Starting phenix.real_space_refine on Wed Apr 8 09:12:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x08_32920/04_2026/7x08_32920.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x08_32920/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/7x08_32920/04_2026/7x08_32920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x08_32920/04_2026/7x08_32920.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x08_32920/04_2026/7x08_32920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x08_32920/04_2026/7x08_32920.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 30 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 dihedrals: 30 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 8.13, per 1000 atoms: 0.22 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: 3.12 Conformation dependent library (CDL) restraints added in 1.5 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: 1.78 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: 10.35 Time building geometry restraints manager: 3.95 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: 20140 17.56 - 35.11: 2082 35.11 - 52.67: 690 52.67 - 70.22: 261 70.22 - 87.78: 44 Dihedral angle restraints: 23217 sinusoidal: 9987 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 23214 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.120 Find NCS groups from input model: 1.010 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:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 16.941 87.781 14568 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 covalent geometry : bond 0.00876 (37230) covalent geometry : angle 0.96496 (50658) SS BOND : bond 0.12111 ( 57) SS BOND : angle 11.54578 ( 114) hydrogen bonds : bond 0.13318 ( 1324) hydrogen bonds : angle 7.34911 ( 3855) link_BETA1-4 : bond 0.21341 ( 24) link_BETA1-4 : angle 15.65353 ( 72) link_NAG-ASN : bond 0.07283 ( 54) link_NAG-ASN : angle 17.21285 ( 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 : 1.195 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: 0.5782 time to fit residues: 594.6817 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 : 1.145 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 HIS ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.194818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142368 restraints weight = 45091.774| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 7.44 r_work: 0.3221 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37365 Z= 0.143 Angle : 0.777 17.921 51006 Z= 0.369 Chirality : 0.052 0.719 5934 Planarity : 0.005 0.072 6441 Dihedral : 8.863 88.927 6694 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.91 % Rotamer: Outliers : 4.44 % Allowed : 19.36 % Favored : 76.20 % 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: -1.82 (0.12), residues: 4530 helix: 0.51 (0.19), residues: 741 sheet: -0.07 (0.14), residues: 1266 loop : -2.48 (0.10), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 567 TYR 0.023 0.002 TYR J 52 PHE 0.026 0.002 PHE L 143 TRP 0.012 0.001 TRP L 189 HIS 0.005 0.001 HIS H 173 Details of bonding type rmsd covalent geometry : bond 0.00308 (37230) covalent geometry : angle 0.71440 (50658) SS BOND : bond 0.00569 ( 57) SS BOND : angle 1.39623 ( 114) hydrogen bonds : bond 0.04915 ( 1324) hydrogen bonds : angle 5.65377 ( 3855) link_BETA1-4 : bond 0.00460 ( 24) link_BETA1-4 : angle 2.85441 ( 72) link_NAG-ASN : bond 0.00646 ( 54) link_NAG-ASN : angle 5.04471 ( 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 480 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 305 time to evaluate : 1.370 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: 0.7178 (OUTLIER) cc_final: 0.6481 (p-80) REVERT: A 215 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.5962 (p0) REVERT: A 309 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: A 516 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6639 (tm-30) REVERT: A 558 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8243 (mptt) REVERT: A 641 ASN cc_start: 0.7910 (m110) cc_final: 0.7700 (m110) REVERT: A 661 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7353 (mp0) REVERT: A 740 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8924 (ttt) REVERT: A 745 ASP cc_start: 0.7825 (m-30) cc_final: 0.7465 (m-30) REVERT: A 796 ASP cc_start: 0.7418 (t70) cc_final: 0.6991 (p0) REVERT: A 823 PHE cc_start: 0.7827 (t80) cc_final: 0.7548 (t80) REVERT: A 1141 LEU cc_start: 0.7827 (tt) cc_final: 0.7589 (tp) REVERT: B 52 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8720 (tt0) REVERT: B 66 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6703 (p-80) REVERT: B 169 GLU cc_start: 0.7916 (tt0) cc_final: 0.7646 (tm-30) REVERT: B 215 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6514 (t70) REVERT: B 249 LEU cc_start: 0.7485 (mt) cc_final: 0.7196 (mp) REVERT: B 259 THR cc_start: 0.7188 (OUTLIER) cc_final: 0.6972 (m) REVERT: B 373 SER cc_start: 0.8691 (p) cc_final: 0.8299 (m) REVERT: B 483 VAL cc_start: 0.8392 (m) cc_final: 0.8118 (p) REVERT: B 505 TYR cc_start: 0.7063 (m-80) cc_final: 0.6746 (t80) REVERT: B 740 MET cc_start: 0.8993 (ttt) cc_final: 0.8659 (ttt) REVERT: B 809 PRO cc_start: 0.6836 (Cg_endo) cc_final: 0.6579 (Cg_exo) REVERT: B 916 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8687 (tt) REVERT: B 1050 MET cc_start: 0.8909 (ptm) cc_final: 0.8641 (ptm) REVERT: B 1139 ASP cc_start: 0.8365 (t0) cc_final: 0.8055 (t70) REVERT: C 66 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.7053 (p-80) REVERT: C 389 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7582 (t0) REVERT: C 516 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: C 529 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8061 (mmtm) REVERT: C 676 THR cc_start: 0.2852 (OUTLIER) cc_final: 0.2294 (m) REVERT: C 847 ARG cc_start: 0.6012 (ttp-110) cc_final: 0.5141 (mmt180) REVERT: C 933 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7922 (mppt) REVERT: H 82 MET cc_start: 0.4843 (mtm) cc_final: 0.4132 (pmm) REVERT: H 151 VAL cc_start: -0.0834 (OUTLIER) cc_final: -0.1111 (t) REVERT: H 179 LEU cc_start: 0.1977 (OUTLIER) cc_final: 0.1771 (tm) REVERT: H 187 LEU cc_start: 0.0647 (OUTLIER) cc_final: 0.0104 (tt) REVERT: I 202 THR cc_start: 0.1521 (OUTLIER) cc_final: 0.0995 (p) REVERT: M 6 GLN cc_start: 0.1905 (OUTLIER) cc_final: 0.0634 (mm-40) REVERT: M 51 SER cc_start: 0.6058 (t) cc_final: 0.5555 (p) REVERT: M 198 GLN cc_start: -0.0360 (OUTLIER) cc_final: -0.0965 (tt0) REVERT: J 116 THR cc_start: 0.3918 (m) cc_final: 0.3711 (p) REVERT: N 51 SER cc_start: 0.5640 (t) cc_final: 0.4825 (p) REVERT: N 99 TRP cc_start: 0.5233 (m100) cc_final: 0.4690 (m100) outliers start: 175 outliers final: 64 residues processed: 450 average time/residue: 0.5532 time to fit residues: 316.1732 Evaluate side-chains 328 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 242 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 213 VAL 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 530 SER 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 66 HIS 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 90 THR Chi-restraints excluded: chain I residue 118 VAL Chi-restraints excluded: chain I residue 122 SER 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 122 SER 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 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 199 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 386 