed : 19.53 % Favored : 76.15 % 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: -1.86 (0.12), residues: 4530 helix: 0.48 (0.19), residues: 741 sheet: -0.11 (0.14), residues: 1266 loop : -2.51 (0.10), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 567 TYR 0.023 0.001 TYR J 52 PHE 0.023 0.001 PHE L 143 TRP 0.011 0.001 TRP B 152 HIS 0.006 0.001 HIS H 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (37230) covalent geometry : angle 0.71582 / 0.35 (50658) SS BOND : bond 0.00747 / 0.51 ( 57) SS BOND : angle 1.46173 / 1.04 ( 114) hydrogen bonds : bond 0.05065 / 3.40 ( 1324) hydrogen bonds : angle 5.70442 / 3.87 ( 3855) link_BETA1-4 : bond 0.00619 / 0.40 ( 24) link_BETA1-4 : angle 2.71843 / 1.84 ( 72) link_NAG-ASN : bond 0.00822 / 0.59 ( 54) link_NAG-ASN : angle 5.36343 / 3.51 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 304 time to evaluate : 1.016 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 66 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6477 (p-80) REVERT: A 215 ASP cc_start: 0.6135 (OUTLIER) cc_final: 0.5909 (p0) REVERT: A 309 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: A 516 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: A 558 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8202 (mptt) REVERT: A 661 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7331 (mp0) REVERT: A 740 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8918 (ttt) REVERT: A 745 ASP cc_start: 0.7839 (m-30) cc_final: 0.7482 (m-30) REVERT: A 796 ASP cc_start: 0.7397 (t70) cc_final: 0.6961 (p0) REVERT: A 823 PHE cc_start: 0.7801 (t80) cc_final: 0.7546 (t80) REVERT: A 1141 LEU cc_start: 0.7792 (tt) cc_final: 0.7555 (tp) REVERT: B 52 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: B 66 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6632 (p-80) REVERT: B 169 GLU cc_start: 0.7901 (tt0) cc_final: 0.7634 (tm-30) REVERT: B 215 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6519 (t70) REVERT: B 249 LEU cc_start: 0.7409 (mt) cc_final: 0.7117 (mp) REVERT: B 259 THR cc_start: 0.7202 (OUTLIER) cc_final: 0.6982 (m) REVERT: B 373 SER cc_start: 0.8687 (p) cc_final: 0.8296 (m) REVERT: B 483 VAL cc_start: 0.8408 (m) cc_final: 0.8122 (p) REVERT: B 505 TYR cc_start: 0.7044 (m-80) cc_final: 0.6740 (t80) REVERT: B 740 MET cc_start: 0.8989 (ttt) cc_final: 0.8657 (ttt) REVERT: B 809 PRO cc_start: 0.6815 (Cg_endo) cc_final: 0.6563 (Cg_exo) REVERT: B 916 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8693 (tt) REVERT: B 1050 MET cc_start: 0.8900 (ptm) cc_final: 0.8659 (ptm) REVERT: B 1139 ASP cc_start: 0.8371 (t0) cc_final: 0.8067 (t70) REVERT: C 389 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7611 (t0) REVERT: C 516 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: C 529 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8070 (mmtm) REVERT: C 676 THR cc_start: 0.3025 (OUTLIER) cc_final: 0.2493 (m) REVERT: C 847 ARG cc_start: 0.5891 (ttp-110) cc_final: 0.5081 (mmt180) REVERT: C 933 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7900 (mppt) REVERT: H 82 MET cc_start: 0.4851 (mtm) cc_final: 0.4125 (pmm) REVERT: H 151 VAL cc_start: -0.0834 (OUTLIER) cc_final: -0.1115 (t) REVERT: H 179 LEU cc_start: 0.1899 (OUTLIER) cc_final: 0.1681 (tm) REVERT: H 187 LEU cc_start: 0.0693 (OUTLIER) cc_final: 0.0120 (tt) REVERT: M 6 GLN cc_start: 0.1826 (OUTLIER) cc_final: 0.0622 (mm-40) REVERT: M 51 SER cc_start: 0.6248 (t) cc_final: 0.5768 (p) REVERT: M 198 GLN cc_start: -0.0346 (OUTLIER) cc_final: -0.0978 (tt0) REVERT: J 116 THR cc_start: 0.3919 (m) cc_final: 0.3712 (p) REVERT: N 51 SER cc_start: 0.5678 (t) cc_final: 0.4865 (p) REVERT: N 99 TRP cc_start: 0.5373 (m100) cc_final: 0.4760 (m100) outliers start: 170 outliers final: 64 residues processed: 446 average time/residue: 0.5258 time to fit residues: 297.9982 Evaluate side-chains 325 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 241 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 198 GLN Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 157 SER Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 198 GLN Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 386 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 128 optimal weight: 0.3980 chunk 264 optimal weight: 10.0000 chunk 245 optimal weight: 0.0030 chunk 317 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 chunk 416 optimal weight: 0.0870 chunk 171 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 328 optimal weight: 3.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 540 ASN B 474 GLN B 519 HIS B 540 ASN B 787 GLN B 935 GLN B1005 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 334 ASN C 540 ASN C 607 GLN C 804 GLN C 957 GLN H 173 HIS L 41 HIS ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 41 HIS ** N 201 HIS ** 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 = 0.4254 r_free = 0.4254 target = 0.195586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147990 restraints weight = 45107.703| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 4.47 r_work: 0.3219 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 37365 Z= 0.117 Angle : 0.676 12.094 51006 Z= 0.324 Chirality : 0.047 0.505 5934 Planarity : 0.004 0.050 6441 Dihedral : 6.499 89.961 4986 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.25 % Favored : 94.61 % Rotamer: Outliers : 3.75 % Allowed : 20.32 % Favored : 75.93 % 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: -1.33 (0.12), residues: 4530 helix: 1.15 (0.20), residues: 741 sheet: 0.11 (0.14), residues: 1287 loop : -2.18 (0.11), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.017 0.001 TYR B1067 