Starting phenix.real_space_refine on Tue Aug 26 11:15:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4x_39771/08_2025/8z4x_39771.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4x_39771/08_2025/8z4x_39771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z4x_39771/08_2025/8z4x_39771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4x_39771/08_2025/8z4x_39771.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z4x_39771/08_2025/8z4x_39771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4x_39771/08_2025/8z4x_39771.map" } resolution = 3.4 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= 0.001 sd= 0.018 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 172 5.16 5 C 22961 2.51 5 N 5898 2.21 5 O 7050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 205 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36081 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 8395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8395 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 52, 'TRANS': 1020} Chain breaks: 6 Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "B" Number of atoms: 8428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8428 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 3 Chain: "A" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8411 Classifications: {'peptide': 1076} Link IDs: {'PTRANS': 52, 'TRANS': 1023} Chain breaks: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" 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: 9.24, per 1000 atoms: 0.26 Number of scatterers: 36081 At special positions: 0 Unit cell: (177.31, 180.88, 238, 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 172 16.00 O 7050 8.00 N 5898 7.00 C 22961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 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 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 E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 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 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 A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.03 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=2.03 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 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 W 2 " - " BMA W 3 " " 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 149 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 149 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C1074 " " NAG D 701 " - " ASN D 322 " " NAG E 701 " - " ASN E 322 " " NAG E 702 " - " ASN E 546 " " NAG F 1 " - " ASN C 17 " " NAG G 1 " - " ASN C 122 " " NAG H 1 " - " ASN C 343 " " NAG I 1 " - " ASN C 709 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN B 17 " " NAG O 1 " - " ASN B 149 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN A 17 " " NAG W 1 " - " ASN A 122 " " NAG X 1 " - " ASN A 331 " " NAG Y 1 " - " ASN A 717 " " NAG Z 1 " - " ASN A 801 " " NAG a 1 " - " ASN A1098 " " NAG b 1 " - " ASN A1134 " Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8288 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 48 sheets defined 35.3% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.020A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.566A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.331A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.628A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.986A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.608A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.806A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.273A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.760A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.041A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.895A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.220A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 82 removed outlier: 3.783A pdb=" N VAL E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 99 removed outlier: 3.596A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.827A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 130 Processing helix chain 'E' and resid 147 through 154 Processing helix chain 'E' and resid 157 through 171 removed outlier: 3.747A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 194 Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.968A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 252 removed outlier: 3.667A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.532A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 299 removed outlier: 3.570A pdb=" N ASP E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.519A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 340 removed outlier: 4.231A pdb=" N VAL E 339 " --> pdb=" O PRO E 336 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN E 340 " --> pdb=" O GLY E 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 336 through 340' Processing helix chain 'E' and resid 366 through 386 removed outlier: 3.521A pdb=" N LEU E 370 " --> pdb=" O MET E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 388 No H-bonds generated for 'chain 'E' and resid 387 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 4.494A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.775A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 removed outlier: 3.531A pdb=" N SER E 507 " --> pdb=" O LEU E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.309A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'E' and resid 581 through 599 Proline residue: E 590 - end of helix Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.763A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 4.231A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.892A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 154 removed outlier: 4.294A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 171 removed outlier: 3.601A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.816A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 326 through 331 removed outlier: 4.020A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 386 removed outlier: 3.519A pdb=" N PHE D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.517A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.227A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.681A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 503 removed outlier: 4.047A pdb=" N LEU D 503 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.178A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.542A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.638A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 removed outlier: 3.507A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Proline residue: D 590 - end of helix Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.931A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.830A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.657A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.054A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.135A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 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: 4.367A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.047A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.790A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.098A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.913A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.835A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.536A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.759A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.796A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.017A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 939 removed outlier: 4.268A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 988 through 1032 removed outlier: 3.996A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.024A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.733A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 212 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.750A pdb=" N PHE C 43 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.764A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.855A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 153 through 154 removed outlier: 7.793A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.126A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.879A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 538 through 539 removed outlier: 5.008A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.656A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.234A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.342A pdb=" N ALA C 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.507A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.513A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.499A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.047A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.632A pdb=" N ARG E 357 " --> pdb=" O TRP E 349 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.773A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.739A pdb=" N THR D 347 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP D 349 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.775A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.775A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.663A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 7.462A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.874A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.464A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.686A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 357 removed outlier: 3.679A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.024A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 702 removed outlier: 5.967A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.614A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.617A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.609A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.505A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 83 through 85 removed outlier: 7.530A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.875A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.387A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.603A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.970A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.509A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.977A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.323A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 1120 through 1122 1475 hydrogen bonds defined for protein. 