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 128 optimal weight: 0.0670 chunk 264 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 317 optimal weight: 8.9990 chunk 298 optimal weight: 1.9990 chunk 416 optimal weight: 0.0030 chunk 171 optimal weight: 7.9990 chunk 279 optimal weight: 1.9990 chunk 328 optimal weight: 7.9990 overall best weight: 1.6134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN B 519 HIS B 779 GLN B 787 GLN B 935 GLN B1005 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 334 ASN C 607 GLN C 804 GLN C 957 GLN ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4219 r_free = 0.4219 target = 0.192360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139914 restraints weight = 44739.638| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 7.51 r_work: 0.3175 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37365 Z= 0.139 Angle : 0.706 14.955 51006 Z= 0.341 Chirality : 0.049 0.444 5934 Planarity : 0.004 0.049 6441 Dihedral : 7.753 80.127 6626 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.61 % Favored : 94.26 % Rotamer: Outliers : 4.54 % Allowed : 19.28 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.12), residues: 4530 helix: 1.11 (0.19), residues: 741 sheet: 0.14 (0.14), residues: 1299 loop : -2.18 (0.11), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 78 TYR 0.019 0.002 TYR C1067 PHE 0.018 0.001 PHE B 898 TRP 0.013 0.001 TRP I 36 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00312 (37230) covalent geometry : angle 0.66016 (50658) SS BOND : bond 0.00495 ( 57) SS BOND : angle 1.35562 ( 114) hydrogen bonds : bond 0.04806 ( 1324) hydrogen bonds : angle 5.37160 ( 3855) link_BETA1-4 : bond 0.00530 ( 24) link_BETA1-4 : angle 2.64589 ( 72) link_NAG-ASN : bond 0.00701 ( 54) link_NAG-ASN : angle 4.01533 ( 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 455 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 276 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6456 (p-80) REVERT: A 309 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: A 357 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7734 (tpm170) REVERT: A 493 GLN cc_start: 0.8480 (mp10) cc_final: 0.8114 (tp-100) REVERT: A 516 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7744 (tp30) REVERT: A 558 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8339 (mptt) REVERT: A 571 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7903 (t70) REVERT: A 661 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7365 (mp0) REVERT: A 740 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8902 (ttt) REVERT: A 745 ASP cc_start: 0.8163 (m-30) cc_final: 0.7770 (m-30) REVERT: A 796 ASP cc_start: 0.7487 (t70) cc_final: 0.7209 (p0) REVERT: A 847 ARG cc_start: 0.5545 (ttp-110) cc_final: 0.4516 (mpt180) REVERT: A 900 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8382 (mtt) REVERT: A 1130 ILE cc_start: 0.8557 (mm) cc_final: 0.8229 (mt) REVERT: B 66 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.6734 (p-80) REVERT: B 169 GLU cc_start: 0.7987 (tt0) cc_final: 0.7727 (tm-30) REVERT: B 182 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.6805 (mmtm) REVERT: B 249 LEU cc_start: 0.7615 (mt) cc_final: 0.7371 (mp) REVERT: B 298 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: B 360 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7606 (p0) REVERT: B 373 SER cc_start: 0.8841 (p) cc_final: 0.8431 (m) REVERT: B 483 VAL cc_start: 0.8340 (m) cc_final: 0.8115 (p) REVERT: B 505 TYR cc_start: 0.7344 (m-80) cc_final: 0.6902 (t80) REVERT: B 740 MET cc_start: 0.9016 (ttt) cc_final: 0.8674 (ttt) REVERT: B 841 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7572 (tt) REVERT: B 916 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8657 (tt) REVERT: B 1005 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8124 (mm110) REVERT: B 1050 MET cc_start: 0.8979 (ptm) cc_final: 0.8738 (ptm) REVERT: C 346 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7519 (ppp-140) REVERT: C 389 ASP cc_start: 0.7866 (m-30) cc_final: 0.7592 (t0) REVERT: C 516 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: C 529 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8220 (mmtt) REVERT: C 661 GLU cc_start: 0.8465 (mp0) cc_final: 0.8236 (mp0) REVERT: C 676 THR cc_start: 0.3462 (OUTLIER) cc_final: 0.3259 (m) REVERT: C 851 CYS cc_start: 0.7940 (m) cc_final: 0.7636 (m) REVERT: C 933 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7805 (mppt) REVERT: H 82 MET cc_start: 0.4832 (mtm) cc_final: 0.4181 (pmm) REVERT: H 151 VAL cc_start: -0.0805 (OUTLIER) cc_final: -0.1025 (t) REVERT: H 187 LEU cc_start: 0.1001 (OUTLIER) cc_final: 0.0373 (tt) REVERT: I 104 ILE cc_start: 0.7201 (mt) cc_final: 0.6958 (mm) REVERT: M 51 SER cc_start: 0.6075 (t) cc_final: 0.5473 (p) REVERT: M 110 LEU cc_start: 0.0121 (OUTLIER) cc_final: -0.0167 (pp) REVERT: J 116 THR cc_start: 0.3940 (m) cc_final: 0.3693 (p) REVERT: N 51 SER cc_start: 0.5686 (t) cc_final: 0.4845 (p) outliers start: 179 outliers final: 84 residues processed: 427 average time/residue: 0.5444 time to fit residues: 295.0998 Evaluate side-chains 336 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 231 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER 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 221 SER 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 357 ARG 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 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET 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 991 VAL 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 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 298 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 360 ASN 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 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 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 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 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 962 LEU 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 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 35 VAL Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 LEU 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 220 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 279 optimal weight: 0.7980 chunk 403 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 63 optimal weight: 0.2980 chunk 39 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 644 GLN A 856 ASN A 957 GLN B 474 GLN B 787 GLN B 856 ASN C 69 HIS C 185 ASN C 607 GLN C 764 ASN C 804 GLN C 935 GLN C 957 GLN H 32 ASN L 41 HIS ** L 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.187607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135158 restraints weight = 44322.361| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 8.28 r_work: 0.3092 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 37365 Z= 0.241 Angle : 0.820 14.061 51006 Z= 0.400 Chirality : 0.054 0.552 5934 Planarity : 0.006 0.071 6441 Dihedral : 8.006 89.103 6612 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.60 % Favored : 93.27 % Rotamer: Outliers : 4.82 % Allowed : 19.41 % Favored : 75.77 % 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: -1.22 (0.12), residues: 4530 helix: 1.06 (0.19), residues: 720 sheet: 0.27 (0.15), residues: 1272 loop : -2.06 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 403 TYR 0.025 0.003 TYR A 265 PHE 0.025 0.003 PHE B 541 TRP 0.023 0.002 TRP N 99 HIS 0.006 