PHE 0.016 0.001 PHE I 92 TRP 0.010 0.001 TRP I 36 HIS 0.007 0.001 HIS H 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (37230) covalent geometry : angle 0.63251 / 0.31 (50658) SS BOND : bond 0.00687 / 0.47 ( 57) SS BOND : angle 1.17475 / 0.86 ( 114) hydrogen bonds : bond 0.04247 / 2.87 ( 1324) hydrogen bonds : angle 5.30226 / 3.59 ( 3855) link_BETA1-4 : bond 0.00534 / 0.35 ( 24) link_BETA1-4 : angle 2.25577 / 1.54 ( 72) link_NAG-ASN : bond 0.00779 / 0.44 ( 54) link_NAG-ASN : angle 3.92533 / 2.60 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 273 time to evaluate : 1.389 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 66 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6602 (p-80) REVERT: A 309 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: A 493 GLN cc_start: 0.8483 (mp10) cc_final: 0.8100 (tp-100) REVERT: A 501 ASN cc_start: 0.8111 (m-40) cc_final: 0.7737 (OUTLIER) REVERT: A 516 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: A 558 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8288 (mptt) REVERT: A 571 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7935 (t70) REVERT: A 661 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7281 (mp0) REVERT: A 740 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8859 (ttt) REVERT: A 745 ASP cc_start: 0.8086 (m-30) cc_final: 0.7741 (m-30) REVERT: A 796 ASP cc_start: 0.7567 (t70) cc_final: 0.7233 (p0) REVERT: A 847 ARG cc_start: 0.5463 (ttp-110) cc_final: 0.4533 (mpt180) REVERT: A 900 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8370 (mtt) REVERT: B 66 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6711 (p-80) REVERT: B 169 GLU cc_start: 0.7975 (tt0) cc_final: 0.7729 (tm-30) REVERT: B 215 ASP cc_start: 0.6806 (OUTLIER) cc_final: 0.5996 (t70) REVERT: B 249 LEU cc_start: 0.7541 (mt) cc_final: 0.7280 (mp) REVERT: B 373 SER cc_start: 0.8548 (p) cc_final: 0.8195 (m) REVERT: B 483 VAL cc_start: 0.8315 (m) cc_final: 0.8098 (p) REVERT: B 505 TYR cc_start: 0.7074 (m-80) cc_final: 0.6715 (t80) REVERT: B 740 MET cc_start: 0.8986 (ttt) cc_final: 0.8685 (ttt) REVERT: B 809 PRO cc_start: 0.6977 (Cg_endo) cc_final: 0.6776 (Cg_exo) REVERT: B 900 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8794 (mtm) REVERT: B 916 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8654 (tt) REVERT: B 936 ASP cc_start: 0.7270 (t0) cc_final: 0.6969 (t0) REVERT: B 1005 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8250 (mm110) REVERT: B 1139 ASP cc_start: 0.8381 (t0) cc_final: 0.8096 (t70) REVERT: C 78 ARG cc_start: 0.7354 (mmm160) cc_final: 0.7118 (mtt-85) REVERT: C 389 ASP cc_start: 0.7843 (m-30) cc_final: 0.7501 (t0) REVERT: C 661 GLU cc_start: 0.8364 (mp0) cc_final: 0.8149 (mp0) REVERT: C 676 THR cc_start: 0.3296 (OUTLIER) cc_final: 0.2975 (m) REVERT: C 933 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7870 (mppt) REVERT: H 82 MET cc_start: 0.4998 (mtm) cc_final: 0.4400 (pmm) REVERT: H 151 VAL cc_start: -0.0861 (OUTLIER) cc_final: -0.1160 (t) REVERT: H 179 LEU cc_start: 0.1834 (OUTLIER) cc_final: 0.1633 (tm) REVERT: H 187 LEU cc_start: 0.1214 (OUTLIER) cc_final: 0.0446 (tt) REVERT: M 6 GLN cc_start: 0.1413 (OUTLIER) cc_final: 0.0742 (mm-40) REVERT: M 51 SER cc_start: 0.6100 (t) cc_final: 0.5577 (p) REVERT: J 116 THR cc_start: 0.4138 (m) cc_final: 0.3835 (p) REVERT: J 165 SER cc_start: 0.1469 (OUTLIER) cc_final: 0.1103 (m) REVERT: N 51 SER cc_start: 0.5490 (t) cc_final: 0.4683 (p) REVERT: N 99 TRP cc_start: 0.5015 (m100) cc_final: 0.4638 (m100) outliers start: 148 outliers final: 67 residues processed: 397 average time/residue: 0.5587 time to fit residues: 280.9777 Evaluate side-chains 316 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 231 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain N residue 157 SER Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 220 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 23 optimal weight: 0.0470 chunk 182 optimal weight: 5.9990 chunk 279 optimal weight: 0.7980 chunk 403 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 overall best weight: 2.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A 613 GLN B 474 GLN B 519 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 607 GLN C 935 GLN H 173 HIS ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.189636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139223 restraints weight = 44672.857| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 5.47 r_work: 0.3098 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37365 Z= 0.180 Angle : 0.751 12.639 51006 Z= 0.365 Chirality : 0.050 0.497 5934 Planarity : 0.005 0.052 6441 Dihedral : 6.438 77.866 4970 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 4.36 % Allowed : 20.04 % Favored : 75.60 % 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: -1.15 (0.12), residues: 4530 helix: 1.13 (0.19), residues: 741 sheet: 0.31 (0.15), residues: 1275 loop : -2.05 (0.11), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 346 TYR 0.023 0.002 TYR M 144 PHE 0.021 0.002 PHE C 898 TRP 0.015 0.001 TRP I 36 HIS 0.007 0.001 HIS H 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (37230) covalent geometry : angle 0.70985 / 0.35 (50658) SS BOND : bond 0.00914 / 0.64 ( 57) SS BOND : angle 1.85086 / 1.43 ( 114) hydrogen bonds : bond 0.05422 / 3.63 ( 1324) hydrogen bonds : angle 5.42216 / 3.69 ( 3855) link_BETA1-4 : bond 0.00557 / 0.36 ( 24) link_BETA1-4 : angle 2.30475 / 1.57 ( 72) link_NAG-ASN : bond 0.00605 / 0.42 ( 54) link_NAG-ASN : angle 3.89321 / 2.56 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 254 time to evaluate : 1.466 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: A 52 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8873 (tt0) REVERT: A 66 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.6525 (p-80) REVERT: A 309 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: A 493 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8144 (tp-100) REVERT: A 516 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7816 (tp30) REVERT: A 558 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8441 (mptt) REVERT: A 571 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8015 (t70) REVERT: A 603 ASN cc_start: 0.6794 (OUTLIER) cc_final: 0.6450 (m-40) REVERT: A 745 ASP cc_start: 0.8237 (m-30) cc_final: 0.7845 (m-30) REVERT: A 796 ASP cc_start: 0.7684 (t70) cc_final: 0.7238 (p0) REVERT: A 847 ARG cc_start: 0.5778 (ttp-110) cc_final: 0.4545 (mpt180) REVERT: A 900 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8411 (mtt) REVERT: A 1130 ILE cc_start: 0.8577 (mm) cc_final: 0.8273 (mt) REVERT: A 1141 LEU cc_start: 0.7918 (tt) cc_final: 0.7693 (tp) REVERT: B 169 GLU cc_start: 0.8098 (tt0) cc_final: 0.7846 (tm-30) REVERT: B 182 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.6723 (mmtm) REVERT: B 249 LEU cc_start: 0.7859 (mt) cc_final: 0.7622 (mp) REVERT: B 483 VAL cc_start: 0.8537 (m) cc_final: 0.8318 (p) REVERT: B 505 TYR cc_start: 0.7550 (m-80) cc_final: 0.7062 (t80) REVERT: B 740 MET cc_start: 0.9060 (ttt) cc_final: 0.8831 (ttt) REVERT: B 841 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7501 (tt) REVERT: B 900 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8981 (mtm) REVERT: B 916 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8659 (tt) REVERT: B 936 ASP cc_start: 0.7542 (t0) cc_final: 0.7293 (t0) REVERT: C 198 ASP cc_start: 0.8369 (m-30) cc_final: 0.7991 (t0) REVERT: C 389 ASP cc_start: 0.7965 (m-30) cc_final: 0.7716 (t0) REVERT: C 516 GLU cc_start: 0.8364 (tt0) cc_final: 0.8120 (tm-30) REVERT: C 661 GLU cc_start: 0.8632 (mp0) cc_final: 0.8392 (mp0) REVERT: C 740 MET cc_start: 0.9057 (mtp) cc_final: 0.8832 (mmm) REVERT: C 851 CYS cc_start: 0.8117 (m) cc_final: 0.7822 (m) REVERT: C 933 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7864 (mppt) REVERT: C 1091 ARG cc_start: 0.8594 (mtt180) cc_final: 0.8374 (mtt90) REVERT: C 1092 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: H 82 MET cc_start: 0.4658 (mtm) cc_final: 0.4024 (pmm) REVERT: H 126 LYS cc_start: 0.2710 (OUTLIER) cc_final: 0.2289 (tppt) REVERT: H 151 VAL cc_start: -0.0816 (OUTLIER) cc_final: -0.1026 (t) REVERT: H 187 LEU cc_start: 0.0870 (OUTLIER) cc_final: 0.0185 (tt) REVERT: I 104 ILE cc_start: 0.7223 (mt) cc_final: 0.7013 (mm) REVERT: M 6 GLN cc_start: 0.1743 (OUTLIER) cc_final: 0.0268 (mt0) REVERT: M 101 PHE cc_start: 0.3611 (OUTLIER) cc_final: 0.2402 (m-10) REVERT: M 157 SER cc_start: 0.0683 (OUTLIER) cc_final: 0.0450 (t) REVERT: J 116 THR cc_start: 0.4038 (m) cc_final: 0.3776 (p) REVERT: J 133 LEU cc_start: 0.1429 (OUTLIER) cc_final: 0.1060 (pp) REVERT: N 51 SER cc_start: 0.5790 (t) cc_final: 0.4793 (p) REVERT: N 101 PHE cc_start: 0.3005 (OUTLIER) cc_final: 0.2007 (m-10) outliers start: 172 outliers final: 82 residues processed: 400 average time/residue: 0.5641 time to fit residues: 285.9883 Evaluate side-chains 333 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 228 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 941 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 157 SER Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 379 optimal weight: 20.0000 chunk 304 optimal weight: 3.9990 chunk 419 optimal weight: 7.9990 chunk 438 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 chunk 364 optimal weight: 0.0170 chunk 6 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 chunk 313 optimal weight: 5.9990 chunk 349 optimal weight: 10.0000 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 613 GLN A 644 GLN A 856 ASN B 474 GLN B 519 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 764 ASN C 935 GLN C 957 GLN H 32 ASN H 39 GLN H 173 HIS L 40 GLN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 40 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS ** N 201 HIS ** 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 = 0.4166 r_free = 0.4166 target = 0.187778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138005 restraints weight = 44289.897| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 5.05 r_work: 0.3059 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 37365 Z= 0.212 Angle : 0.778 12.211 51006 Z= 0.382 Chirality : 0.052 0.524 5934 Planarity : 0.005 0.051 6441 Dihedral : 6.521 86.907 4964 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.16 % Favored : 93.71 % Rotamer: Outliers : 4.49 % Allowed : 19.96 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.10 (0.12), residues: 4530 helix: 1.17 (0.19), residues: 720 sheet: 0.28 (0.14), residues: 1329 loop : -1.99 (0.11), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 78 TYR 0.023 0.002 TYR A 265 PHE 0.023 0.002 PHE C 898 TRP 0.030 0.002 TRP N 99 HIS 0.011 0.001 HIS H 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (37230) covalent geometry : angle 0.73706 / 0.37 (50658) SS BOND : bond 0.00903 / 0.62 ( 57) SS BOND : angle 2.04408 / 1.53 ( 114) hydrogen bonds : bond 0.05773 / 3.86 ( 1324) hydrogen bonds : angle 5.50439 / 3.75 ( 3855) link_BETA1-4 : bond 0.00547 / 0.32 ( 24) link_BETA1-4 : angle 2.26217 / 1.53 ( 72) link_NAG-ASN : bond 0.00756 / 0.56 ( 54) link_NAG-ASN : angle 3.94874 / 2.66 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 253 time to evaluate : 1.501 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: A 52 