4188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.62 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11466 1.34 - 1.46: 9282 1.46 - 1.58: 15948 1.58 - 1.70: 0 1.70 - 1.82: 244 Bond restraints: 36940 Sorted by residual: bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C THR C 630 " pdb=" N PRO C 631 " ideal model delta sigma weight residual 1.333 1.357 -0.023 1.01e-02 9.80e+03 5.32e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C1 BMA K 3 " pdb=" C2 BMA K 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 ... (remaining 36935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 49527 1.77 - 3.54: 643 3.54 - 5.30: 51 5.30 - 7.07: 12 7.07 - 8.84: 6 Bond angle restraints: 50239 Sorted by residual: angle pdb=" C ASN B 196 " pdb=" N ILE B 197 " pdb=" CA ILE B 197 " ideal model delta sigma weight residual 122.96 120.45 2.51 9.50e-01 1.11e+00 6.97e+00 angle pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " pdb=" CG LEU A 517 " ideal model delta sigma weight residual 116.30 125.14 -8.84 3.50e+00 8.16e-02 6.38e+00 angle pdb=" CA LEU B 517 " pdb=" CB LEU B 517 " pdb=" CG LEU B 517 " ideal model delta sigma weight residual 116.30 124.99 -8.69 3.50e+00 8.16e-02 6.16e+00 angle pdb=" N ILE B 197 " pdb=" CA ILE B 197 " pdb=" C ILE B 197 " ideal model delta sigma weight residual 106.42 110.13 -3.71 1.51e+00 4.39e-01 6.05e+00 angle pdb=" C3 NAG O 1 " pdb=" C4 NAG O 1 " pdb=" O4 NAG O 1 " ideal model delta sigma weight residual 107.29 114.51 -7.22 3.00e+00 1.11e-01 5.78e+00 ... (remaining 50234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 22477 21.76 - 43.52: 435 43.52 - 65.28: 32 65.28 - 87.04: 32 87.04 - 108.80: 28 Dihedral angle restraints: 23004 sinusoidal: 10119 harmonic: 12885 Sorted by residual: dihedral pdb=" O4 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C5 BMA K 3 " pdb=" O5 BMA K 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.91 108.80 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.96 108.75 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.99 108.72 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 23001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 5016 0.057 - 0.113: 729 0.113 - 0.170: 50 0.170 - 0.226: 0 0.226 - 0.283: 7 Chirality restraints: 5802 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 5799 not shown) Planarity restraints: 6447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 321 " 0.031 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 322 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 322 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 322 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO B 337 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 337 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.023 5.00e-02 4.00e+02 ... (remaining 6444 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3661 2.75 - 3.29: 34764 3.29 - 3.82: 59241 3.82 - 4.36: 66905 4.36 - 4.90: 118679 Nonbonded interactions: 283250 Sorted by model distance: nonbonded pdb=" OG SER C 383 " pdb=" OE2 GLU B 988 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP E 382 " pdb=" OH TYR E 385 " model vdw 2.246 3.040 nonbonded pdb=" OG SER B 884 " pdb=" OG1 THR B 887 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASN B 439 " pdb=" OG SER B 443 " model vdw 2.259 3.040 ... (remaining 283245 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 69 or resid 77 through 244 or resid 254 through \ 1309)) selection = (chain 'B' and (resid 14 through 69 or resid 77 through 244 or resid 254 through \ 1309)) selection = (chain 'C' and (resid 14 through 621 or resid 640 through 1309)) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 19 through 701) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'R' selection = chain 'W' selection = chain 'a' } 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: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.800 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.003 0.068 37070 Z= 0.138 Angle : 0.473 17.202 50581 Z= 0.219 Chirality : 0.041 0.283 5802 Planarity : 0.003 0.048 6393 Dihedral : 9.569 108.799 14572 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.68 % Allowed : 3.95 % Favored : 94.37 % 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 aren not related in a simple way. whole: -1.80 (0.11), residues: 4382 helix: 0.48 (0.13), residues: 1353 sheet: -1.26 (0.18), residues: 668 loop : -2.27 (0.11), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1014 TYR 0.017 0.001 TYR D 385 PHE 0.006 0.001 PHE A 133 TRP 0.004 0.000 TRP D 69 HIS 0.001 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00270 (36940) covalent geometry : angle 0.46112 (50239) SS BOND : bond 0.00106 ( 48) SS BOND : angle 0.45962 ( 96) hydrogen bonds : bond 0.18875 ( 1468) hydrogen bonds : angle 7.09651 ( 4188) link_BETA1-4 : bond 0.00825 ( 28) link_BETA1-4 : angle 2.12101 ( 84) link_NAG-ASN : bond 0.00239 ( 54) link_NAG-ASN : angle 1.19601 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 982 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 ASN cc_start: 0.8345 (p0) cc_final: 0.7670 (p0) REVERT: C 88 ASP cc_start: 0.7714 (m-30) cc_final: 0.7424 (m-30) REVERT: C 116 SER cc_start: 0.7824 (m) cc_final: 0.6886 (p) REVERT: C 120 VAL cc_start: 0.7722 (t) cc_final: 0.7330 (m) REVERT: C 129 LYS cc_start: 0.7436 (ttmt) cc_final: 0.6929 (tptp) REVERT: C 195 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8178 (mtpt) REVERT: C 196 ASN cc_start: 0.7368 (t0) cc_final: 0.7105 (t0) REVERT: C 308 VAL cc_start: 0.8117 (t) cc_final: 0.7689 (p) REVERT: C 324 GLU cc_start: 0.7180 (pt0) cc_final: 0.6618 (mt-10) REVERT: C 394 ASN cc_start: 0.8204 (p0) cc_final: 0.7471 (p0) REVERT: C 395 VAL cc_start: 0.7930 (t) cc_final: 0.7544 (t) REVERT: C 434 ILE cc_start: 0.7362 (mt) cc_final: 0.7138 (mt) REVERT: C 436 TRP cc_start: 0.7029 (p90) cc_final: 0.6790 (p90) REVERT: C 546 LEU cc_start: 0.8126 (tp) cc_final: 0.7914 (tt) REVERT: C 555 SER cc_start: 0.8277 (t) cc_final: 0.7551 (p) REVERT: C 584 ILE cc_start: 0.7871 (mm) cc_final: 0.7352 (mm) REVERT: C 596 SER cc_start: 0.8026 (t) cc_final: 0.7648 (p) REVERT: C 659 SER cc_start: 0.8472 (m) cc_final: 0.8230 (m) REVERT: C 661 GLU cc_start: 0.6308 (tt0) cc_final: 0.6096 (tt0) REVERT: C 703 ASN cc_start: 0.7877 (t0) cc_final: 0.7617 (t0) REVERT: C 739 THR cc_start: 0.8104 (m) cc_final: 0.7863 (p) REVERT: C 751 ASN cc_start: 0.8387 (m-40) cc_final: 0.8111 (m-40) REVERT: C 785 VAL cc_start: 0.5578 (m) cc_final: 0.4233 (t) REVERT: C 821 LEU cc_start: 0.8299 (mp) cc_final: 0.7968 (mp) REVERT: C 921 LYS cc_start: 0.8106 (mmtp) cc_final: 0.7835 (mmtp) REVERT: C 1010 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6972 (mm110) REVERT: C 1072 GLU cc_start: 0.7899 (pm20) cc_final: 0.6926 (mp0) REVERT: C 1094 VAL cc_start: 0.7783 (p) cc_final: 0.6924 (t) REVERT: C 1122 VAL cc_start: 0.8068 (t) cc_final: 0.7754 (m) REVERT: E 49 ASN cc_start: 0.8044 (m-40) cc_final: 0.7793 (t0) REVERT: E 72 PHE cc_start: 0.7825 (t80) cc_final: 0.7136 (t80) REVERT: E 83 TYR cc_start: 0.5873 (m-80) cc_final: 0.4289 (m-80) REVERT: E 170 SER cc_start: 0.9182 (m) cc_final: 0.7028 (p) REVERT: E 180 TYR cc_start: 0.3182 (t80) cc_final: 0.1998 (t80) REVERT: E 314 PHE cc_start: 0.7861 (t80) cc_final: 0.7536 (t80) REVERT: E 315 PHE cc_start: 0.6187 (m-80) cc_final: 0.5377 (m-80) REVERT: E 329 GLU cc_start: 0.7817 (pt0) cc_final: 0.7569 (pt0) REVERT: E 360 MET cc_start: -0.0942 (ttt) cc_final: -0.1755 (ttp) REVERT: E 391 LEU cc_start: 0.8933 (mt) cc_final: 0.8142 (pt) REVERT: E 408 MET cc_start: 0.5723 (mpt) cc_final: 0.5249 (mpt) REVERT: E 460 ARG cc_start: 0.6970 (mtp180) cc_final: 0.6436 (tpp80) REVERT: E 480 MET cc_start: 0.7432 (mtp) cc_final: 0.6991 (mtp) REVERT: E 510 TYR cc_start: 0.7106 (m-80) cc_final: 0.6831 (m-80) REVERT: E 514 ARG cc_start: 0.8120 (ptp-170) cc_final: 0.7571 (ptp-170) REVERT: E 559 ARG cc_start: 0.7231 (ptm-80) cc_final: 0.7018 (tpm170) REVERT: E 563 SER cc_start: 0.6570 (p) cc_final: 0.5969 (p) REVERT: D 26 LYS cc_start: 0.7233 (mtmm) cc_final: 0.6846 (tptp) REVERT: D 72 PHE cc_start: 0.7838 (t80) cc_final: 0.7498 (t80) REVERT: D 76 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7735 (tp40) REVERT: D 100 LEU cc_start: 0.0505 (tp) cc_final: 0.0297 (tp) REVERT: D 144 LEU