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00583 (37230) covalent geometry : angle 0.77226 (50658) SS BOND : bond 0.00873 ( 57) SS BOND : angle 2.03332 ( 114) hydrogen bonds : bond 0.06128 ( 1324) hydrogen bonds : angle 5.61843 ( 3855) link_BETA1-4 : bond 0.00536 ( 24) link_BETA1-4 : angle 2.73396 ( 72) link_NAG-ASN : bond 0.00673 ( 54) link_NAG-ASN : angle 4.34578 ( 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 443 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 253 time to evaluate : 1.412 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: 0.9140 (OUTLIER) cc_final: 0.8861 (tt0) REVERT: A 66 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.6426 (p-80) REVERT: A 357 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7577 (tpm170) REVERT: A 493 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: A 516 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7997 (tp30) REVERT: A 558 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8442 (mptt) REVERT: A 571 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7740 (t70) REVERT: A 796 ASP cc_start: 0.7867 (t70) cc_final: 0.7388 (p0) REVERT: A 825 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8081 (mptp) REVERT: A 847 ARG cc_start: 0.5650 (ttp-110) cc_final: 0.4532 (mpt180) REVERT: A 1130 ILE cc_start: 0.8539 (mm) cc_final: 0.8277 (mt) REVERT: B 20 THR cc_start: 0.6948 (m) cc_final: 0.6713 (p) REVERT: B 169 GLU cc_start: 0.8224 (tt0) cc_final: 0.7910 (tm-30) REVERT: B 182 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6739 (mmtm) REVERT: B 249 LEU cc_start: 0.7616 (mt) cc_final: 0.7413 (mp) REVERT: B 483 VAL cc_start: 0.8565 (m) cc_final: 0.8307 (p) REVERT: B 505 TYR cc_start: 0.7621 (m-80) cc_final: 0.7080 (t80) REVERT: B 740 MET cc_start: 0.9105 (ttt) cc_final: 0.8775 (ttt) REVERT: B 811 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6659 (mptm) REVERT: B 841 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7547 (tt) REVERT: B 936 ASP cc_start: 0.7665 (t0) cc_final: 0.7418 (t0) REVERT: B 1050 MET cc_start: 0.9126 (ptm) cc_final: 0.8838 (ptm) REVERT: C 167 THR cc_start: 0.8406 (m) cc_final: 0.8146 (t) REVERT: C 198 ASP cc_start: 0.8380 (m-30) cc_final: 0.8044 (t0) REVERT: C 516 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: C 529 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8357 (mmtm) REVERT: C 569 ILE cc_start: 0.7988 (tt) cc_final: 0.7668 (pt) REVERT: C 661 GLU cc_start: 0.8617 (mp0) cc_final: 0.8309 (mp0) REVERT: C 851 CYS cc_start: 0.8049 (m) cc_final: 0.7733 (m) REVERT: C 933 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7869 (mppt) REVERT: C 1092 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: H 82 MET cc_start: 0.4425 (mtm) cc_final: 0.3848 (pmm) REVERT: H 126 LYS cc_start: 0.2815 (OUTLIER) cc_final: 0.2369 (tppt) REVERT: H 151 VAL cc_start: -0.0374 (OUTLIER) cc_final: -0.0576 (t) REVERT: H 187 LEU cc_start: 0.1037 (OUTLIER) cc_final: 0.0407 (tt) REVERT: L 101 PHE cc_start: 0.3496 (OUTLIER) cc_final: 0.2155 (m-10) REVERT: M 6 GLN cc_start: 0.1905 (OUTLIER) cc_final: 0.0498 (mt0) REVERT: M 49 MET cc_start: 0.5652 (tpp) cc_final: 0.5235 (mmt) REVERT: M 101 PHE cc_start: 0.3529 (OUTLIER) cc_final: 0.2520 (m-10) REVERT: J 116 THR cc_start: 0.3774 (m) cc_final: 0.3525 (p) REVERT: J 133 LEU cc_start: 0.1142 (OUTLIER) cc_final: 0.0834 (pp) REVERT: N 159 VAL cc_start: -0.1234 (OUTLIER) cc_final: -0.1530 (t) REVERT: N 184 LEU cc_start: 0.0193 (OUTLIER) cc_final: -0.0380 (mp) outliers start: 190 outliers final: 103 residues processed: 416 average time/residue: 0.5981 time to fit residues: 311.4304 Evaluate side-chains 355 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 229 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR 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 357 ARG 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 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET 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 916 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 88 ASP 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 469 SER 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 676 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 811 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 216 LEU 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 516 GLU 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 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 962 LEU Chi-restraints excluded: chain C residue 1092 GLU 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 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 18 VAL 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 100 ILE 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 92 SER Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 109 VAL 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 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 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 6 GLN Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 184 LEU 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: 9.9990 chunk 304 optimal weight: 0.8980 chunk 419 optimal weight: 20.0000 chunk 438 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 chunk 364 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 331 optimal weight: 9.9990 chunk 313 optimal weight: 0.9980 chunk 349 optimal weight: 9.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 644 GLN B 474 GLN B 519 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1005 GLN C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 804 GLN C 935 GLN H 39 GLN 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** J 180 GLN N 6 GLN ** N 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.189785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137633 restraints weight = 44392.840| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 7.77 r_work: 0.3141 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37365 Z= 0.130 Angle : 0.675 11.852 51006 Z= 0.329 Chirality : 0.047 0.327 5934 Planarity : 0.005 0.063 6441 Dihedral : 7.401 85.743 6606 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.32 % Favored : 94.57 % Rotamer: Outliers : 4.11 % Allowed : 20.27 % 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: -0.92 (0.12), residues: 4530 helix: 1.46 (0.20), residues: 723 sheet: 0.44 (0.15), residues: 1287 loop : -1.93 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.018 0.001 TYR C1067 PHE 0.014 0.001 PHE I 92 TRP 0.014 0.001 TRP A 152 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00291 (37230) covalent geometry : angle 0.63538 (50658) SS BOND : bond 0.00488 ( 57) SS BOND : angle 1.59667 ( 114) hydrogen bonds : bond 0.04789 ( 1324) hydrogen bonds : angle 5.28370 ( 3855) link_BETA1-4 : bond 0.00464 ( 24) link_BETA1-4 : angle 2.18573 ( 72) link_NAG-ASN : bond 0.00639 ( 54) link_NAG-ASN : angle 3.62673 ( 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 420 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 258 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8849 (tt0) REVERT: A 66 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.6594 (p-80) REVERT: A 294 ASP cc_start: 0.7257 (m-30) cc_final: 0.6904 (m-30) REVERT: A 357 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7553 (tpm170) REVERT: A 493 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8100 (tp-100) REVERT: A 516 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7808 (tp30) REVERT: A 558 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8416 (mptt) REVERT: A 796 ASP cc_start: 0.7760 (t70) cc_final: 0.7338 (p0) REVERT: A 921 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8250 (mptt) REVERT: A 1130 ILE cc_start: 0.8508 (mm) cc_final: 0.8283 (mt) REVERT: B 20 THR cc_start: 0.7034 (m) cc_final: 0.6804 (p) REVERT: B 52 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8618 (tt0) REVERT: B 169 GLU cc_start: 0.8150 (tt0) cc_final: 0.7853 (tm-30) REVERT: B 249 LEU cc_start: 0.7854 (mt) cc_final: 0.7640 (mp) REVERT: B 355 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8244 (ttt180) REVERT: B 421 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7642 (p90) REVERT: B 483 VAL cc_start: 0.8503 (m) cc_final: 0.8262 (p) REVERT: B 505 TYR cc_start: 0.7552 (m-80) cc_final: 0.6942 (t80) REVERT: B 617 CYS cc_start: 0.6643 (m) cc_final: 0.6245 (p) REVERT: B 740 MET cc_start: 0.9078 (ttt) cc_final: 0.8757 (ttt) REVERT: B 811 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6773 (mmtp) REVERT: B 841 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7644 (tt) REVERT: B 900 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8326 (mtm) REVERT: B 916 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8692 (tt) REVERT: B 936 ASP cc_start: 0.7603 (t0) cc_final: 0.7381 (t0) REVERT: B 1050 MET cc_start: 0.9051 (ptm) cc_final: 0.8768 (ptm) REVERT: C 198 ASP cc_start: 0.8344 (m-30) cc_final: 0.8084 (t0) REVERT: C 529 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8355 (mmtm) REVERT: C 661 GLU cc_start: 0.8594 (mp0) cc_final: 0.8305 (mp0) REVERT: C 759 PHE cc_start: 0.7208 (m-80) cc_final: 0.6997 (m-80) REVERT: C 851 CYS cc_start: 0.7915 (m) cc_final: 0.7615 (m) REVERT: C 933 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7727 (mppt) REVERT: C 1091 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8256 (mtt90) REVERT: H 82 MET cc_start: 0.4521 (mtm) cc_final: 0.3908 (pmm) REVERT: H 126 LYS cc_start: 0.2431 (OUTLIER) cc_final: 0.2030 (tppt) REVERT: H 187 LEU cc_start: 0.0923 (OUTLIER) cc_final: 0.0262 (tt) REVERT: M 49 MET cc_start: 0.5551 (tpp) cc_final: 0.5314 (mmt) REVERT: J 133 LEU cc_start: 0.1479 (OUTLIER) cc_final: 0.1112 (pp) REVERT: J 187 LEU cc_start: 0.0046 (OUTLIER) cc_final: -0.0333 (pt) REVERT: N 49 MET cc_start: 0.6672 (mmm) cc_final: 0.6297 (mpp) REVERT: N 51 SER cc_start: 0.5541 (t) cc_final: 0.4731 (p) REVERT: N 101 PHE cc_start: 0.2968 (OUTLIER) cc_final: 0.2090 (m-80) REVERT: N 159 VAL cc_start: -0.1236 (OUTLIER) cc_final: -0.1543 (t) outliers start: 162 outliers final: 83 residues processed: 396 average time/residue: 0.5902 time to fit residues: 293.6000 Evaluate side-chains 342 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 238 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 357 ARG 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 498 GLN 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 597 VAL Chi-restraints excluded: chain A residue 719 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 52 GLN Chi-restraints excluded: chain B residue 66 HIS 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 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 355 ARG 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 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 LYS 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 16 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 359 SER 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 719 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1091 ARG 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 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 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 118 VAL 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 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 109 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 39 GLN Chi-restraints excluded: chain N residue 101 PHE Chi-restraints excluded: chain N residue 105 THR 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: 5.9990 chunk 283 optimal weight: 9.9990 chunk 341 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 290 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 328 optimal weight: 20.0000 chunk 265 optimal weight: 0.7980 chunk 401 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN B 474 GLN B 519 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1005 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 607 GLN C 804 GLN C 935 GLN L 40 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.189727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142028 restraints weight = 44545.774| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 4.40 r_work: 0.3074 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37365 Z= 0.159 Angle : 0.716 19.439 51006 Z= 0.351 Chirality : 0.049 0.481 5934 Planarity : 0.005 0.063 6441 Dihedral : 7.349 78.924 6602 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.05 % Favored : 93.84 % Rotamer: Outliers : 4.24 % Allowed : 19.94 % Favored : 75.82 % 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: -0.85 (0.12), residues: 4530 helix: 1.46 (0.20), residues: 723 sheet: 0.49 (0.14), residues: 1311 loop : -1.88 (0.11), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.020 0.002 TYR B 265 PHE 0.018 0.002 PHE C 898 TRP 0.015 0.001 TRP I 36 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00372 (37230) covalent geometry : angle 0.67530 (50658) SS BOND : bond 0.00592 ( 57) SS BOND : angle 2.31266 ( 114) hydrogen bonds : bond 0.05123 ( 1324) hydrogen bonds : angle 5.30227 ( 3855) link_BETA1-4 : bond 0.00597 ( 24) link_BETA1-4 : angle 2.18558 ( 72) link_NAG-ASN : bond 0.00602 ( 54) link_NAG-ASN : angle 3.59661 ( 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 423 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 256 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8945 (tt0) REVERT: A 66 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.6639 (p-80) REVERT: A 177 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.6007 (ttp) REVERT: A 294 ASP cc_start: 0.7511 (m-30) cc_final: 0.7132 (m-30) REVERT: A 357 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7642 (tpm170) REVERT: A 493 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8200 (tp-100) REVERT: A 516 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: A 558 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8388 (mptt) REVERT: A 571 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8039 (t70) REVERT: A 603 ASN cc_start: 0.7767 (p0) cc_final: 0.6959 (m110) REVERT: A 690 GLN cc_start: 0.6901 (mm110) cc_final: 0.6670 (mm-40) REVERT: A 796 ASP cc_start: 0.8107 (t70) cc_final: 0.7615 (p0) REVERT: A 825 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8605 (tppt) REVERT: A 841 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8126 (tt) REVERT: A 921 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8384 (mptt) REVERT: A 1073 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8590 (tttp) REVERT: A 1130 ILE cc_start: 0.8578 (mm) cc_final: 0.8359 (mt) REVERT: B 52 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8751 (tt0) REVERT: B 169 GLU cc_start: 0.8474 (tt0) cc_final: 0.8139 (tm-30) REVERT: B 421 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7741 (p90) REVERT: B 483 VAL cc_start: 0.8666 (m) cc_final: 0.8427 (p) REVERT: B 505 TYR cc_start: 0.7632 (m-80) cc_final: 0.7032 (t80) REVERT: B 617 CYS cc_start: 0.7142 (m) cc_final: 0.6788 (p) REVERT: B 740 MET cc_start: 0.9067 (ttt) cc_final: 0.8759 (ttt) REVERT: B 811 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6890 (mttm) REVERT: B 841 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7652 (tt) REVERT: B 900 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8409 (mtm) REVERT: B 916 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8706 (tt) REVERT: B 1005 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8329 (mm110) REVERT: B 1050 MET cc_start: 0.9064 (ptm) cc_final: 0.8770 (ptm) REVERT: C 198 ASP cc_start: 0.8505 (m-30) cc_final: 0.8236 (t0) REVERT: C 516 GLU cc_start: 0.8433 (tt0) cc_final: 0.8180 (tm-30) REVERT: C 529 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8393 (mmtm) REVERT: C 661 GLU cc_start: 0.8685 (mp0) cc_final: 0.8468 (mp0) REVERT: C 851 CYS cc_start: 0.8128 (m) cc_final: 0.7872 (m) REVERT: C 933 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7883 (mppt) REVERT: C 1091 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8103 (mtt-85) REVERT: H 126 LYS cc_start: 0.2149 (OUTLIER) cc_final: 0.1651 (mppt) REVERT: H 187 LEU cc_start: 0.0954 (OUTLIER) cc_final: 0.0179 (tt) REVERT: J 133 LEU cc_start: 0.1344 (OUTLIER) cc_final: 0.0997 (pp) REVERT: J 187 LEU cc_start: 0.0165 (OUTLIER) cc_final: -0.0323 (pt) REVERT: N 101 PHE cc_start: 0.3454 (OUTLIER) cc_final: 0.2516 (m-80) REVERT: N 159 VAL cc_start: -0.1372 (OUTLIER) cc_final: -0.1742 (t) outliers start: 167 outliers final: 99 residues processed: 400 average time/residue: 0.5928 time to fit residues: 296.5752 Evaluate side-chains 368 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 243 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR 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 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 357 ARG 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 597 VAL Chi-restraints excluded: chain A residue 676 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 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 991 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 52 GLN 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 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 676 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 LYS 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 B residue 1114 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 THR 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 455 LEU 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 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 962 LEU 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 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 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 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 147 LEU 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 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 109 VAL Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 153 LYS 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 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 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 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: 50.0000 chunk 66 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 297 optimal weight: 9.9990 chunk 335 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 249 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 344 optimal weight: 50.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 607 GLN H 180 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 39 GLN N 40 GLN ** 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 = 0.4149 r_free = 0.4149 target = 0.186758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137047 restraints weight = 44274.398| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.76 r_work: 0.3206 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 37365 Z= 0.210 Angle : 0.773 14.679 51006 Z= 0.379 Chirality : 0.051 0.400 5934 Planarity : 0.005 0.055 6441 Dihedral : 7.642 77.984 6602 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.11 % Favored : 93.77 % Rotamer: Outliers : 4.41 % Allowed : 20.14 % 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: -0.94 (0.12), residues: 4530 helix: 1.20 (0.19), residues: 723 sheet: 0.40 (0.15), residues: 1308 loop : -1.85 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 509 TYR 0.022 0.002 TYR A 265 PHE 0.021 0.002 PHE C 898 TRP 0.018 0.002 TRP I 36 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00505 (37230) covalent geometry : angle 0.72772 (50658) SS BOND : bond 0.00797 ( 57) SS BOND : angle 2.43208 ( 114) hydrogen bonds : bond 0.05760 ( 1324) hydrogen bonds : angle 5.47564 ( 3855) link_BETA1-4 : bond 0.00531 ( 24) link_BETA1-4 : angle 2.24699 ( 72) link_NAG-ASN : bond 0.00551 ( 54) link_NAG-ASN : angle 4.02200 ( 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 423 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 249 time to evaluate : 1.374 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 52 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8927 (tt0) REVERT: A 281 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8339 (pp20) REVERT: A 321 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8341 (mp10) REVERT: A 357 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7629 (tpm170) REVERT: A 493 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8136 (tp40) REVERT: A 516 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.6934 (tm-30) REVERT: A 571 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7817 (t70) REVERT: A 675 GLN cc_start: 0.7339 (tm-30) cc_final: 0.7058 (tm130) REVERT: A 796 ASP cc_start: 0.8101 (t70) cc_final: 0.7688 (p0) REVERT: A 825 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8520 (ttmm) REVERT: A 841 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 921 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8428 (mptt) REVERT: A 1073 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8543 (tttp) REVERT: A 1130 ILE cc_start: 0.8549 (mm) cc_final: 0.8316 (mt) REVERT: A 1141 LEU cc_start: 0.8025 (tt) cc_final: 0.7798 (tp) REVERT: B 52 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8764 (tt0) REVERT: B 169 GLU cc_start: 0.8299 (tt0) cc_final: 0.8061 (tm-30) REVERT: B 355 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8244 (ttt180) REVERT: B 421 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7657 (p90) REVERT: B 484 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6554 (mt-10) REVERT: B 505 TYR cc_start: 0.7801 (m-80) cc_final: 0.7147 (t80) REVERT: B 726 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9081 (mt) REVERT: B 740 MET cc_start: 0.9028 (ttt) cc_final: 0.8699 (ttt) REVERT: B 811 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7092 (mtmm) REVERT: B 841 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7694 (tt) REVERT: B 900 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8401 (mtm) REVERT: B 935 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6965 (tp-100) REVERT: C 458 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7992 (mptt) REVERT: C 516 GLU cc_start: 0.8287 (tt0) cc_final: 0.8061 (tm-30) REVERT: C 529 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8448 (mmtm) REVERT: C 661 GLU cc_start: 0.8639 (mp0) cc_final: 0.8412 (mp0) REVERT: C 851 CYS cc_start: 0.8076 (m) cc_final: 0.7792 (m) REVERT: C 933 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7877 (mppt) REVERT: C 1091 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8047 (mtt-85) REVERT: H 126 LYS cc_start: 0.2232 (OUTLIER) cc_final: 0.1808 (tppt) REVERT: H 187 LEU cc_start: 0.1025 (OUTLIER) cc_final: 0.0280 (tt) REVERT: M 39 GLN cc_start: 0.3233 (OUTLIER) cc_final: 0.2376 (tp40) REVERT: M 49 MET cc_start: 0.5633 (tpt) cc_final: 0.5083 (mmm) REVERT: M 171 GLN cc_start: 0.0301 (OUTLIER) cc_final: -0.0587 (mm-40) REVERT: J 133 LEU cc_start: 0.1301 (OUTLIER) cc_final: 0.0950 (pp) REVERT: J 187 LEU cc_start: 0.0388 (OUTLIER) cc_final: -0.0115 (pt) REVERT: N 101 PHE cc_start: 0.3335 (OUTLIER) cc_final: 0.2449 (m-80) REVERT: N 159 VAL cc_start: -0.1352 (OUTLIER) cc_final: -0.1742 (t) outliers start: 174 outliers final: 100 residues processed: 398 average time/residue: 0.6077 time to fit residues: 301.8646 Evaluate side-chains 361 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 231 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR 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 137 ASN 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 321 GLN Chi-restraints excluded: chain A residue 357 ARG 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 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 991 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 52 GLN 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 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 355 ARG 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 676 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 THR 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 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 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 962 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 100 ILE Chi-restraints excluded: chain H residue 126 LYS 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 39 GLN Chi-restraints excluded: chain L residue 54 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 100 ILE Chi-restraints excluded: chain I residue 147 LEU 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 109 VAL Chi-restraints excluded: chain M residue 157 SER 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 315 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 296 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 0.0670 chunk 231 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN B 66 HIS B 474 GLN B 519 HIS ** 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 804 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 = 0.4160 r_free = 0.4160 target = 0.187686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.143540 restraints weight = 44181.555| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.70 r_work: 0.3239 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37365 Z= 0.168 Angle : 0.737 15.070 51006 Z= 0.360 Chirality : 0.051 0.826 5934 Planarity : 0.005 0.050 6441 Dihedral : 7.473 76.032 6597 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.14 % Favored : 93.75 % Rotamer: Outliers : 4.24 % Allowed : 20.52 % Favored : 75.24 % 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: -0.85 (0.12), residues: 4530 helix: 1.35 (0.19), residues: 723 sheet: 0.44 (0.15), residues: 1308 loop : -1.81 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 983 TYR 0.028 0.002 TYR B 248 PHE 0.017 0.002 PHE C 898 TRP 0.022 0.001 TRP N 99 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00397 (37230) covalent geometry : angle 0.69228 (50658) SS BOND : bond 0.00623 ( 57) SS BOND : angle 2.28757 ( 114) hydrogen bonds : bond 0.05261 ( 1324) hydrogen bonds : angle 5.37629 ( 3855) link_BETA1-4 : bond 0.00431 ( 24) link_BETA1-4 : angle 2.03871 ( 72) link_NAG-ASN : bond 0.00794 ( 54) link_NAG-ASN : angle 3.93977 ( 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 412 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 245 time to evaluate : 1.306 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 52 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8935 (tt0) REVERT: A 66 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.6673 (p-80) REVERT: A 294 ASP cc_start: 0.7463 (m-30) cc_final: 0.7130 (m-30) REVERT: A 321 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8345 (mp10) REVERT: A 357 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7606 (tpm170) REVERT: A 455 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8555 (tt) REVERT: A 493 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8294 (tp40) REVERT: A 516 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7841 (tp30) REVERT: A 571 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7743 (t70) REVERT: A 603 ASN cc_start: 0.7908 (p0) cc_final: 0.7034 (m110) REVERT: A 675 GLN cc_start: 0.7351 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 796 ASP cc_start: 0.8130 (t70) cc_final: 0.7725 (p0) REVERT: A 825 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8493 (ttmm) REVERT: A 841 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8161 (tt) REVERT: A 921 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8407 (mptt) REVERT: A 1073 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8534 (tttp) REVERT: A 1130 ILE cc_start: 0.8555 (mm) cc_final: 0.8341 (mt) REVERT: B 52 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8737 (tt0) REVERT: B 169 GLU cc_start: 0.8266 (tt0) cc_final: 0.8039 (tm-30) REVERT: B 355 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8254 (ttt180) REVERT: B 421 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7770 (p90) REVERT: B 484 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6561 (mt-10) REVERT: B 505 TYR cc_start: 0.7705 (m-80) cc_final: 0.7091 (t80) REVERT: B 726 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9073 (mt) REVERT: B 740 MET cc_start: 0.9059 (ttt) cc_final: 0.8729 (ttt) REVERT: B 811 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6975 (mtmm) REVERT: B 841 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7706 (tt) REVERT: B 900 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8352 (mtm) REVERT: B 916 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8800 (tt) REVERT: C 458 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7972 (mptt) REVERT: C 516 GLU cc_start: 0.8282 (tt0) cc_final: 0.8018 (tm-30) REVERT: C 529 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8403 (mmtm) REVERT: C 661 GLU cc_start: 0.8542 (mp0) cc_final: 0.8263 (mp0) REVERT: C 851 CYS cc_start: 0.8031 (m) cc_final: 0.7731 (m) REVERT: C 933 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7804 (mppt) REVERT: C 1091 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8140 (mtt-85) REVERT: H 210 LYS cc_start: 0.1283 (OUTLIER) cc_final: 0.1034 (ptpt) REVERT: M 49 MET cc_start: 0.5847 (tpt) cc_final: 0.5541 (mmt) REVERT: M 171 GLN cc_start: 0.0356 (OUTLIER) cc_final: -0.0480 (mm-40) REVERT: J 105 MET cc_start: 0.6951 (mtt) cc_final: 0.6715 (mtt) REVERT: J 133 LEU cc_start: 0.1359 (OUTLIER) cc_final: 0.1007 (pp) REVERT: J 187 LEU cc_start: 0.0143 (OUTLIER) cc_final: -0.0256 (pt) REVERT: N 159 VAL cc_start: -0.1395 (OUTLIER) cc_final: -0.1746 (t) outliers start: 167 outliers final: 107 residues processed: 386 average time/residue: 0.6168 time to fit residues: 296.2968 Evaluate side-chains 371 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 236 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU 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 137 ASN 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 357 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 455 LEU 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 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 825 LYS 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 1073 LYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 52 GLN 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 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 355 ARG Chi-restraints excluded: chain B residue 360 ASN 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 676 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 841 LEU 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 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 THR 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 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 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 916 LEU Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 962 LEU 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 162 SER Chi-restraints excluded: chain H residue 179 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 54 SER Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 171 GLN 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 100 ILE 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 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 53 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 157 SER 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 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 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: 0.9980 chunk 177 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 228 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 391 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 369 optimal weight: 0.0170 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 66 HIS B 474 GLN B 519 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN C 66 HIS C 540 ASN C 607 GLN C 935 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.188978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128353 restraints weight = 44428.923| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.38 r_work: 0.3220 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4007 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= 0.123 Angle : 0.671 20.980 51006 Z= 0.328 Chirality : 0.048 0.598 5934 Planarity : 0.004 0.065 6441 Dihedral : 7.065 70.019 6597 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 3.45 % Allowed : 21.21 % Favored : 75.34 % 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: -0.67 (0.12), residues: 4530 helix: 1.68 (0.20), residues: 723 sheet: 0.56 (0.15), residues: 1302 loop : -1.74 (0.11), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.025 0.001 TYR B 248 PHE 0.016 0.001 PHE I 92 TRP 0.018 0.001 TRP N 99 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00273 (37230) covalent geometry : angle 0.63145 (50658) SS BOND : bond 0.00576 ( 57) SS BOND : angle 2.12548 ( 114) hydrogen bonds : bond 0.04402 ( 1324) hydrogen bonds : angle 5.13709 ( 3855) link_BETA1-4 : bond 0.00408 ( 24) link_BETA1-4 : angle 1.76776 ( 72) link_NAG-ASN : bond 0.00594 ( 54) link_NAG-ASN : angle 3.55917 ( 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 395 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 259 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.6695 (p-80) REVERT: A 294 ASP cc_start: 0.7356 (m-30) cc_final: 0.6957 (m-30) REVERT: A 321 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8283 (mp10) REVERT: A 357 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7494 (tpm170) REVERT: A 455 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8528 (tt) REVERT: A 493 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8180 (tp-100) REVERT: A 516 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: A 571 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7921 (t70) REVERT: A 603 ASN cc_start: 0.7856 (p0) cc_final: 0.7015 (m110) REVERT: A 675 GLN cc_start: 0.7281 (tm-30) cc_final: 0.6956 (tm130) REVERT: A 796 ASP cc_start: 0.8195 (t70) cc_final: 0.7660 (p0) REVERT: A 825 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8433 (ttmm) REVERT: A 900 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8560 (mtt) REVERT: A 921 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8316 (mptt) REVERT: A 1073 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8577 (tttp) REVERT: A 1130 ILE cc_start: 0.8534 (mm) cc_final: 0.8307 (mt) REVERT: B 169 GLU cc_start: 0.8299 (tt0) cc_final: 0.7968 (tm-30) REVERT: B 421 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7858 (p90) REVERT: B 505 TYR cc_start: 0.7636 (m-80) cc_final: 0.6859 (t80) REVERT: B 740 MET cc_start: 0.9069 (ttt) cc_final: 0.8713 (ttt) REVERT: B 900 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8368 (mtm) REVERT: B 916 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8767 (tt) REVERT: B 1130 ILE cc_start: 0.8775 (mm) cc_final: 0.8501 (mt) REVERT: C 458 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7937 (mptt) REVERT: C 516 GLU cc_start: 0.8320 (tt0) cc_final: 0.8062 (tm-30) REVERT: C 529 LYS cc_start: 0.8635 (mmtt) cc_final: 0.8356 (mmtm) REVERT: C 661 GLU cc_start: 0.8671 (mp0) cc_final: 0.8328 (mp0) REVERT: C 851 CYS cc_start: 0.7979 (m) cc_final: 0.7733 (m) REVERT: C 1091 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8344 (mtt90) REVERT: M 171 GLN cc_start: 0.1150 (OUTLIER) cc_final: 0.0158 (mm-40) REVERT: J 105 MET cc_start: 0.6779 (mtt) cc_final: 0.6516 (mtt) REVERT: J 133 LEU cc_start: 0.1410 (OUTLIER) cc_final: 0.1063 (pp) REVERT: J 187 LEU cc_start: 0.0249 (OUTLIER) cc_final: -0.0055 (pt) REVERT: N 101 PHE cc_start: 0.3136 (OUTLIER) cc_final: 0.2239 (m-80) REVERT: N 159 VAL cc_start: -0.1332 (OUTLIER) cc_final: -0.1603 (t) outliers start: 136 outliers final: 77 residues processed: 376 average time/residue: 0.6198 time to fit residues: 289.5852 Evaluate side-chains 346 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 249 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 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 357 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 455 LEU 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 676 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 825 LYS 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 1073 LYS 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 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 676 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 286 THR 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 458 LYS 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 962 LEU Chi-restraints excluded: chain C residue 1034 LEU 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 82 MET Chi-restraints excluded: chain H residue 100 ILE 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 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 171 GLN Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 147 LEU 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 53 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 157 SER 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 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 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 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 146 