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8945 (tt0) REVERT: A 66 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.6623 (p-80) REVERT: A 493 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: A 516 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7932 (tp30) REVERT: A 558 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8469 (mptt) REVERT: A 571 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7786 (t70) REVERT: A 702 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: A 796 ASP cc_start: 0.7929 (t70) cc_final: 0.7447 (p0) REVERT: A 825 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8163 (mptp) REVERT: A 841 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8191 (tt) REVERT: A 921 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8372 (mptt) REVERT: A 1130 ILE cc_start: 0.8556 (mm) cc_final: 0.8320 (mt) REVERT: A 1141 LEU cc_start: 0.7853 (tt) cc_final: 0.7639 (tp) REVERT: B 20 THR cc_start: 0.6980 (m) cc_final: 0.6761 (p) REVERT: B 169 GLU cc_start: 0.8229 (tt0) cc_final: 0.7956 (tm-30) REVERT: B 182 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6739 (mmtm) REVERT: B 249 LEU cc_start: 0.7858 (mt) cc_final: 0.7653 (mp) REVERT: B 421 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7750 (p90) REVERT: B 483 VAL cc_start: 0.8647 (m) cc_final: 0.8397 (p) REVERT: B 505 TYR cc_start: 0.7617 (m-80) cc_final: 0.7022 (t80) REVERT: B 567 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8548 (mtt180) REVERT: B 617 CYS cc_start: 0.7096 (m) cc_final: 0.6674 (p) REVERT: B 841 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7590 (tt) REVERT: B 900 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.9015 (mtm) REVERT: B 916 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8700 (tt) REVERT: C 198 ASP cc_start: 0.8442 (m-30) cc_final: 0.8115 (t0) REVERT: C 516 GLU cc_start: 0.8351 (tt0) cc_final: 0.8087 (tm-30) REVERT: C 661 GLU cc_start: 0.8673 (mp0) cc_final: 0.8437 (mp0) REVERT: C 851 CYS cc_start: 0.8120 (m) cc_final: 0.7832 (m) REVERT: C 933 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7876 (mppt) REVERT: H 82 MET cc_start: 0.4306 (mtm) cc_final: 0.3879 (pmm) REVERT: H 126 LYS cc_start: 0.2632 (OUTLIER) cc_final: 0.2078 (tppt) REVERT: H 187 LEU cc_start: 0.0992 (OUTLIER) cc_final: 0.0265 (tt) REVERT: L 101 PHE cc_start: 0.3451 (OUTLIER) cc_final: 0.1961 (m-10) REVERT: M 49 MET cc_start: 0.5624 (tpp) cc_final: 0.5338 (mmt) REVERT: N 159 VAL cc_start: -0.1253 (OUTLIER) cc_final: -0.1579 (t) outliers start: 177 outliers final: 91 residues processed: 410 average time/residue: 0.5592 time to fit residues: 289.3921 Evaluate side-chains 343 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 232 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 226 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 341 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 170 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 328 optimal weight: 20.0000 chunk 265 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 474 GLN B 519 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 607 GLN C 935 GLN H 173 HIS L 40 GLN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN M 40 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN N 41 HIS ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.187526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126046 restraints weight = 44381.217| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.72 r_work: 0.3190 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37365 Z= 0.172 Angle : 0.766 23.459 51006 Z= 0.369 Chirality : 0.051 0.721 5934 Planarity : 0.005 0.051 6441 Dihedral : 6.346 81.749 4958 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.03 % Favored : 93.86 % Rotamer: Outliers : 4.29 % Allowed : 20.09 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.98 (0.12), residues: 4530 helix: 1.33 (0.19), residues: 723 sheet: 0.31 (0.14), residues: 1320 loop : -1.89 (0.11), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 78 TYR 0.020 0.002 TYR A 265 PHE 0.019 0.002 PHE B 898 TRP 0.015 0.001 TRP I 36 HIS 0.009 0.001 HIS H 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (37230) covalent geometry : angle 0.70964 / 0.35 (50658) SS BOND : bond 0.00675 / 0.46 ( 57) SS BOND : angle 2.21252 / 1.90 ( 114) hydrogen bonds : bond 0.05261 / 3.53 ( 1324) hydrogen bonds : angle 5.39794 / 3.69 ( 3855) link_BETA1-4 : bond 0.00475 / 0.30 ( 24) link_BETA1-4 : angle 2.03040 / 1.37 ( 72) link_NAG-ASN : bond 0.00712 / 0.51 ( 54) link_NAG-ASN : angle 4.71075 / 3.25 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 255 time to evaluate : 1.391 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 66 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.6497 (p-80) REVERT: A 177 MET cc_start: 0.6092 (OUTLIER) cc_final: 0.5804 (ttp) REVERT: A 294 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: A 493 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8237 (tp40) REVERT: A 516 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: A 558 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8316 (mptt) REVERT: A 571 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7792 (t70) REVERT: A 690 GLN cc_start: 0.6751 (mm110) cc_final: 0.6422 (mm-40) REVERT: A 796 ASP cc_start: 0.8019 (t70) cc_final: 0.7517 (p0) REVERT: A 825 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8254 (mptp) REVERT: A 921 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8333 (mptt) REVERT: A 1130 ILE cc_start: 0.8540 (mm) cc_final: 0.8315 (mt) REVERT: B 20 THR cc_start: 0.7062 (m) cc_final: 0.6837 (p) REVERT: B 169 GLU cc_start: 0.8297 (tt0) cc_final: 0.7994 (tm-30) REVERT: B 249 LEU cc_start: 0.7853 (mt) cc_final: 0.7638 (mp) REVERT: B 355 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8255 (ttt180) REVERT: B 483 VAL cc_start: 0.8648 (m) cc_final: 0.8404 (p) REVERT: B 505 TYR cc_start: 0.7651 (m-80) cc_final: 0.6992 (t80) REVERT: B 567 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8511 (mtt180) REVERT: B 606 ASN cc_start: 0.8107 (t0) cc_final: 0.7895 (t0) REVERT: B 740 MET cc_start: 0.9137 (ttt) cc_final: 0.8825 (ttt) REVERT: B 841 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7613 (tt) REVERT: B 900 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.9029 (mtm) REVERT: B 916 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8684 (tt) REVERT: B 1005 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8377 (mm-40) REVERT: C 198 ASP cc_start: 0.8447 (m-30) cc_final: 0.8170 (t0) REVERT: C 458 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8166 (mttt) REVERT: C 516 GLU cc_start: 0.8329 (tt0) cc_final: 0.8066 (tm-30) REVERT: C 661 GLU cc_start: 0.8662 (mp0) cc_final: 0.8349 (mp0) REVERT: C 851 CYS cc_start: 0.8097 (m) cc_final: 0.7829 (m) REVERT: C 933 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7826 (mppt) REVERT: H 82 MET cc_start: 0.4331 (mtm) cc_final: 0.4082 (pmm) REVERT: H 126 LYS cc_start: 0.2917 (OUTLIER) cc_final: 0.2400 (tppt) REVERT: H 187 LEU cc_start: 0.0616 (OUTLIER) cc_final: 0.0105 (tt) REVERT: H 210 LYS cc_start: 0.1441 (OUTLIER) cc_final: 0.1216 (ptpt) REVERT: M 159 VAL cc_start: 0.1741 (OUTLIER) cc_final: 0.1432 (t) REVERT: J 133 LEU cc_start: 0.1412 (OUTLIER) cc_final: 0.1057 (pp) REVERT: J 187 LEU cc_start: 0.0065 (OUTLIER) cc_final: -0.0254 (pt) REVERT: N 101 PHE cc_start: 0.3287 (OUTLIER) cc_final: 0.2350 (m-80) REVERT: N 159 VAL cc_start: -0.1254 (OUTLIER) cc_final: -0.1568 (t) outliers start: 169 outliers final: 92 residues processed: 398 average time/residue: 0.5836 time to fit residues: 292.2749 Evaluate side-chains 362 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 246 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 335 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 249 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 344 optimal weight: 50.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 474 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 935 GLN H 173 HIS ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN N 40 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.186700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144472 restraints weight = 44366.602| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.63 r_work: 0.3231 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 37365 Z= 0.220 Angle : 0.798 19.936 51006 Z= 0.390 Chirality : 0.052 0.533 5934 Planarity : 0.005 0.053 6441 Dihedral : 6.472 78.358 4958 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.64 % Favored : 93.27 % Rotamer: Outliers : 4.41 % Allowed : 19.99 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.12), residues: 4530 helix: 1.16 (0.19), residues: 723 sheet: 0.29 (0.14), residues: 1329 loop : -1.91 (0.11), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 509 TYR 0.023 0.002 TYR A 265 PHE 0.022 0.002 PHE C 898 TRP 0.019 0.002 TRP I 36 HIS 0.008 0.001 HIS H 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (37230) covalent geometry : angle 0.75231 / 0.38 (50658) SS BOND : bond 0.00903 / 0.61 ( 57) SS BOND : angle 2.41195 / 2.00 ( 114) hydrogen bonds : bond 0.05864 / 3.91 ( 1324) hydrogen bonds : angle 5.53208 / 3.78 ( 3855) link_BETA1-4 : bond 0.00461 / 0.28 ( 24) link_BETA1-4 : angle 2.16620 / 1.45 ( 72) link_NAG-ASN : bond 0.00578 / 0.42 ( 54) link_NAG-ASN : angle 4.18802 / 2.83 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 243 time to evaluate : 1.383 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 177 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.6029 (ttp) REVERT: A 321 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8416 (mp10) REVERT: A 493 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8140 (tp40) REVERT: A 516 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: A 571 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7832 (t70) REVERT: A 616 ASN cc_start: 0.8109 (t0) cc_final: 0.7415 (m110) REVERT: A 675 GLN cc_start: 0.7352 (tm-30) cc_final: 0.7077 (tm130) REVERT: A 690 GLN cc_start: 0.6972 (mm110) cc_final: 0.6649 (mm-40) REVERT: A 702 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: A 796 ASP cc_start: 0.8086 (t70) cc_final: 0.7695 (p0) REVERT: A 825 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8523 (ttmm) REVERT: A 841 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8167 (tt) REVERT: A 921 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8458 (mptt) REVERT: A 1130 ILE cc_start: 0.8565 (mm) cc_final: 0.8345 (mt) REVERT: B 169 GLU cc_start: 0.8279 (tt0) cc_final: 0.8041 (tm-30) REVERT: B 298 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: B 421 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7678 (p90) REVERT: B 484 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6605 (mt-10) REVERT: B 505 TYR cc_start: 0.7773 (m-80) cc_final: 0.7181 (t80) REVERT: B 617 CYS cc_start: 0.7177 (m) cc_final: 0.6965 (p) REVERT: B 661 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: B 740 MET cc_start: 0.9095 (ttt) cc_final: 0.8796 (ttt) REVERT: B 841 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7754 (tt) REVERT: B 900 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8969 (mtm) REVERT: B 916 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8693 (tt) REVERT: B 935 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6991 (tp-100) REVERT: B 1005 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8273 (mm-40) REVERT: C 66 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7566 (p-80) REVERT: C 458 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7983 (mptt) REVERT: C 516 GLU cc_start: 0.8377 (tt0) cc_final: 0.8143 (tm-30) REVERT: C 661 GLU cc_start: 0.8733 (mp0) cc_final: 0.8471 (mp0) REVERT: C 851 CYS cc_start: 0.8149 (m) cc_final: 0.7879 (m) REVERT: C 933 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7909 (mppt) REVERT: C 1091 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8048 (mtt-85) REVERT: H 187 LEU cc_start: 0.0957 (OUTLIER) cc_final: 0.0241 (tt) REVERT: M 49 MET cc_start: 0.6072 (OUTLIER) cc_final: 0.5531 (ttm) REVERT: M 171 GLN cc_start: 0.0415 (OUTLIER) cc_final: -0.0645 (mm-40) REVERT: J 133 LEU cc_start: 0.1341 (OUTLIER) cc_final: 0.0970 (pp) REVERT: J 187 LEU cc_start: 0.0205 (OUTLIER) cc_final: -0.0270 (pt) REVERT: N 101 PHE cc_start: 0.3427 (OUTLIER) cc_final: 0.2336 (m-80) REVERT: N 159 VAL cc_start: -0.1349 (OUTLIER) cc_final: -0.1734 (t) outliers start: 174 outliers final: 104 residues processed: 391 average time/residue: 0.5707 time to fit residues: 281.6820 Evaluate side-chains 365 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 233 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 171 GLN Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 315 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 0.0050 chunk 231 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 66 HIS B 474 GLN B 519 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN H 173 HIS H 180 GLN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.186095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135144 restraints weight = 44155.247| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 5.80 r_work: 0.3098 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 37365 Z= 0.219 Angle : 0.800 17.375 51006 Z= 0.392 Chirality : 0.052 0.476 5934 Planarity : 0.005 0.052 6441 Dihedral : 6.459 78.622 4956 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 4.44 % Allowed : 20.12 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.12), residues: 4530 helix: 1.09 (0.19), residues: 726 sheet: 0.31 (0.15), residues: 1305 loop : -1.91 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 509 TYR 0.023 0.002 TYR A 265 PHE 0.021 0.002 PHE C 898 TRP 0.015 0.002 TRP B 152 HIS 0.025 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (37230) covalent geometry : angle 0.75414 / 0.38 (50658) SS BOND : bond 0.00765 / 0.52 ( 57) SS BOND : angle 2.62901 / 2.03 ( 114) hydrogen bonds : bond 0.05825 / 3.89 ( 1324) hydrogen bonds : angle 5.55964 / 3.81 ( 3855) link_BETA1-4 : bond 0.00462 / 0.28 ( 24) link_BETA1-4 : angle 2.08921 / 1.39 ( 72) link_NAG-ASN : bond 0.00577 / 0.42 ( 54) link_NAG-ASN : angle 4.07762 / 2.78 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 251 time to evaluate : 1.513 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 177 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.6025 (ttp) REVERT: A 321 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8310 (mp10) REVERT: A 389 ASP cc_start: 0.8080 (m-30) cc_final: 0.7803 (m-30) REVERT: A 493 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8075 (tp40) REVERT: A 516 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7906 (tp30) REVERT: A 571 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7790 (t70) REVERT: A 675 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 690 GLN cc_start: 0.7021 (mm110) cc_final: 0.6744 (mm-40) REVERT: A 702 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: A 796 ASP cc_start: 0.8165 (t70) cc_final: 0.7756 (p0) REVERT: A 825 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8481 (ttmm) REVERT: A 841 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 921 LYS cc_start: 0.8671 (mtmm) cc_final: 0.8407 (mptt) REVERT: A 1130 ILE cc_start: 0.8537 (mm) cc_final: 0.8311 (mt) REVERT: B 169 GLU cc_start: 0.8248 (tt0) cc_final: 0.8009 (tm-30) REVERT: B 298 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: B 421 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7817 (p90) REVERT: B 484 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6493 (mt-10) REVERT: B 505 TYR cc_start: 0.7781 (m-80) cc_final: 0.7077 (t80) REVERT: B 661 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: B 740 MET cc_start: 0.9074 (ttt) cc_final: 0.8755 (ttt) REVERT: B 841 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7677 (tt) REVERT: B 916 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8691 (tt) REVERT: B 935 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6982 (tp-100) REVERT: B 1005 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8240 (mm-40) REVERT: C 66 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.6978 (p90) REVERT: C 94 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8507 (t) REVERT: C 458 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7894 (mptt) REVERT: C 516 GLU cc_start: 0.8279 (tt0) cc_final: 0.8031 (tm-30) REVERT: C 661 GLU cc_start: 0.8658 (mp0) cc_final: 0.8384 (mp0) REVERT: C 851 CYS cc_start: 0.8078 (m) cc_final: 0.7784 (m) REVERT: C 933 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7850 (mppt) REVERT: C 1091 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8071 (mtt-85) REVERT: M 39 GLN cc_start: 0.3254 (OUTLIER) cc_final: 0.2330 (tp40) REVERT: M 49 MET cc_start: 0.5875 (tpt) cc_final: 0.5220 (mmm) REVERT: M 159 VAL cc_start: 0.1518 (OUTLIER) cc_final: 0.1088 (t) REVERT: M 171 GLN cc_start: 0.0164 (OUTLIER) cc_final: -0.0877 (mm-40) REVERT: J 133 LEU cc_start: 0.1387 (OUTLIER) cc_final: 0.1009 (pp) REVERT: J 187 LEU cc_start: 0.0106 (OUTLIER) cc_final: -0.0321 (pt) REVERT: N 101 PHE cc_start: 0.3254 (OUTLIER) cc_final: 0.2330 (m-80) REVERT: N 159 VAL cc_start: -0.1349 (OUTLIER) cc_final: -0.1723 (t) outliers start: 175 outliers final: 114 residues processed: 395 average time/residue: 0.5775 time to fit residues: 287.6710 Evaluate side-chains 377 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 235 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 GLN Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 31 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 228 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 391 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 369 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN B 66 HIS B 474 GLN B 519 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1005 GLN C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 450 ASN C 607 GLN C1083 HIS H 173 HIS ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 41 HIS ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.189341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128831 restraints weight = 44653.382| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.47 r_work: 0.3235 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 37365 Z= 0.114 Angle : 0.673 22.218 51006 Z= 0.328 Chirality : 0.047 0.452 5934 Planarity : 0.004 0.052 6441 Dihedral : 5.878 69.658 4955 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 2.61 % Allowed : 21.99 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.74 (0.12), residues: 4530 helix: 1.64 (0.20), residues: 723 sheet: 0.48 (0.14), residues: 1314 loop : -1.78 (0.11), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 847 TYR 0.025 0.001 TYR B 248 PHE 0.016 0.001 PHE I 92 TRP 0.022 0.001 TRP A 152 HIS 0.011 0.001 HIS H 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (37230) covalent geometry : angle 0.63517 / 0.32 (50658) SS BOND : bond 0.00566 / 0.39 ( 57) SS BOND : angle 2.35705 / 1.81 ( 114) hydrogen bonds : bond 0.04209 / 2.84 ( 1324) hydrogen bonds : angle 5.15522 / 3.53 ( 3855) link_BETA1-4 : bond 0.00401 / 0.25 ( 24) link_BETA1-4 : angle 1.67054 / 1.11 ( 72) link_NAG-ASN : bond 0.00653 / 0.49 ( 54) link_NAG-ASN : angle 3.34585 / 2.26 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 271 time to evaluate : 1.383 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: A 66 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.6615 (p-80) REVERT: A 294 ASP cc_start: 0.7238 (m-30) cc_final: 0.6945 (m-30) REVERT: A 321 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8273 (mp10) REVERT: A 493 GLN cc_start: 0.8445 (mp10) cc_final: 0.8155 (tp-100) REVERT: A 516 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7828 (tp30) REVERT: A 675 GLN cc_start: 0.7327 (tm-30) cc_final: 0.7016 (tm130) REVERT: A 690 GLN cc_start: 0.6856 (mm110) cc_final: 0.6607 (mm-40) REVERT: A 796 ASP cc_start: 0.8377 (t70) cc_final: 0.7689 (p0) REVERT: A 841 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8114 (tt) REVERT: A 900 MET cc_start: 0.8887 (mtm) cc_final: 0.8558 (mtt) REVERT: A 921 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8298 (mptt) REVERT: A 1130 ILE cc_start: 0.8517 (mm) cc_final: 0.8287 (mt) REVERT: B 169 GLU cc_start: 0.8306 (tt0) cc_final: 0.7931 (tm-30) REVERT: B 298 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: B 421 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7768 (p90) REVERT: B 484 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: B 505 TYR cc_start: 0.7610 (m-80) cc_final: 0.6834 (t80) REVERT: B 606 ASN cc_start: 0.8017 (t0) cc_final: 0.7773 (t0) REVERT: B 740 MET cc_start: 0.8986 (ttt) cc_final: 0.8662 (ttt) REVERT: B 916 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8696 (tt) REVERT: B 1005 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8433 (mm110) REVERT: C 516 GLU cc_start: 0.8298 (tt0) cc_final: 0.8044 (tm-30) REVERT: C 661 GLU cc_start: 0.8616 (mp0) cc_final: 0.8278 (mp0) REVERT: C 851 CYS cc_start: 0.7963 (m) cc_final: 0.7719 (m) REVERT: C 1091 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8303 (mtt90) REVERT: M 39 GLN cc_start: 0.3283 (OUTLIER) cc_final: 0.2972 (tp40) REVERT: M 49 MET cc_start: 0.5845 (tpt) cc_final: 0.4827 (ttm) REVERT: M 159 VAL cc_start: 0.2058 (OUTLIER) cc_final: 0.1691 (t) REVERT: M 171 GLN cc_start: 0.0933 (OUTLIER) cc_final: 0.0213 (mm-40) REVERT: J 133 LEU cc_start: 0.1425 (OUTLIER) cc_final: 0.1066 (pp) REVERT: J 187 LEU cc_start: 0.0151 (OUTLIER) cc_final: -0.0195 (pt) REVERT: N 55 LYS cc_start: 0.5751 (tptm) cc_final: 0.5498 (tppp) REVERT: N 159 VAL cc_start: -0.1338 (OUTLIER) cc_final: -0.1612 (t) outliers start: 103 outliers final: 59 residues processed: 361 average time/residue: 0.6036 time to fit residues: 272.6870 Evaluate side-chains 321 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 246 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 173 HIS Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 171 GLN Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 146 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 344 optimal weight: 50.0000 chunk 416 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 362 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 420 optimal weight: 10.0000 chunk 374 optimal weight: 6.9990 chunk 200 optimal weight: 0.0370 overall best weight: 6.