cc_start: -0.3972 (OUTLIER) cc_final: -0.4554 (tt) REVERT: D 152 MET cc_start: -0.4010 (mmm) cc_final: -0.4259 (mmm) REVERT: D 309 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7259 (mmtt) REVERT: D 314 PHE cc_start: 0.8023 (t80) cc_final: 0.7564 (t80) REVERT: D 455 MET cc_start: 0.5237 (tmm) cc_final: 0.4793 (tmm) REVERT: D 525 PHE cc_start: 0.1508 (m-10) cc_final: 0.1267 (m-80) REVERT: B 42 VAL cc_start: 0.8272 (t) cc_final: 0.7875 (t) REVERT: B 50 SER cc_start: 0.8838 (m) cc_final: 0.8466 (p) REVERT: B 63 THR cc_start: 0.8332 (m) cc_final: 0.8015 (p) REVERT: B 81 ASN cc_start: 0.8256 (p0) cc_final: 0.7898 (p0) REVERT: B 99 ASN cc_start: 0.7190 (m-40) cc_final: 0.6897 (m-40) REVERT: B 138 ASP cc_start: 0.7278 (m-30) cc_final: 0.7036 (m-30) REVERT: B 152 TRP cc_start: 0.5339 (m100) cc_final: 0.4820 (m100) REVERT: B 153 MET cc_start: 0.6497 (ptm) cc_final: 0.6290 (ptm) REVERT: B 206 LYS cc_start: 0.7572 (tptt) cc_final: 0.7357 (tptm) REVERT: B 216 LEU cc_start: 0.7517 (tp) cc_final: 0.7123 (mt) REVERT: B 220 PHE cc_start: 0.8075 (t80) cc_final: 0.7803 (t80) REVERT: B 244 LEU cc_start: 0.6375 (mt) cc_final: 0.5961 (mt) REVERT: B 327 VAL cc_start: 0.8013 (t) cc_final: 0.7566 (m) REVERT: B 365 TYR cc_start: 0.6972 (m-80) cc_final: 0.6770 (m-80) REVERT: B 374 PHE cc_start: 0.7392 (m-80) cc_final: 0.7030 (m-80) REVERT: B 551 VAL cc_start: 0.9010 (p) cc_final: 0.8638 (m) REVERT: B 553 THR cc_start: 0.8233 (t) cc_final: 0.8025 (p) REVERT: B 604 THR cc_start: 0.8236 (m) cc_final: 0.7927 (p) REVERT: B 610 VAL cc_start: 0.8452 (t) cc_final: 0.8222 (t) REVERT: B 860 VAL cc_start: 0.8594 (t) cc_final: 0.8129 (m) REVERT: B 901 GLN cc_start: 0.7656 (tt0) cc_final: 0.7406 (tt0) REVERT: B 918 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6881 (mt-10) REVERT: B 1017 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6822 (mt-10) REVERT: B 1019 ARG cc_start: 0.6721 (ttm110) cc_final: 0.6334 (ttm110) REVERT: B 1072 GLU cc_start: 0.7870 (pm20) cc_final: 0.6651 (mp0) REVERT: B 1073 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7662 (mtpp) REVERT: B 1119 ASN cc_start: 0.7360 (m110) cc_final: 0.7125 (m-40) REVERT: B 1142 GLN cc_start: 0.8077 (tp40) cc_final: 0.7332 (tp40) REVERT: A 52 GLN cc_start: 0.7602 (tm130) cc_final: 0.6856 (tm-30) REVERT: A 90 VAL cc_start: 0.8237 (m) cc_final: 0.7873 (p) REVERT: A 104 TRP cc_start: 0.7351 (m-90) cc_final: 0.7143 (m-90) REVERT: A 116 SER cc_start: 0.7925 (m) cc_final: 0.7533 (p) REVERT: A 138 ASP cc_start: 0.7809 (m-30) cc_final: 0.7563 (t0) REVERT: A 194 PHE cc_start: 0.7910 (m-80) cc_final: 0.7315 (m-10) REVERT: A 221 SER cc_start: 0.8434 (m) cc_final: 0.8083 (p) REVERT: A 241 LEU cc_start: 0.7875 (mt) cc_final: 0.7616 (mt) REVERT: A 276 LEU cc_start: 0.8763 (tp) cc_final: 0.8465 (tt) REVERT: A 294 ASP cc_start: 0.7272 (p0) cc_final: 0.6756 (p0) REVERT: A 297 SER cc_start: 0.8098 (t) cc_final: 0.7853 (m) REVERT: A 362 VAL cc_start: 0.6031 (OUTLIER) cc_final: 0.5761 (p) REVERT: A 569 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8521 (mp) REVERT: A 654 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6659 (mt-10) REVERT: A 673 SER cc_start: 0.8824 (t) cc_final: 0.8345 (m) REVERT: A 710 ASN cc_start: 0.7031 (p0) cc_final: 0.6828 (p0) REVERT: A 735 SER cc_start: 0.7776 (t) cc_final: 0.7360 (p) REVERT: A 774 GLN cc_start: 0.7302 (mm-40) cc_final: 0.7083 (mp10) REVERT: A 821 LEU cc_start: 0.8252 (mp) cc_final: 0.7996 (mt) REVERT: A 823 PHE cc_start: 0.7375 (m-80) cc_final: 0.7136 (m-10) REVERT: A 878 LEU cc_start: 0.8464 (tt) cc_final: 0.8158 (tp) REVERT: A 918 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6622 (mt-10) REVERT: A 950 ASP cc_start: 0.6984 (t70) cc_final: 0.6680 (t0) REVERT: A 1010 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7284 (mm-40) REVERT: A 1019 ARG cc_start: 0.7128 (ttp-110) cc_final: 0.6683 (ttp80) REVERT: A 1028 LYS cc_start: 0.8680 (mttp) cc_final: 0.8398 (mttm) REVERT: A 1038 LYS cc_start: 0.8322 (mttt) cc_final: 0.7992 (mttm) REVERT: A 1077 THR cc_start: 0.8562 (t) cc_final: 0.8337 (t) outliers start: 65 outliers final: 28 residues processed: 1034 average time/residue: 0.2417 time to fit residues: 396.7397 Evaluate side-chains 829 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 798 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 1004 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 0.1980 chunk 424 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN C 188 ASN C 271 GLN C 474 GLN C 501 ASN C 519 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 580 GLN C 613 GLN C 641 ASN C 787 GLN C 954 GLN C 955 ASN C 957 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1011 GLN E 53 ASN E 58 ASN E 61 ASN E 81 GLN E 96 GLN E 134 ASN E 239 HIS E 300 GLN E 442 GLN E 472 GLN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN E 531 GLN E 540 HIS E 552 GLN D 81 GLN D 89 GLN D 134 ASN D 137 ASN D 239 HIS D 373 HIS D 380 GLN D 442 GLN D 493 HIS D 524 GLN D 531 GLN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 146 HIS B 164 ASN B 173 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 218 GLN B 388 ASN B 414 GLN B 422 ASN B 437 ASN B 460 ASN B 493 GLN B 563 GLN B 655 HIS B 690 GLN B 764 ASN B 856 ASN B 919 ASN B1011 GLN B1071 GLN B1108 ASN B1119 ASN A 52 GLN A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 183 GLN A 218 GLN A 414 GLN A 422 ASN A 460 ASN A 493 GLN A 506 GLN A 544 ASN A 563 GLN A 641 ASN A 690 GLN A 960 ASN A1011 GLN A1071 GLN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.200000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150182 restraints weight = 64029.235| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.07 r_work: 0.3615 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 37070 Z= 0.205 Angle : 0.629 17.145 50581 Z= 0.310 Chirality : 0.045 0.353 5802 Planarity : 0.004 0.050 6393 Dihedral : 7.992 89.139 6510 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.87 % Allowed : 9.12 % Favored : 88.02 % 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 aren not related in a simple way. whole: -0.87 (0.12), residues: 4382 helix: 1.28 (0.14), residues: 1368 sheet: -0.57 (0.18), residues: 699 loop : -1.80 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 192 TYR 0.025 0.002 TYR E 196 PHE 0.028 0.002 PHE A 643 TRP 0.021 0.001 TRP C 353 HIS 0.006 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00449 (36940) covalent geometry : angle 0.60688 (50239) SS BOND : bond 0.00949 ( 48) SS BOND : angle 2.20126 ( 96) hydrogen bonds : bond 0.04328 ( 1468) hydrogen bonds : angle 5.31011 ( 4188) link_BETA1-4 : bond 0.01181 ( 28) link_BETA1-4 : angle 2.58530 ( 84) link_NAG-ASN : bond 0.00484 ( 54) link_NAG-ASN : angle 1.67335 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 827 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 LYS cc_start: 0.8438 (mttm) cc_final: 0.8153 (mttm) REVERT: C 53 ASP cc_start: 0.7401 (t70) cc_final: 0.7166 (t70) REVERT: C 116 SER cc_start: 0.6918 (m) cc_final: 0.6640 (p) REVERT: C 129 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7277 (tppt) REVERT: C 156 GLU cc_start: 0.6065 (mt-10) cc_final: 0.5763 (mt-10) REVERT: C 196 ASN cc_start: 0.7983 (t0) cc_final: 0.7746 (t0) REVERT: C 298 GLU cc_start: 0.7548 (tp30) cc_final: 0.7250 (tp30) REVERT: C 307 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8263 (p) REVERT: C 308 VAL cc_start: 0.8411 (t) cc_final: 0.8033 (p) REVERT: C 319 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.7356 (ttm110) REVERT: C 392 PHE cc_start: 0.7285 (m-80) cc_final: 0.6990 (m-80) REVERT: C 394 ASN cc_start: 0.8375 (p0) cc_final: 0.7754 (p0) REVERT: C 430 THR cc_start: 0.7163 (m) cc_final: 0.6869 (t) REVERT: C 432 CYS cc_start: 0.5294 (OUTLIER) cc_final: 0.4871 (m) REVERT: C 436 TRP cc_start: 0.6904 (p90) cc_final: 0.6643 (p90) REVERT: C 514 SER cc_start: 0.7587 (p) cc_final: 0.7339 (m) REVERT: C 546 LEU cc_start: 0.8378 (tp) cc_final: 0.8005 (tt) REVERT: C 555 SER cc_start: 0.8317 (t) cc_final: 0.8090 (t) REVERT: C 558 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7681 (mmmt) REVERT: C 574 ASP cc_start: 0.7986 (p0) cc_final: 0.7446 (t0) REVERT: C 577 ARG cc_start: 0.7632 (ttm170) cc_final: 0.7367 (ttm-80) REVERT: C 596 SER cc_start: 0.8306 (t) cc_final: 0.7979 (p) REVERT: C 615 VAL cc_start: 0.8457 (t) cc_final: 0.8249 (p) REVERT: C 703 ASN cc_start: 0.8075 (t0) cc_final: 0.7777 (t0) REVERT: C 776 LYS cc_start: 0.8565 (tttt) cc_final: 0.8087 (ttmm) REVERT: C 785 VAL cc_start: 0.6620 (m) cc_final: 0.5368 (t) REVERT: C 900 MET cc_start: 0.8627 (mmm) cc_final: 0.8107 (mtp) REVERT: C 921 LYS cc_start: 0.8347 (mmtp) cc_final: 0.8135 (mmmm) REVERT: C 947 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8088 (mtpp) REVERT: C 1019 ARG cc_start: 0.7991 (ttp80) cc_final: 0.6524 (ttp-170) REVERT: C 1072 GLU cc_start: 0.8310 (pm20) cc_final: 0.7727 (pm20) REVERT: C 1073 LYS cc_start: 0.8273 (mttt) cc_final: 0.7859 (mtpp) REVERT: C 1091 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7527 (mtp85) REVERT: E 26 LYS cc_start: 0.6706 (tppt) cc_final: 0.6140 (tppt) REVERT: E 63 ASN cc_start: 0.7705 (m-40) cc_final: 0.7468 (m-40) REVERT: E 72 PHE cc_start: 0.7711 (t80) cc_final: 0.7191 (t80) REVERT: E 83 TYR cc_start: 0.5785 (m-80) cc_final: 0.5527 (m-80) REVERT: E 180 TYR cc_start: 0.3613 (t80) cc_final: 0.2352 (t80) REVERT: E 308 PHE cc_start: 0.8841 (m-80) cc_final: 0.8235 (m-80) REVERT: E 314 PHE cc_start: 0.8224 (t80) cc_final: 0.8005 (t80) REVERT: E 315 PHE cc_start: 0.6588 (m-80) cc_final: 0.5682 (m-80) REVERT: E 329 GLU cc_start: 0.8056 (pt0) cc_final: 0.7721 (pp20) REVERT: E 370 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6589 (mp) REVERT: E 408 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.5499 (mpt) REVERT: E 455 MET cc_start: 0.8496 (ppp) cc_final: 0.8149 (ppp) REVERT: E 480 MET cc_start: 0.7654 (mtp) cc_final: 0.7116 (mtp) REVERT: E 491 VAL cc_start: 0.2185 (OUTLIER) cc_final: 0.1512 (p) REVERT: E 510 TYR cc_start: 0.7461 (m-80) cc_final: 0.6825 (m-80) REVERT: E 514 ARG cc_start: 0.8196 (ptp-170) cc_final: 0.7821 (ptp-170) REVERT: E 560 LEU cc_start: 0.6173 (mt) cc_final: 0.5760 (mt) REVERT: D 31 LYS cc_start: 0.6736 (tmtp) cc_final: 0.6513 (mtmm) REVERT: D 72 PHE cc_start: 0.8196 (t80) cc_final: 0.7868 (t80) REVERT: D 76 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7867 (tp40) REVERT: D 144 LEU cc_start: -0.3775 (OUTLIER) cc_final: -0.4176 (tt) REVERT: D 152 MET cc_start: -0.4241 (mmm) cc_final: -0.4451 (mmm) REVERT: D 309 LYS cc_start: 0.7476 (mmtt) cc_final: 0.7225 (mmtt) REVERT: D 314 PHE cc_start: 0.8590 (t80) cc_final: 0.8268 (t80) REVERT: D 323 MET cc_start: 0.3757 (mmm) cc_final: 0.3037 (tpp) REVERT: D 383 MET cc_start: 0.2929 (mtm) cc_final: 0.2436 (mtp) REVERT: D 404 VAL cc_start: 0.7425 (t) cc_final: 0.7100 (m) REVERT: D 455 MET cc_start: 0.5656 (tmm) cc_final: 0.5296 (tmm) REVERT: D 461 TRP cc_start: 0.3451 (t60) cc_final: 0.3014 (t-100) REVERT: D 579 MET cc_start: 0.0033 (OUTLIER) cc_final: -0.0789 (tpp) REVERT: B 50 SER cc_start: 0.9055 (m) cc_final: 0.8717 (p) REVERT: B 52 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 99 ASN cc_start: 0.8246 (m-40) cc_final: 0.7890 (m-40) REVERT: B 140 PHE cc_start: 0.8078 (p90) cc_final: 0.7641 (p90) REVERT: B 152 TRP cc_start: 0.5843 (m100) cc_final: 0.5301 (m100) REVERT: B 153 MET cc_start: 0.7331 (ptm) cc_final: 0.7111 (ptm) REVERT: B 216 LEU cc_start: 0.7711 (tp) cc_final: 0.7368 (mt) REVERT: B 220 PHE cc_start: 0.8121 (t80) cc_final: 0.7872 (t80) REVERT: B 244 LEU cc_start: 0.6349 (mt) cc_final: 0.6075 (mt) REVERT: B 291 CYS cc_start: 0.6580 (m) cc_final: 0.6359 (m) REVERT: B 327 VAL cc_start: 0.8439 (t) cc_final: 0.8119 (m) REVERT: B 365 TYR cc_start: 0.7821 (m-80) cc_final: 0.7413 (m-80) REVERT: B 539 VAL cc_start: 0.8576 (m) cc_final: 0.8350 (p) REVERT: B 551 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8707 (m) REVERT: B 553 THR cc_start: 0.8679 (t) cc_final: 0.8364 (p) REVERT: B 559 PHE cc_start: 0.8295 (m-10) cc_final: 0.8031 (m-10) REVERT: B 604 THR cc_start: 0.8523 (m) cc_final: 0.8174 (p) REVERT: B 654 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7889 (tt0) REVERT: B 781 VAL cc_start: 0.8498 (t) cc_final: 0.7536 (m) REVERT: B 820 ASP cc_start: 0.7844 (m-30) cc_final: 0.7492 (t0) REVERT: B 860 VAL cc_start: 0.8683 (t) cc_final: 0.8365 (m) REVERT: B 901 GLN cc_start: 0.8160 (tt0) cc_final: 0.7825 (tt0) REVERT: B 979 ASP cc_start: 0.8121 (m-30) cc_final: 0.7708 (t0) REVERT: B 986 LYS cc_start: 0.7243 (ttmm) cc_final: 0.6848 (ttmm) REVERT: B 1005 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7971 (mm-40) REVERT: B 1017 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7565 (mt-10) REVERT: B 1073 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7865 (ttmm) REVERT: B 1107 ARG cc_start: 0.7544 (mtt90) cc_final: 0.7136 (mtt90) REVERT: B 1142 GLN cc_start: 0.8405 (tp40) cc_final: 0.7580 (tp40) REVERT: A 28 TYR cc_start: 0.8003 (m-80) cc_final: 0.7700 (m-80) REVERT: A 52 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 90 VAL cc_start: 0.8437 (m) cc_final: 0.8233 (p) REVERT: A 96 GLU cc_start: 0.6932 (pm20) cc_final: 0.6135 (pt0) REVERT: A 104 TRP cc_start: 0.7834 (m-90) cc_final: 0.7518 (m-10) REVERT: A 113 LYS cc_start: 0.8148 (mptp) cc_final: 0.7936 (mptp) REVERT: A 116 SER cc_start: 0.7832 (m) cc_final: 0.7438 (p) REVERT: A 138 ASP cc_start: 0.7856 (m-30) cc_final: 0.7575 (t0) REVERT: A 149 ASN cc_start: 0.5990 (OUTLIER) cc_final: 0.5579 (p0) REVERT: A 194 PHE cc_start: 0.8164 (m-80) cc_final: 0.7405 (m-10) REVERT: A 203 ILE cc_start: 0.8577 (mt) cc_final: 0.8258 (tt) REVERT: A 266 TYR cc_start: 0.8420 (m-80) cc_final: 0.7791 (m-80) REVERT: A 276 LEU cc_start: 0.8745 (tp) cc_final: 0.8530 (tt) REVERT: A 294 ASP cc_start: 0.7646 (p0) cc_final: 0.7373 (p0) REVERT: A 307 THR cc_start: 0.7482 (p) cc_final: 0.7281 (p) REVERT: A 319 ARG cc_start: 0.8182 (ptp90) cc_final: 0.7896 (ptp90) REVERT: A 539 VAL cc_start: 0.8264 (m) cc_final: 0.8033 (p) REVERT: A 584 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7513 (tp) REVERT: A 644 GLN cc_start: 0.8465 (tp40) cc_final: 0.7899 (tm-30) REVERT: A 673 SER cc_start: 0.8904 (t) cc_final: 0.8499 (m) REVERT: A 710 ASN cc_start: 0.7675 (p0) cc_final: 0.7416 (p0) REVERT: A 735 SER cc_start: 0.8433 (t) cc_final: 0.8062 (p) REVERT: A 823 PHE cc_start: 0.7697 (m-80) cc_final: 0.7484 (m-10) REVERT: A 878 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8473 (tp) REVERT: A 904 TYR cc_start: 0.8091 (m-10) cc_final: 0.7659 (m-10) REVERT: A 949 GLN cc_start: 0.8421 (tp40) cc_final: 0.8104 (mm-40) REVERT: A 950 ASP cc_start: 0.7654 (t70) cc_final: 0.7331 (t0) REVERT: A 1019 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7271 (ttp80) REVERT: A 1038 LYS cc_start: 0.8639 (mttt) cc_final: 0.8303 (mttm) REVERT: A 1068 VAL cc_start: 0.7898 (t) cc_final: 0.7584 (m) REVERT: A 1107 ARG cc_start: 0.8118 (mtt90) cc_final: 0.7853 (mtt90) REVERT: A 1141 LEU cc_start: 0.8507 (mt) cc_final: 0.8297 (tp) outliers start: 111 outliers final: 66 residues processed: 894 average time/residue: 0.2535 time to fit residues: 359.5791 Evaluate side-chains 839 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 762 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 349 optimal weight: 0.5980 chunk 311 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 400 optimal weight: 0.3980 chunk 401 optimal weight: 0.0670 chunk 79 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 777 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 505 HIS E 524 GLN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 764 ASN B1101 HIS A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 271 GLN A 317 ASN A 955 ASN A 957 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.200683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151202 restraints weight = 64625.599| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.81 r_work: 0.3632 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 37070 Z= 0.144 Angle : 0.595 15.994 50581 Z= 0.289 Chirality : 0.044 0.347 5802 Planarity : 0.004 0.070 6393 Dihedral : 6.766 81.556 6501 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.00 % Allowed : 10.95 % Favored : 86.05 % 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 aren not related in a simple way. whole: -0.50 (0.12), residues: 4382 helix: 1.64 (0.14), residues: 1369 sheet: -0.30 (0.18), residues: 709 loop : -1.65 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 559 TYR 0.027 0.001 TYR E 497 PHE 0.025 0.002 PHE A 106 TRP 0.024 0.001 TRP C 353 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00323 (36940) covalent geometry : angle 0.57267 (50239) SS BOND : bond 0.00476 ( 48) SS BOND : angle 2.39530 ( 96) hydrogen bonds : bond 0.03845 ( 1468) hydrogen bonds : angle 5.04750 ( 4188) link_BETA1-4 : bond 0.00845 ( 28) link_BETA1-4 : angle 2.40944 ( 84) link_NAG-ASN : bond 0.00299 ( 54) link_NAG-ASN : angle 1.57374 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 768 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 ASN cc_start: 0.8861 (p0) cc_final: 0.8642 (p0) REVERT: C 87 ASN cc_start: 0.8218 (p0) cc_final: 0.7956 (p0) REVERT: C 116 SER cc_start: 0.7194 (m) cc_final: 0.6598 (p) REVERT: C 129 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7436 (tptp) REVERT: C 196 ASN cc_start: 0.7943 (t0) cc_final: 0.7682 (t0) REVERT: C 307 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8199 (p) REVERT: C 308 VAL cc_start: 0.8417 (t) cc_final: 0.8027 (p) REVERT: C 356 LYS cc_start: 0.8585 (tptt) cc_final: 0.8227 (tppt) REVERT: C 390 LEU cc_start: 0.8340 (tt) cc_final: 0.8083 (mt) REVERT: C 394 ASN cc_start: 0.8294 (p0) cc_final: 0.7791 (p0) REVERT: C 430 THR cc_start: 0.7072 (m) cc_final: 0.6820 (t) REVERT: C 432 CYS cc_start: 0.5189 (OUTLIER) cc_final: 0.4672 (m) REVERT: C 436 TRP cc_start: 0.6843 (p90) cc_final: 0.6483 (p90) REVERT: C 514 SER cc_start: 0.7741 (p) cc_final: 0.7435 (m) REVERT: C 537 LYS cc_start: 0.7330 (mmmt) cc_final: 0.7090 (mtpp) REVERT: C 546 LEU cc_start: 0.8269 (tp) cc_final: 0.7905 (tt) REVERT: C 558 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7656 (mmmt) REVERT: C 596 SER cc_start: 0.8382 (t) cc_final: 0.8064 (p) REVERT: C 615 VAL cc_start: 0.8463 (t) cc_final: 0.8258 (p) REVERT: C 703 ASN cc_start: 0.8090 (t0) cc_final: 0.7799 (t0) REVERT: C 725 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7572 (tm-30) REVERT: C 762 GLN cc_start: 0.8048 (tt0) cc_final: 0.7769 (mt0) REVERT: C 773 GLU cc_start: 0.7410 (pt0) cc_final: 0.6749 (tp30) REVERT: C 775 ASP cc_start: 0.7644 (m-30) cc_final: 0.7400 (m-30) REVERT: C 776 LYS cc_start: 0.8536 (tttt) cc_final: 0.8089 (ttmm) REVERT: C 785 VAL cc_start: 0.6874 (m) cc_final: 0.5765 (t) REVERT: C 804 GLN cc_start: 0.8400 (mt0) cc_final: 0.8130 (mt0) REVERT: C 811 LYS cc_start: 0.7634 (tmtt) cc_final: 0.7234 (tmtt) REVERT: C 900 MET cc_start: 0.8586 (mmm) cc_final: 0.8149 (mtp) REVERT: C 921 LYS cc_start: 0.8411 (mmtp) cc_final: 0.8136 (mmmm) REVERT: C 935 GLN cc_start: 0.8382 (tt0) cc_final: 0.7949 (tt0) REVERT: C 947 LYS cc_start: 0.8275 (mtpp) cc_final: 0.8025 (mtpp) REVERT: C 1002 GLN cc_start: 0.8236 (tt0) cc_final: 0.7995 (tp40) REVERT: C 1010 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7464 (mp-120) REVERT: C 1019 ARG cc_start: 0.7632 (ttp80) cc_final: 0.6531 (ttp-170) REVERT: C 1073 LYS cc_start: 0.8307 (mttt) cc_final: 0.7852 (mtpp) REVERT: C 1091 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7239 (mtp180) REVERT: C 1107 ARG cc_start: 0.7506 (mtt90) cc_final: 0.7236 (mtt90) REVERT: C 1144 GLU cc_start: 0.8301 (tp30) cc_final: 0.8012 (mm-30) REVERT: E 40 PHE cc_start: 0.6688 (t80) cc_final: 0.6345 (t80) REVERT: E 61 ASN cc_start: 0.8016 (m110) cc_final: 0.7047 (m110) REVERT: E 63 ASN cc_start: 0.7710 (m-40) cc_final: 0.7470 (m-40) REVERT: E 72 PHE cc_start: 0.7935 (t80) cc_final: 0.7356 (t80) REVERT: E 83 TYR cc_start: 0.5881 (m-80) cc_final: 0.5674 (m-80) REVERT: E 273 ARG cc_start: 0.5256 (mmt180) cc_final: 0.4860 (mmt-90) REVERT: E 308 PHE cc_start: 0.8870 (m-80) cc_final: 0.8277 (m-80) REVERT: E 314 PHE cc_start: 0.8136 (t80) cc_final: 0.7910 (t80) REVERT: E 315 PHE cc_start: 0.6568 (m-80) cc_final: 0.5757 (m-80) REVERT: E 329 GLU cc_start: 0.8352 (pt0) cc_final: 0.8004 (pp20) REVERT: E 408 MET cc_start: 0.5889 (mpt) cc_final: 0.5446 (mpt) REVERT: E 452 PHE cc_start: 0.5985 (t80) cc_final: 0.5572 (t80) REVERT: E 455 MET cc_start: 0.8514 (ppp) cc_final: 0.8227 (ppp) REVERT: E 480 MET cc_start: 0.7678 (mtp) cc_final: 0.7165 (mtp) REVERT: E 510 TYR cc_start: 0.7109 (m-80) cc_final: 0.6710 (m-80) REVERT: E 514 ARG cc_start: 0.8213 (ptp-170) cc_final: 0.7927 (ptp-170) REVERT: D 72 PHE cc_start: 0.8125 (t80) cc_final: 0.7805 (t80) REVERT: D 76 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7852 (tp40) REVERT: D 144 LEU cc_start: -0.3802 (OUTLIER) cc_final: -0.4245 (tt) REVERT: D 152 MET cc_start: -0.4212 (mmm) cc_final: -0.4536 (mmm) REVERT: D 314 PHE cc_start: 0.8479 (t80) cc_final: 0.8169 (t80) REVERT: D 323 MET cc_start: 0.3771 (mmm) cc_final: 0.2907 (tpp) REVERT: D 370 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.3606 (mm) REVERT: D 383 MET cc_start: 0.2758 (mtm) cc_final: 0.2192 (mtp) REVERT: D 455 MET cc_start: 0.5789 (tmm) cc_final: 0.5034 (tmm) REVERT: D 461 TRP cc_start: 0.3424 (t60) cc_final: 0.2762 (t-100) REVERT: D 462 MET cc_start: 0.7435 (mtm) cc_final: 0.7226 (mtm) REVERT: D 475 LYS cc_start: 0.8797 (tmmt) cc_final: 0.8575 (tmmt) REVERT: D 579 MET cc_start: -0.0268 (ttt) cc_final: -0.0949 (tpp) REVERT: B 28 TYR cc_start: 0.8185 (m-80) cc_final: 0.7668 (m-10) REVERT: B 50 SER cc_start: 0.9020 (m) cc_final: 0.8672 (p) REVERT: B 52 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 99 ASN cc_start: 0.8349 (m-40) cc_final: 0.7923 (m-40) REVERT: B 140 PHE cc_start: 0.8191 (p90) cc_final: 0.7645 (p90) REVERT: B 152 TRP cc_start: 0.5803 (m100) cc_final: 0.5389 (m100) REVERT: B 153 MET cc_start: 0.7335 (ptm) cc_final: 0.7072 (ptm) REVERT: B 216 LEU cc_start: 0.7727 (tp) cc_final: 0.7367 (mt) REVERT: B 220 PHE cc_start: 0.8131 (t80) cc_final: 0.7861 (t80) REVERT: B 244 LEU cc_start: 0.6293 (mt) cc_final: 0.5951 (mt) REVERT: B 327 VAL cc_start: 0.8426 (t) cc_final: 0.8213 (m) REVERT: B 365 TYR cc_start: 0.7851 (m-80) cc_final: 0.7369 (m-80) REVERT: B 376 THR cc_start: 0.8143 (p) cc_final: 0.7932 (t) REVERT: B 406 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7240 (tp30) REVERT: B 542 ASN cc_start: 0.9064 (t0) cc_final: 0.8739 (t0) REVERT: B 551 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8708 (m) REVERT: B 553 THR cc_start: 0.8682 (t) cc_final: 0.8398 (p) REVERT: B 559 PHE cc_start: 0.8360 (m-10) cc_final: 0.8034 (m-10) REVERT: B 604 THR cc_start: 0.8548 (m) cc_final: 0.8156 (p) REVERT: B 654 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7871 (tt0) REVERT: B 755 GLN cc_start: 0.7835 (mt0) cc_final: 0.7546 (pt0) REVERT: B 758 SER cc_start: 0.8789 (m) cc_final: 0.8509 (p) REVERT: B 790 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7716 (mtmm) REVERT: B 820 ASP cc_start: 0.7810 (m-30) cc_final: 0.7453 (t0) REVERT: B 860 VAL cc_start: 0.8671 (t) cc_final: 0.8374 (m) REVERT: B 904 TYR cc_start: 0.7876 (m-10) cc_final: 0.7667 (m-10) REVERT: B 918 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7685 (mt-10) REVERT: B 921 LYS cc_start: 0.8286 (mmtp) cc_final: 0.7947 (mmtp) REVERT: B 925 ASN cc_start: 0.8621 (m-40) cc_final: 0.8421 (m-40) REVERT: B 979 ASP cc_start: 0.8080 (m-30) cc_final: 0.7648 (t0) REVERT: B 1005 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7927 (mm-40) REVERT: B 1073 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7849 (ttmm) REVERT: B 1107 ARG cc_start: 0.7481 (mtt90) cc_final: 0.7075 (mtt90) REVERT: B 1139 ASP cc_start: 0.7859 (t0) cc_final: 0.7613 (t0) REVERT: B 1142 GLN cc_start: 0.8421 (tp40) cc_final: 0.7535 (tp40) REVERT: A 28 TYR cc_start: 0.8033 (m-80) cc_final: 0.7745 (m-80) REVERT: A 52 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 113 LYS cc_start: 0.8231 (mptp) cc_final: 0.8013 (mptp) REVERT: A 138 ASP cc_start: 0.7939 (m-30) cc_final: 0.7486 (t0) REVERT: A 149 ASN cc_start: 0.5853 (OUTLIER) cc_final: 0.5536 (p0) REVERT: A 203 ILE cc_start: 0.8576 (mt) cc_final: 0.8241 (tt) REVERT: A 266 TYR cc_start: 0.8315 (m-80) cc_final: 0.7865 (m-80) REVERT: A 276 LEU cc_start: 0.8758 (tp) cc_final: 0.8408 (tt) REVERT: A 294 ASP cc_start: 0.7585 (p0) cc_final: 0.7361 (p0) REVERT: A 307 THR cc_start: 0.7545 (p) cc_final: 0.7304 (p) REVERT: A 319 ARG cc_start: 0.8184 (ptp90) cc_final: 0.7958 (ptp90) REVERT: A 362 VAL cc_start: 0.6668 (OUTLIER) cc_final: 0.6338 (p) REVERT: A 539 VAL cc_start: 0.8227 (m) cc_final: 0.7982 (p) REVERT: A 673 SER cc_start: 0.8899 (t) cc_final: 0.8480 (m) REVERT: A 710 ASN cc_start: 0.7722 (p0) cc_final: 0.7508 (p0) REVERT: A 735 SER cc_start: 0.8384 (t) cc_final: 0.8060 (p) REVERT: A 748 GLU cc_start: 0.7122 (pm20) cc_final: 0.6906 (pm20) REVERT: A 858 LEU cc_start: 0.8716 (mm) cc_final: 0.8457 (mt) REVERT: A 878 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8443 (tp) REVERT: A 904 TYR cc_start: 0.8108 (m-10) cc_final: 0.7634 (m-10) REVERT: A 949 GLN cc_start: 0.8384 (tp40) cc_final: 0.8046 (mm-40) REVERT: A 950 ASP cc_start: 0.7649 (t70) cc_final: 0.7315 (t0) REVERT: A 957 GLN cc_start: 0.8407 (tt0) cc_final: 0.8058 (tt0) REVERT: A 981 LEU cc_start: 0.8755 (mt) cc_final: 0.8234 (mt) REVERT: A 1017 GLU cc_start: 0.7512 (tp30) cc_final: 0.6634 (tp30) REVERT: A 1019 ARG cc_start: 0.7762 (ttp-110) cc_final: 0.7524 (ttp80) REVERT: A 1038 LYS cc_start: 0.8714 (mttt) cc_final: 0.8356 (mttm) REVERT: A 1107 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7836 (mtt90) REVERT: A 1122 VAL cc_start: 0.8871 (m) cc_final: 0.8580 (p) REVERT: A 1135 ASN cc_start: 0.8153 (t0) cc_final: 0.7944 (t0) REVERT: A 1136 THR cc_start: 0.8589 (t) cc_final: 0.8387 (p) REVERT: A 1141 LEU cc_start: 0.8476 (mt) cc_final: 0.8260 (tp) outliers start: 116 outliers final: 80 residues processed: 834 average time/residue: 0.2521 time to fit residues: 333.0448 Evaluate side-chains 831 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 742 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1004 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 308 optimal weight: 0.9990 chunk 343 optimal weight: 1.9990 chunk 318 optimal weight: 0.9990 chunk 426 optimal weight: 0.9990 chunk 428 optimal weight: 1.9990 chunk 433 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 chunk 258 optimal weight: 4.9990 chunk 414 optimal weight: 0.0970 chunk 84 optimal weight: 0.9990 chunk 324 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1010 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 487 ASN A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.199277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149631 restraints weight = 64213.977| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.85 r_work: 0.3608 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 37070 Z= 0.171 Angle : 0.602 16.579 50581 Z= 0.294 Chirality : 0.044 0.341 5802 Planarity : 0.004 0.042 6393 Dihedral : 6.017 75.103 6499 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.18 % Allowed : 11.83 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.12), residues: 4382 helix: 1.75 (0.14), residues: 1367 sheet: -0.31 (0.18), residues: 731 loop : -1.52 (0.12), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 319 TYR 0.022 0.001 TYR E 385 PHE 0.028 0.002 PHE E 452 TRP 0.030 0.001 TRP A 104 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00386 (36940) covalent geometry : angle 0.57957 (50239) SS BOND : bond 0.00427 ( 48) SS BOND : angle 2.38994 ( 96) hydrogen bonds : bond 0.03813 ( 1468) hydrogen bonds : angle 4.95154 ( 4188) link_BETA1-4 : bond 0.00854 ( 28) link_BETA1-4 : angle 2.43835 ( 84) link_NAG-ASN : bond 0.00284 ( 54) link_NAG-ASN : angle 1.60128 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 748 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 TRP cc_start: 0.7698 (m-90) cc_final: 0.7243 (m-10) REVERT: C 116 SER cc_start: 0.7272 (m) cc_final: 0.6805 (p) REVERT: C 129 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7553 (tptp) REVERT: C 191 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7737 (mt-10) REVERT: C 196 ASN cc_start: 0.7937 (t0) cc_final: 0.7670 (t0) REVERT: C 307 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8283 (p) REVERT: C 308 VAL cc_start: 0.8431 (t) cc_final: 0.8010 (p) REVERT: C 390 LEU cc_start: 0.8322 (tt) cc_final: 0.8111 (mt) REVERT: C 