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 344 optimal weight: 50.0000 chunk 416 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 chunk 5 optimal weight: 0.1980 chunk 420 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 474 GLN A1058 HIS B 66 HIS B 474 GLN B 519 HIS B 606 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1005 GLN C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 146 HIS C 607 GLN C 935 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 = 0.4127 r_free = 0.4127 target = 0.184695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134685 restraints weight = 44183.952| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.74 r_work: 0.3176 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 37365 Z= 0.282 Angle : 0.875 23.878 51006 Z= 0.430 Chirality : 0.056 0.596 5934 Planarity : 0.006 0.069 6441 Dihedral : 7.847 80.442 6596 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.17 % Favored : 92.76 % Rotamer: Outliers : 3.35 % Allowed : 21.56 % Favored : 75.09 % 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: 1.04 (0.19), residues: 723 sheet: 0.46 (0.15), residues: 1308 loop : -1.88 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 509 TYR 0.031 0.003 TYR C 380 PHE 0.028 0.003 PHE B 541 TRP 0.026 0.002 TRP N 99 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00689 (37230) covalent geometry : angle 0.82594 (50658) SS BOND : bond 0.00998 ( 57) SS BOND : angle 3.04600 ( 114) hydrogen bonds : bond 0.06514 ( 1324) hydrogen bonds : angle 5.65930 ( 3855) link_BETA1-4 : bond 0.00487 ( 24) link_BETA1-4 : angle 2.28175 ( 72) link_NAG-ASN : bond 0.00641 ( 54) link_NAG-ASN : angle 4.36549 ( 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 368 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 236 time to evaluate : 1.316 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: 0.7711 (OUTLIER) cc_final: 0.6538 (p90) REVERT: A 281 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8341 (pp20) REVERT: A 321 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8366 (mp10) REVERT: A 357 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7656 (tpm170) REVERT: A 389 ASP cc_start: 0.8179 (m-30) cc_final: 0.7872 (m-30) REVERT: A 516 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: A 571 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7777 (t70) REVERT: A 675 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7157 (tm130) REVERT: A 796 ASP cc_start: 0.8411 (t70) cc_final: 0.7890 (p0) REVERT: A 825 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8538 (ttmm) REVERT: A 921 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8476 (mptt) REVERT: A 1073 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8563 (tttp) REVERT: A 1130 ILE cc_start: 0.8575 (mm) cc_final: 0.8338 (mt) REVERT: B 169 GLU cc_start: 0.8285 (tt0) cc_final: 0.8022 (tm-30) REVERT: B 421 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7850 (p90) REVERT: B 505 TYR cc_start: 0.7945 (m-80) cc_final: 0.7214 (t80) REVERT: B 661 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: B 740 MET cc_start: 0.9061 (ttt) cc_final: 0.8754 (ttt) REVERT: C 458 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7996 (mptt) REVERT: C 516 GLU cc_start: 0.8350 (tt0) cc_final: 0.8082 (tm-30) REVERT: C 529 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8430 (mmtm) REVERT: C 661 GLU cc_start: 0.8728 (mp0) cc_final: 0.8467 (mp0) REVERT: C 851 CYS cc_start: 0.8078 (m) cc_final: 0.7782 (m) REVERT: C 1091 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8038 (mtt-85) REVERT: M 49 MET cc_start: 0.5966 (tpt) cc_final: 0.5526 (mmt) REVERT: M 171 GLN cc_start: 0.0203 (OUTLIER) cc_final: -0.0664 (mm-40) REVERT: J 133 LEU cc_start: 0.1342 (OUTLIER) cc_final: 0.0976 (pp) REVERT: J 187 LEU cc_start: 0.0050 (OUTLIER) cc_final: -0.0388 (pt) REVERT: N 159 VAL cc_start: -0.1346 (OUTLIER) cc_final: -0.1688 (t) outliers start: 132 outliers final: 90 residues processed: 344 average time/residue: 0.6316 time to fit residues: 269.5009 Evaluate side-chains 337 residues out of total 3942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 231 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU 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 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 321 GLN Chi-restraints excluded: chain A residue 357 ARG 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 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 676 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 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 1073 LYS Chi-restraints excluded: chain A residue 1128 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 108 THR Chi-restraints excluded: chain B residue 161 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 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 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 518 LEU Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 19 THR 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 455 LEU Chi-restraints excluded: chain C residue 458 LYS 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 962 LEU Chi-restraints excluded: chain C residue 1034 LEU 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 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 149 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain I residue 90 THR 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 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 53 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 101 PHE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 157 SER 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 234 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 420 optimal weight: 8.9990 chunk 259 optimal weight: 0.8980 chunk 369 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 368 optimal weight: 30.0000 chunk 70 optimal weight: 0.7980 chunk 389 optimal weight: 5.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 474 GLN B 519 HIS B 606 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 450 ASN C 607 GLN C 935 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.185681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133184 restraints weight = 43962.595| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 7.57 r_work: 0.3081 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 37365 Z= 0.195 Angle : 0.983 59.171 51006 Z= 0.519 Chirality : 0.053 0.803 5934 Planarity : 0.006 0.064 6441 Dihedral : 7.835 79.970 6596 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 3.04 % Allowed : 21.77 % Favored : 75.19 % Cbeta Deviations : 0.05 % 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: -1.00 (0.12), residues: 4530 helix: 1.02 (0.19), residues: 723 sheet: 0.44 (0.15), residues: 1308 loop : -1.90 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 78 TYR 0.029 0.002 TYR C 380 PHE 0.024 0.002 PHE B 541 TRP 0.022 0.002 TRP N 99 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00447 (37230) covalent geometry : angle 0.94109 (50658) SS BOND : bond 0.00633 ( 57) SS BOND : angle 2.95118 ( 114) hydrogen bonds : bond 0.06105 ( 1324) hydrogen bonds : angle 5.64197 ( 3855) link_BETA1-4 : bond 0.00397 ( 24) link_BETA1-4 : angle 2.21458 ( 72) link_NAG-ASN : bond 0.00589 ( 54) link_NAG-ASN : angle 4.34194 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16637.62 seconds wall clock time: 283 minutes 2.74 seconds (16982.74 seconds total)