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 137 ASN A 613 GLN B 66 HIS B 317 ASN B 474 GLN B 519 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 146 HIS C 607 GLN H 173 HIS ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 HIS N 112 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.184233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142462 restraints weight = 44308.217| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.64 r_work: 0.3201 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 37365 Z= 0.345 Angle : 0.942 24.760 51006 Z= 0.464 Chirality : 0.059 0.403 5934 Planarity : 0.006 0.082 6441 Dihedral : 6.689 82.404 4954 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.42 % Favored : 92.49 % Rotamer: Outliers : 3.09 % Allowed : 21.77 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.12), residues: 4530 helix: 0.83 (0.19), residues: 723 sheet: 0.32 (0.14), residues: 1353 loop : -1.97 (0.11), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 509 TYR 0.034 0.003 TYR C 380 PHE 0.032 0.003 PHE B 541 TRP 0.021 0.002 TRP I 36 HIS 0.013 0.002 HIS H 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.34 (37230) covalent geometry : angle 0.89095 / 0.45 (50658) SS BOND : bond 0.01134 / 0.75 ( 57) SS BOND : angle 3.21576 / 2.39 ( 114) hydrogen bonds : bond 0.07005 / 4.64 ( 1324) hydrogen bonds : angle 5.77417 / 3.95 ( 3855) link_BETA1-4 : bond 0.00573 / 0.34 ( 24) link_BETA1-4 : angle 2.44935 / 1.63 ( 72) link_NAG-ASN : bond 0.00699 / 0.50 ( 54) link_NAG-ASN : angle 4.58810 / 3.00 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 240 time to evaluate : 1.380 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: A 52 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8970 (tt0) REVERT: A 321 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: A 389 ASP cc_start: 0.8137 (m-30) cc_final: 0.7800 (m-30) REVERT: A 516 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: A 675 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7175 (tm-30) REVERT: A 796 ASP cc_start: 0.8485 (t70) cc_final: 0.7999 (p0) REVERT: A 841 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8231 (tt) REVERT: A 1130 ILE cc_start: 0.8659 (mm) cc_final: 0.8430 (mt) REVERT: B 259 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7775 (t) REVERT: B 298 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: B 421 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7822 (p90) REVERT: B 484 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6534 (mt-10) REVERT: B 505 TYR cc_start: 0.7942 (m-80) cc_final: 0.7261 (t80) REVERT: B 740 MET cc_start: 0.9057 (ttt) cc_final: 0.8744 (ttt) REVERT: B 935 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7121 (tp-100) REVERT: C 421 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7471 (p90) REVERT: C 516 GLU cc_start: 0.8439 (tt0) cc_final: 0.8222 (tm-30) REVERT: C 661 GLU cc_start: 0.8618 (mp0) cc_final: 0.8340 (mp0) REVERT: C 851 CYS cc_start: 0.8179 (m) cc_final: 0.7891 (m) REVERT: M 49 MET cc_start: 0.5731 (tpt) cc_final: 0.5321 (ttm) REVERT: M 171 GLN cc_start: 0.0245 (OUTLIER) cc_final: -0.0622 (mm-40) REVERT: J 133 LEU cc_start: 0.1012 (OUTLIER) cc_final: 0.0724 (pp) REVERT: J 187 LEU cc_start: 0.0375 (OUTLIER) cc_final: -0.0070 (pt) REVERT: N 159 VAL cc_start: -0.1279 (OUTLIER) cc_final: -0.1639 (t) outliers start: 122 outliers final: 83 residues processed: 342 average time/residue: 0.5935 time to fit residues: 254.0338 Evaluate side-chains 327 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 230 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 167 THR Chi-restraints excluded: chain M residue 171 GLN Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 74 SER Chi-restraints excluded: chain J residue 101 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 THR Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 207 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 234 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 420 optimal weight: 9.9990 chunk 259 optimal weight: 0.8980 chunk 369 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 368 optimal weight: 50.0000 chunk 70 optimal weight: 1.9990 chunk 389 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 474 GLN A 613 GLN A 690 GLN B 66 HIS B 474 GLN B 519 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN B1005 GLN C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 450 ASN C 607 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.188990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.147774 restraints weight = 44189.316| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.63 r_work: 0.3281 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37365 Z= 0.121 Angle : 0.700 20.862 51006 Z= 0.340 Chirality : 0.048 0.317 5934 Planarity : 0.004 0.056 6441 Dihedral : 6.055 73.517 4954 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.77 % Rotamer: Outliers : 2.59 % Allowed : 22.35 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.81 (0.12), residues: 4530 helix: 1.41 (0.20), residues: 723 sheet: 0.50 (0.15), residues: 1305 loop : -1.81 (0.11), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 847 TYR 0.024 0.001 TYR B 248 PHE 0.016 0.001 PHE I 92 TRP 0.018 0.001 TRP A 152 HIS 0.009 0.001 HIS H 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (37230) covalent geometry : angle 0.65766 / 0.33 (50658) SS BOND : bond 0.00617 / 0.37 ( 57) SS BOND : angle 2.38527 / 1.82 ( 114) hydrogen bonds : bond 0.04567 / 3.08 ( 1324) hydrogen bonds : angle 5.29540 / 3.63 ( 3855) link_BETA1-4 : bond 0.00406 / 0.25 ( 24) link_BETA1-4 : angle 1.72427 / 1.14 ( 72) link_NAG-ASN : bond 0.00537 / 0.35 ( 54) link_NAG-ASN : angle 3.71783 / 2.46 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16013.06 seconds wall clock time: 272 minutes 45.55 seconds (16365.55 seconds total)