394 ASN cc_start: 0.8294 (p0) cc_final: 0.7807 (p0) REVERT: C 430 THR cc_start: 0.7156 (m) cc_final: 0.6907 (t) REVERT: C 432 CYS cc_start: 0.5252 (OUTLIER) cc_final: 0.4728 (m) REVERT: C 436 TRP cc_start: 0.6829 (p90) cc_final: 0.6496 (p90) REVERT: C 514 SER cc_start: 0.7815 (p) cc_final: 0.7518 (m) REVERT: C 537 LYS cc_start: 0.7465 (mmmt) cc_final: 0.7222 (mtpp) REVERT: C 546 LEU cc_start: 0.8327 (tp) cc_final: 0.7966 (tt) REVERT: C 596 SER cc_start: 0.8407 (t) cc_final: 0.8185 (p) REVERT: C 674 TYR cc_start: 0.8547 (t80) cc_final: 0.8263 (t80) REVERT: C 703 ASN cc_start: 0.8098 (t0) cc_final: 0.7856 (t0) REVERT: C 775 ASP cc_start: 0.7638 (m-30) cc_final: 0.7363 (m-30) REVERT: C 776 LYS cc_start: 0.8586 (tttt) cc_final: 0.8129 (ttmm) REVERT: C 804 GLN cc_start: 0.8436 (mt0) cc_final: 0.8129 (mt0) REVERT: C 900 MET cc_start: 0.8577 (mmm) cc_final: 0.8276 (mtp) REVERT: C 921 LYS cc_start: 0.8461 (mmtp) cc_final: 0.8184 (mmmm) REVERT: C 935 GLN cc_start: 0.8409 (tt0) cc_final: 0.7949 (tt0) REVERT: C 947 LYS cc_start: 0.8248 (mtpp) cc_final: 0.8016 (mtpp) REVERT: C 1002 GLN cc_start: 0.8305 (tt0) cc_final: 0.8085 (tp40) REVERT: C 1019 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7223 (ttp-170) REVERT: C 1072 GLU cc_start: 0.8217 (pm20) cc_final: 0.7848 (pm20) REVERT: C 1073 LYS cc_start: 0.8300 (mttt) cc_final: 0.7913 (mtpp) REVERT: E 26 LYS cc_start: 0.6852 (tppt) cc_final: 0.6284 (mmtm) REVERT: E 63 ASN cc_start: 0.7790 (m-40) cc_final: 0.7520 (m-40) REVERT: E 72 PHE cc_start: 0.7950 (t80) cc_final: 0.7420 (t80) REVERT: E 308 PHE cc_start: 0.8867 (m-80) cc_final: 0.8297 (m-80) REVERT: E 314 PHE cc_start: 0.8201 (t80) cc_final: 0.7951 (t80) REVERT: E 329 GLU cc_start: 0.8425 (pt0) cc_final: 0.8032 (pp20) REVERT: E 383 MET cc_start: 0.8630 (mtm) cc_final: 0.8294 (mtm) REVERT: E 393 ARG cc_start: 0.7653 (ptp-110) cc_final: 0.7425 (ptp-110) REVERT: E 408 MET cc_start: 0.5895 (mpt) cc_final: 0.5385 (mpt) REVERT: E 455 MET cc_start: 0.8578 (ppp) cc_final: 0.8224 (ppp) REVERT: E 480 MET cc_start: 0.7742 (mtp) cc_final: 0.7252 (mtp) REVERT: E 510 TYR cc_start: 0.7187 (m-80) cc_final: 0.6774 (m-80) REVERT: E 514 ARG cc_start: 0.8283 (ptp-170) cc_final: 0.7975 (ptp-170) REVERT: E 555 PHE cc_start: 0.8166 (t80) cc_final: 0.7694 (t80) REVERT: E 579 MET cc_start: 0.2946 (ttp) cc_final: 0.2676 (mtp) REVERT: D 72 PHE cc_start: 0.8136 (t80) cc_final: 0.7627 (t80) REVERT: D 144 LEU cc_start: -0.3654 (OUTLIER) cc_final: -0.4118 (tt) REVERT: D 152 MET cc_start: -0.4221 (mmm) cc_final: -0.4547 (mmm) REVERT: D 314 PHE cc_start: 0.8458 (t80) cc_final: 0.8222 (t80) REVERT: D 323 MET cc_start: 0.4141 (mmm) cc_final: 0.3296 (tpp) REVERT: D 452 PHE cc_start: 0.5881 (t80) cc_final: 0.5589 (t80) REVERT: D 455 MET cc_start: 0.4842 (tmm) cc_final: 0.4625 (tmm) REVERT: D 461 TRP cc_start: 0.3321 (t60) cc_final: 0.2758 (t-100) REVERT: D 579 MET cc_start: 0.0201 (OUTLIER) cc_final: -0.0981 (tpp) REVERT: B 50 SER cc_start: 0.8981 (m) cc_final: 0.8610 (p) REVERT: B 52 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 54 LEU cc_start: 0.8368 (mt) cc_final: 0.8139 (mp) REVERT: B 99 ASN cc_start: 0.8122 (m-40) cc_final: 0.7756 (m-40) REVERT: B 140 PHE cc_start: 0.8231 (p90) cc_final: 0.7772 (p90) REVERT: B 152 TRP cc_start: 0.5852 (m100) cc_final: 0.5475 (m100) REVERT: B 153 MET cc_start: 0.7405 (ptm) cc_final: 0.7123 (ptm) REVERT: B 216 LEU cc_start: 0.7774 (tp) cc_final: 0.7420 (mt) REVERT: B 220 PHE cc_start: 0.8166 (t80) cc_final: 0.7865 (t80) REVERT: B 244 LEU cc_start: 0.6364 (mt) cc_final: 0.6044 (mt) REVERT: B 327 VAL cc_start: 0.8439 (t) cc_final: 0.8233 (m) REVERT: B 365 TYR cc_start: 0.7978 (m-80) cc_final: 0.7562 (m-80) REVERT: B 542 ASN cc_start: 0.9026 (t0) cc_final: 0.8726 (t0) REVERT: B 551 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8705 (m) REVERT: B 553 THR cc_start: 0.8737 (t) cc_final: 0.8432 (p) REVERT: B 555 SER cc_start: 0.8712 (t) cc_final: 0.8295 (p) REVERT: B 604 THR cc_start: 0.8564 (m) cc_final: 0.8195 (p) REVERT: B 755 GLN cc_start: 0.7797 (mt0) cc_final: 0.7496 (pt0) REVERT: B 758 SER cc_start: 0.8837 (m) cc_final: 0.8524 (p) REVERT: B 790 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7676 (mtmm) REVERT: B 820 ASP cc_start: 0.7845 (m-30) cc_final: 0.7509 (t0) REVERT: B 860 VAL cc_start: 0.8678 (t) cc_final: 0.8404 (m) REVERT: B 918 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7801 (mt-10) REVERT: B 921 LYS cc_start: 0.8344 (mmtp) cc_final: 0.8105 (mmtp) REVERT: B 979 ASP cc_start: 0.8087 (m-30) cc_final: 0.7749 (t0) REVERT: B 1005 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7979 (mm-40) REVERT: B 1073 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7873 (ttmm) REVERT: B 1142 GLN cc_start: 0.8419 (tp40) cc_final: 0.7541 (tp40) REVERT: B 1144 GLU cc_start: 0.7836 (mp0) cc_final: 0.7565 (mp0) REVERT: A 28 TYR cc_start: 0.8057 (m-80) cc_final: 0.7806 (m-80) REVERT: A 52 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 109 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7536 (p) REVERT: A 113 LYS cc_start: 0.8330 (mptp) cc_final: 0.8100 (mptp) REVERT: A 116 SER cc_start: 0.7968 (m) cc_final: 0.7478 (p) REVERT: A 138 ASP cc_start: 0.8047 (m-30) cc_final: 0.7622 (t0) REVERT: A 149 ASN cc_start: 0.6038 (OUTLIER) cc_final: 0.5678 (p0) REVERT: A 190 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7826 (mtm180) REVERT: A 203 ILE cc_start: 0.8552 (mt) cc_final: 0.8243 (tt) REVERT: A 266 TYR cc_start: 0.8322 (m-80) cc_final: 0.7960 (m-80) REVERT: A 276 LEU cc_start: 0.8728 (tp) cc_final: 0.8409 (tt) REVERT: A 294 ASP cc_start: 0.7640 (p0) cc_final: 0.7422 (p0) REVERT: A 362 VAL cc_start: 0.6905 (OUTLIER) cc_final: 0.6616 (p) REVERT: A 539 VAL cc_start: 0.8374 (m) cc_final: 0.8112 (p) REVERT: A 654 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 673 SER cc_start: 0.8909 (t) cc_final: 0.8450 (m) REVERT: A 735 SER cc_start: 0.8384 (t) cc_final: 0.8077 (p) REVERT: A 878 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8554 (tp) REVERT: A 902 MET cc_start: 0.8202 (tpp) cc_final: 0.7577 (tpt) REVERT: A 949 GLN cc_start: 0.8464 (tp40) cc_final: 0.8103 (mm-40) REVERT: A 950 ASP cc_start: 0.7759 (t70) cc_final: 0.7430 (t0) REVERT: A 957 GLN cc_start: 0.8428 (tt0) cc_final: 0.8157 (tt0) REVERT: A 963 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8708 (t) REVERT: A 981 LEU cc_start: 0.8796 (mt) cc_final: 0.8563 (mt) REVERT: A 1019 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7464 (ttp80) REVERT: A 1038 LYS cc_start: 0.8706 (mttt) cc_final: 0.8371 (mttm) REVERT: A 1045 LYS cc_start: 0.8384 (mmmm) cc_final: 0.8094 (mmmm) REVERT: A 1086 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7949 (mtmm) REVERT: A 1107 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7844 (mtt90) REVERT: A 1122 VAL cc_start: 0.8886 (m) cc_final: 0.8588 (p) REVERT: A 1135 ASN cc_start: 0.8140 (t0) cc_final: 0.7922 (t0) REVERT: A 1141 LEU cc_start: 0.8567 (mt) cc_final: 0.8360 (tp) outliers start: 123 outliers final: 92 residues processed: 817 average time/residue: 0.2256 time to fit residues: 291.5331 Evaluate side-chains 838 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 736 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1004 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 196 optimal weight: 0.7980 chunk 213 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 358 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 379 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN C 218 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 53 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 388 ASN B 641 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.196057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146080 restraints weight = 63871.987| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.84 r_work: 0.3562 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 37070 Z= 0.292 Angle : 0.671 16.432 50581 Z= 0.334 Chirality : 0.047 0.344 5802 Planarity : 0.004 0.044 6393 Dihedral : 5.988 71.390 6497 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.72 % Allowed : 12.37 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.44 (0.12), residues: 4382 helix: 1.68 (0.14), residues: 1358 sheet: -0.50 (0.18), residues: 747 loop : -1.51 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 646 TYR 0.019 0.002 TYR E 385 PHE 0.030 0.002 PHE E 452 TRP 0.027 0.002 TRP C 353 HIS 0.011 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00653 (36940) covalent geometry : angle 0.64797 (50239) SS BOND : bond 0.00516 ( 48) SS BOND : angle 2.59262 ( 96) hydrogen bonds : bond 0.04439 ( 1468) hydrogen bonds : angle 5.10957 ( 4188) link_BETA1-4 : bond 0.00860 ( 28) link_BETA1-4 : angle 2.42677 ( 84) link_NAG-ASN : bond 0.00450 ( 54) link_NAG-ASN : angle 1.84159 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 784 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 SER cc_start: 0.7376 (m) cc_final: 0.6866 (p) REVERT: C 129 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7503 (tptp) REVERT: C 140 PHE cc_start: 0.8521 (p90) cc_final: 0.8290 (p90) REVERT: C 196 ASN cc_start: 0.8019 (t0) cc_final: 0.7750 (t0) REVERT: C 307 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8300 (p) REVERT: C 308 VAL cc_start: 0.8384 (t) cc_final: 0.7968 (p) REVERT: C 392 PHE cc_start: 0.7636 (m-10) cc_final: 0.7312 (m-80) REVERT: C 394 ASN cc_start: 0.8274 (p0) cc_final: 0.7790 (p0) REVERT: C 432 CYS cc_start: 0.5319 (OUTLIER) cc_final: 0.4877 (m) REVERT: C 524 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8220 (m) REVERT: C 546 LEU cc_start: 0.8344 (tp) cc_final: 0.7967 (tt) REVERT: C 574 ASP cc_start: 0.8109 (p0) cc_final: 0.7664 (t0) REVERT: C 596 SER cc_start: 0.8516 (t) cc_final: 0.8158 (p) REVERT: C 661 GLU cc_start: 0.7473 (tp30) cc_final: 0.7067 (tp30) REVERT: C 674 TYR cc_start: 0.8595 (t80) cc_final: 0.8344 (t80) REVERT: C 703 ASN cc_start: 0.8105 (t0) cc_final: 0.7865 (t0) REVERT: C 767 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8262 (mt) REVERT: C 773 GLU cc_start: 0.7592 (pt0) cc_final: 0.6964 (tp30) REVERT: C 776 LYS cc_start: 0.8636 (tttt) cc_final: 0.8271 (tttp) REVERT: C 804 GLN cc_start: 0.8392 (mt0) cc_final: 0.8027 (mt0) REVERT: C 811 LYS cc_start: 0.7672 (tmtt) cc_final: 0.7439 (ttmm) REVERT: C 824 ASN cc_start: 0.8259 (m-40) cc_final: 0.7956 (m-40) REVERT: C 900 MET cc_start: 0.8603 (mmm) cc_final: 0.8377 (mtp) REVERT: C 921 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8224 (mmmm) REVERT: C 935 GLN cc_start: 0.8432 (tt0) cc_final: 0.7983 (tt0) REVERT: C 947 LYS cc_start: 0.8296 (mtpp) cc_final: 0.8057 (mtpp) REVERT: C 1002 GLN cc_start: 0.8288 (tt0) cc_final: 0.8063 (tp40) REVERT: C 1019 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7487 (ttp-170) REVERT: C 1073 LYS cc_start: 0.8260 (mttt) cc_final: 0.8010 (mmmm) REVERT: C 1081 ILE cc_start: 0.8481 (mm) cc_final: 0.8156 (mt) REVERT: C 1107 ARG cc_start: 0.7738 (mtt90) cc_final: 0.7190 (mtt90) REVERT: C 1132 ILE cc_start: 0.9041 (tt) cc_final: 0.8811 (tt) REVERT: C 1144 GLU cc_start: 0.8392 (tp30) cc_final: 0.8097 (mm-30) REVERT: E 63 ASN cc_start: 0.7993 (m-40) cc_final: 0.7743 (m-40) REVERT: E 72 PHE cc_start: 0.7939 (t80) cc_final: 0.7439 (t80) REVERT: E 269 ASP cc_start: 0.3678 (t0) cc_final: 0.2962 (m-30) REVERT: E 308 PHE cc_start: 0.8852 (m-80) cc_final: 0.8308 (m-80) REVERT: E 314 PHE cc_start: 0.8164 (t80) cc_final: 0.7936 (t80) REVERT: E 329 GLU cc_start: 0.8317 (pt0) cc_final: 0.7968 (pp20) REVERT: E 408 MET cc_start: 0.5962 (mpt) cc_final: 0.5437 (mpt) REVERT: E 455 MET cc_start: 0.8561 (ppp) cc_final: 0.8199 (ppp) REVERT: E 480 MET cc_start: 0.7776 (mtp) cc_final: 0.7265 (mtp) REVERT: E 510 TYR cc_start: 0.7373 (m-80) cc_final: 0.6747 (m-80) REVERT: E 555 PHE cc_start: 0.8101 (t80) cc_final: 0.7627 (t80) REVERT: D 76 GLN cc_start: 0.8425 (mm-40) cc_final: 0.7409 (tp40) REVERT: D 79 LEU cc_start: 0.8226 (mt) cc_final: 0.7806 (pp) REVERT: D 100 LEU cc_start: 0.1184 (tp) cc_final: 0.0899 (tp) REVERT: D 144 LEU cc_start: -0.3501 (OUTLIER) cc_final: -0.3768 (tt) REVERT: D 190 MET cc_start: 0.9283 (ppp) cc_final: 0.9023 (ppp) REVERT: D 270 MET cc_start: 0.5218 (tpp) cc_final: 0.4694 (ttm) REVERT: D 314 PHE cc_start: 0.8437 (t80) cc_final: 0.8207 (t80) REVERT: D 323 MET cc_start: 0.4204 (mmm) cc_final: 0.3606 (tpp) REVERT: D 452 PHE cc_start: 0.5884 (t80) cc_final: 0.5676 (t80) REVERT: D 455 MET cc_start: 0.4753 (tmm) cc_final: 0.4548 (tmm) REVERT: D 461 TRP cc_start: 0.3364 (t60) cc_final: 0.2796 (t-100) REVERT: D 579 MET cc_start: 0.0061 (OUTLIER) cc_final: -0.1012 (tpp) REVERT: B 45 SER cc_start: 0.8372 (t) cc_final: 0.7899 (p) REVERT: B 52 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 54 LEU cc_start: 0.8378 (mt) cc_final: 0.8145 (mp) REVERT: B 99 ASN cc_start: 0.8314 (m-40) cc_final: 0.8006 (m110) REVERT: B 140 PHE cc_start: 0.8185 (p90) cc_final: 0.7687 (p90) REVERT: B 152 TRP cc_start: 0.5905 (m100) cc_final: 0.5580 (m100) REVERT: B 153 MET cc_start: 0.7383 (ptm) cc_final: 0.7088 (ptm) REVERT: B 220 PHE cc_start: 0.8279 (t80) cc_final: 0.7987 (t80) REVERT: B 244 LEU cc_start: 0.6551 (mt) cc_final: 0.6106 (mt) REVERT: B 327 VAL cc_start: 0.8469 (t) cc_final: 0.8196 (m) REVERT: B 365 TYR cc_start: 0.8128 (m-80) cc_final: 0.7747 (m-80) REVERT: B 386 LYS cc_start: 0.8864 (mmtm) cc_final: 0.8602 (pttt) REVERT: B 539 VAL cc_start: 0.8741 (p) cc_final: 0.8494 (m) REVERT: B 551 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8636 (m) REVERT: B 553 THR cc_start: 0.8816 (t) cc_final: 0.8520 (p) REVERT: B 555 SER cc_start: 0.8750 (t) cc_final: 0.8322 (p) REVERT: B 654 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 705 VAL cc_start: 0.8711 (t) cc_final: 0.8414 (m) REVERT: B 735 SER cc_start: 0.8381 (m) cc_final: 0.8167 (p) REVERT: B 755 GLN cc_start: 0.7844 (mt0) cc_final: 0.7496 (pt0) REVERT: B 758 SER cc_start: 0.8999 (m) cc_final: 0.8542 (p) REVERT: B 820 ASP cc_start: 0.7930 (m-30) cc_final: 0.7565 (t0) REVERT: B 860 VAL cc_start: 0.8684 (t) cc_final: 0.8448 (m) REVERT: B 904 TYR cc_start: 0.7861 (m-10) cc_final: 0.7473 (m-10) REVERT: B 960 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7882 (m-40) REVERT: B 979 ASP cc_start: 0.8104 (m-30) cc_final: 0.7832 (t0) REVERT: B 1005 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8014 (mm-40) REVERT: B 1073 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7895 (ttmm) REVERT: B 1142 GLN cc_start: 0.8428 (tp40) cc_final: 0.7591 (tp40) REVERT: B 1144 GLU cc_start: 0.7940 (mp0) cc_final: 0.7580 (mp0) REVERT: A 52 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 96 GLU cc_start: 0.7296 (mp0) cc_final: 0.6589 (mt-10) REVERT: A 113 LYS cc_start: 0.8542 (mptp) cc_final: 0.8270 (mptp) REVERT: A 138 ASP cc_start: 0.8101 (m-30) cc_final: 0.7610 (t0) REVERT: A 149 ASN cc_start: 0.6095 (OUTLIER) cc_final: 0.5648 (p0) REVERT: A 190 ARG cc_start: 0.8024 (mtt-85) cc_final: 0.7676 (mtt-85) REVERT: A 203 ILE cc_start: 0.8536 (mt) cc_final: 0.8191 (tt) REVERT: A 276 LEU cc_start: 0.8779 (tp) cc_final: 0.8452 (tt) REVERT: A 294 ASP cc_start: 0.7733 (p0) cc_final: 0.7503 (p0) REVERT: A 346 ARG cc_start: 0.7253 (mmm160) cc_final: 0.6792 (mmm160) REVERT: A 362 VAL cc_start: 0.6989 (OUTLIER) cc_final: 0.6700 (p) REVERT: A 539 VAL cc_start: 0.8395 (m) cc_final: 0.8153 (p) REVERT: A 574 ASP cc_start: 0.7935 (p0) cc_final: 0.7598 (t0) REVERT: A 654 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 673 SER cc_start: 0.8881 (t) cc_final: 0.8423 (m) REVERT: A 725 GLU cc_start: 0.7640 (tt0) cc_final: 0.7424 (tm-30) REVERT: A 735 SER cc_start: 0.8386 (t) cc_final: 0.8055 (p) REVERT: A 736 VAL cc_start: 0.8571 (t) cc_final: 0.8339 (p) REVERT: A 878 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8602 (tp) REVERT: A 902 MET cc_start: 0.8280 (tpp) cc_final: 0.8027 (tpt) REVERT: A 918 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 933 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8073 (mttm) REVERT: A 949 GLN cc_start: 0.8552 (tp40) cc_final: 0.8170 (mm-40) REVERT: A 950 ASP cc_start: 0.7794 (t70) cc_final: 0.7387 (t0) REVERT: A 955 ASN cc_start: 0.7939 (t0) cc_final: 0.7626 (m-40) REVERT: A 957 GLN cc_start: 0.8494 (tt0) cc_final: 0.8280 (tt0) REVERT: A 988 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7375 (mt-10) REVERT: A 1019 ARG cc_start: 0.7750 (ttp-110) cc_final: 0.7472 (ttp80) REVERT: A 1031 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7549 (mt-10) REVERT: A 1038 LYS cc_start: 0.8685 (mttt) cc_final: 0.8358 (mttm) REVERT: A 1072 GLU cc_start: 0.8193 (pm20) cc_final: 0.7937 (pm20) REVERT: A 1086 LYS cc_start: 0.8289 (mtpp) cc_final: 0.7946 (mtmm) REVERT: A 1107 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7879 (mtt90) REVERT: A 1122 VAL cc_start: 0.8867 (m) cc_final: 0.8597 (p) REVERT: A 1123 SER cc_start: 0.8598 (t) cc_final: 0.8149 (p) outliers start: 144 outliers final: 97 residues processed: 871 average time/residue: 0.2559 time to fit residues: 351.9687 Evaluate side-chains 853 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 745 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1004 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 10 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 chunk 371 optimal weight: 0.0070 chunk 73 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 405 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 365 optimal weight: 6.9990 chunk 435 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN C 218 GLN C 564 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 GLN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 644 GLN A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.197968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148699 restraints weight = 63612.436| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.77 r_work: 0.3596 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 37070 Z= 0.150 Angle : 0.614 16.651 50581 Z= 0.302 Chirality : 0.044 0.344 5802 Planarity : 0.004 0.046 6393 Dihedral : 5.640 66.413 6497 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.28 % Allowed : 13.87 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.28 (0.13), residues: 4382 helix: 1.86 (0.14), residues: 1356 sheet: -0.45 (0.18), residues: 752 loop : -1.42 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 765 TYR 0.018 0.001 TYR E 385 PHE 0.031 0.002 PHE E 369 TRP 0.029 0.001 TRP C 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00338 (36940) covalent geometry : angle 0.59176 (50239) SS BOND : bond 0.00391 ( 48) SS BOND : angle 2.52312 ( 96) hydrogen bonds : bond 0.03762 ( 1468) hydrogen bonds : angle 4.95005 ( 4188) link_BETA1-4 : bond 0.00842 ( 28) link_BETA1-4 : angle 2.31611 ( 84) link_NAG-ASN : bond 0.00250 ( 54) link_NAG-ASN : angle 1.62693 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 755 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 ASN cc_start: 0.8342 (p0) cc_final: 0.8091 (p0) REVERT: C 116 SER cc_start: 0.7239 (m) cc_final: 0.6717 (p) REVERT: C 129 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7454 (tptp) REVERT: C 196 ASN cc_start: 0.7962 (t0) cc_final: 0.7721 (t0) REVERT: C 308 VAL cc_start: 0.8374 (t) cc_final: 0.7972 (p) REVERT: C 394 ASN cc_start: 0.8097 (p0) cc_final: 0.7657 (p0) REVERT: C 432 CYS cc_start: 0.5184 (OUTLIER) cc_final: 0.4657 (m) REVERT: C 514 SER cc_start: 0.7807 (p) cc_final: 0.7531 (m) REVERT: C 524 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8111 (p) REVERT: C 546 LEU cc_start: 0.8369 (tp) cc_final: 0.7996 (tt) REVERT: C 555 SER cc_start: 0.8316 (t) cc_final: 0.7827 (m) REVERT: C 574 ASP cc_start: 0.8040 (p0) cc_final: 0.7565 (t0) REVERT: C 588 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8369 (p) REVERT: C 596 SER cc_start: 0.8468 (t) cc_final: 0.8119 (p) REVERT: C 606 ASN cc_start: 0.8608 (m-40) cc_final: 0.8289 (m-40) REVERT: C 661 GLU cc_start: 0.7463 (tp30) cc_final: 0.7111 (tp30) REVERT: C 674 TYR cc_start: 0.8530 (t80) cc_final: 0.8297 (t80) REVERT: C 767 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8086 (mp) REVERT: C 773 GLU cc_start: 0.7508 (pt0) cc_final: 0.6967 (tp30) REVERT: C 776 LYS cc_start: 0.8628 (tttt) cc_final: 0.8248 (tttp) REVERT: C 803 SER cc_start: 0.8660 (t) cc_final: 0.8173 (p) REVERT: C 804 GLN cc_start: 0.8320 (mt0) cc_final: 0.7963 (mt0) REVERT: C 824 ASN cc_start: 0.8249 (m-40) cc_final: 0.7933 (m-40) REVERT: C 900 MET cc_start: 0.8464 (mmm) cc_final: 0.8255 (mtp) REVERT: C 921 LYS cc_start: 0.8529 (mmtp) cc_final: 0.8222 (mmmm) REVERT: C 947 LYS cc_start: 0.8240 (mtpp) cc_final: 0.8009 (mtpp) REVERT: C 1002 GLN cc_start: 0.8286 (tt0) cc_final: 0.8077 (tp40) REVERT: C 1019 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7435 (ttp-170) REVERT: C 1073 LYS cc_start: 0.8289 (mttt) cc_final: 0.8032 (mmmm) REVERT: C 1107 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7498 (mtt90) REVERT: C 1132 ILE cc_start: 0.8956 (tt) cc_final: 0.8735 (tt) REVERT: C 1144 GLU cc_start: 0.8351 (tp30) cc_final: 0.8040 (mm-30) REVERT: E 63 ASN cc_start: 0.7778 (m-40) cc_final: 0.7542 (m-40) REVERT: E 72 PHE cc_start: 0.7959 (t80) cc_final: 0.7457 (t80) REVERT: E 269 ASP cc_start: 0.4236 (t0) cc_final: 0.2813 (m-30) REVERT: E 308 PHE cc_start: 0.8838 (m-80) cc_final: 0.8280 (m-80) REVERT: E 314 PHE cc_start: 0.8202 (t80) cc_final: 0.7964 (t80) REVERT: E 329 GLU cc_start: 0.8411 (pt0) cc_final: 0.8016 (pp20) REVERT: E 408 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5501 (mpt) REVERT: E 455 MET cc_start: 0.8545 (ppp) cc_final: 0.8111 (ppp) REVERT: E 480 MET cc_start: 0.7745 (mtp) cc_final: 0.7219 (mtp) REVERT: E 510 TYR cc_start: 0.7016 (m-80) cc_final: 0.6710 (m-80) REVERT: E 555 PHE cc_start: 0.8132 (t80) cc_final: 0.7648 (t80) REVERT: D 144 LEU cc_start: -0.3353 (OUTLIER) cc_final: -0.3827 (tt) REVERT: D 190 MET cc_start: 0.9277 (ppp) cc_final: 0.8991 (ppp) REVERT: D 314 PHE cc_start: 0.8342 (t80) cc_final: 0.8139 (t80) REVERT: D 323 MET cc_start: 0.4267 (mmm) cc_final: 0.3497 (tpp) REVERT: D 455 MET cc_start: 0.4707 (tmm) cc_final: 0.4496 (tmm) REVERT: D 461 TRP cc_start: 0.3547 (t60) cc_final: 0.2845 (t-100) REVERT: D 579 MET cc_start: -0.0039 (OUTLIER) cc_final: -0.1018 (tpp) REVERT: B 28 TYR cc_start: 0.8174 (m-80) cc_final: 0.7697 (m-10) REVERT: B 99 ASN cc_start: 0.8295 (m-40) cc_final: 0.7999 (m110) REVERT: B 140 PHE cc_start: 0.8198 (p90) cc_final: 0.7793 (p90) REVERT: B 152 TRP cc_start: 0.5900 (m100) cc_final: 0.5612 (m100) REVERT: B 153 MET cc_start: 0.7410 (ptm) cc_final: 0.7103 (ptm) REVERT: B 216 LEU cc_start: 0.7621 (tp) cc_final: 0.7406 (mt) REVERT: B 220 PHE cc_start: 0.8234 (t80) cc_final: 0.7962 (t80) REVERT: B 244 LEU cc_start: 0.6531 (mt) cc_final: 0.6109 (mt) REVERT: B 365 TYR cc_start: 0.8056 (m-80) cc_final: 0.7717 (m-80) REVERT: B 378 LYS cc_start: 0.8367 (tptt) cc_final: 0.8008 (tmtt) REVERT: B 542 ASN cc_start: 0.8991 (t0) cc_final: 0.8727 (t0) REVERT: B 551 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8687 (m) REVERT: B 553 THR cc_start: 0.8816 (t) cc_final: 0.8501 (p) REVERT: B 555 SER cc_start: 0.8773 (t) cc_final: 0.8305 (p) REVERT: B 705 VAL cc_start: 0.8685 (t) cc_final: 0.8412 (m) REVERT: B 755 GLN cc_start: 0.7797 (mt0) cc_final: 0.7482 (pt0) REVERT: B 758 SER cc_start: 0.8972 (m) cc_final: 0.8520 (p) REVERT: B 790 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7650 (mtmm) REVERT: B 820 ASP cc_start: 0.7785 (m-30) cc_final: 0.7417 (t0) REVERT: B 860 VAL cc_start: 0.8663 (t) cc_final: 0.8411 (m) REVERT: B 934 ILE cc_start: 0.8449 (tt) cc_final: 0.8206 (tt) REVERT: B 960 ASN cc_start: 0.8026 (t0) cc_final: 0.7787 (m-40) REVERT: B 979 ASP cc_start: 0.8074 (m-30) cc_final: 0.7822 (t0) REVERT: B 1005 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7958 (mm-40) REVERT: B 1073 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7865 (ttmm) REVERT: B 1142 GLN cc_start: 0.8364 (tp40) cc_final: 0.7526 (tp40) REVERT: B 1144 GLU cc_start: 0.7916 (mp0) cc_final: 0.7531 (mp0) REVERT: A 52 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 96 GLU cc_start: 0.7260 (mp0) cc_final: 0.6581 (mt-10) REVERT: A 113 LYS cc_start: 0.8320 (mptp) cc_final: 0.8032 (mptp) REVERT: A 138 ASP cc_start: 0.8093 (m-30) cc_final: 0.7579 (t0) REVERT: A 149 ASN cc_start: 0.5966 (OUTLIER) cc_final: 0.5596 (p0) REVERT: A 190 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7660 (mtt90) REVERT: A 203 ILE cc_start: 0.8516 (mt) cc_final: 0.8210 (tt) REVERT: A 276 LEU cc_start: 0.8743 (tp) cc_final: 0.8422 (tt) REVERT: A 294 ASP cc_start: 0.7654 (p0) cc_final: 0.7416 (p0) REVERT: A 323 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8226 (p) REVERT: A 346 ARG cc_start: 0.7275 (mmm160) cc_final: 0.6730 (mmm160) REVERT: A 362 VAL cc_start: 0.7108 (OUTLIER) cc_final: 0.6827 (p) REVERT: A 539 VAL cc_start: 0.8302 (m) cc_final: 0.8040 (p) REVERT: A 574 ASP cc_start: 0.7890 (p0) cc_final: 0.7543 (t0) REVERT: A 654 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 673 SER cc_start: 0.8900 (t) cc_final: 0.8437 (m) REVERT: A 735 SER cc_start: 0.8348 (t) cc_final: 0.8079 (p) REVERT: A 736 VAL cc_start: 0.8559 (t) cc_final: 0.8307 (p) REVERT: A 823 PHE cc_start: 0.7765 (m-80) cc_final: 0.7552 (m-10) REVERT: A 878 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8557 (tp) REVERT: A 933 LYS cc_start: 0.8359 (mtmm) cc_final: 0.8024 (mttm) REVERT: A 949 GLN cc_start: 0.8481 (tp40) cc_final: 0.8086 (mm-40) REVERT: A 950 ASP cc_start: 0.7739 (t70) cc_final: 0.7343 (t0) REVERT: A 955 ASN cc_start: 0.7970 (t0) cc_final: 0.7632 (m-40) REVERT: A 957 GLN cc_start: 0.8514 (tt0) cc_final: 0.8298 (tt0) REVERT: A 963 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8768 (t) REVERT: A 981 LEU cc_start: 0.8799 (mt) cc_final: 0.8524 (mt) REVERT: A 1019 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.7401 (ttp80) REVERT: A 1038 LYS cc_start: 0.8731 (mttt) cc_final: 0.8389 (mttm) REVERT: A 1086 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7950 (mtmm) REVERT: A 1122 VAL cc_start: 0.8875 (m) cc_final: 0.8590 (p) REVERT: A 1123 SER cc_start: 0.8541 (t) cc_final: 0.8085 (p) outliers start: 127 outliers final: 86 residues processed: 833 average time/residue: 0.2590 time to fit residues: 339.7348 Evaluate side-chains 839 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 739 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 369 PHE Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1004 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 99 optimal weight: 0.5980 chunk 101 optimal weight: 0.0050 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 298 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 354 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN C 394 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN E 42 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 644 GLN B 957 GLN A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.197380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147831 restraints weight = 63843.631| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.84 r_work: 0.3591 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37070 Z= 0.170 Angle : 0.617 16.355 50581 Z= 0.304 Chirality : 0.044 0.342 5802 Planarity : 0.004 0.078 6393 Dihedral : 5.504 61.358 6497 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.43 % Allowed : 14.28 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.26 (0.13), residues: 4382 helix: 1.77 (0.14), residues: 1375 sheet: -0.41 (0.18), residues: 759 loop : -1.37 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 273 TYR 0.033 0.001 TYR D 385 PHE 0.045 0.002 PHE C 157 TRP 0.034 0.001 TRP D 473 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00384 (36940) covalent geometry : angle 0.59728 (50239) SS BOND : bond 0.00380 ( 48) SS BOND : angle 2.19335 ( 96) hydrogen bonds : bond 0.03802 ( 1468) hydrogen bonds : angle 4.92761 ( 4188) link_BETA1-4 : bond 0.00812 ( 28) link_BETA1-4 : angle 2.28055 ( 84) link_NAG-ASN : bond 0.00256 ( 54) link_NAG-ASN : angle 1.62531 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 735 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 ASN cc_start: 0.8869 (p0) cc_final: 0.8529 (p0) REVERT: C 116 SER cc_start: 0.7230 (m) cc_final: 0.6664 (p) REVERT: C 120 VAL cc_start: 0.8275 (t) cc_final: 0.7909 (m) REVERT: C 129 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7472 (tptp) REVERT: C 196 ASN cc_start: 0.7991 (t0) cc_final: 0.7736 (t0) REVERT: C 218 GLN cc_start: 0.8026 (tp40) cc_final: 0.7572 (tp40) REVERT: C 308 VAL cc_start: 0.8410 (t) cc_final: 0.7998 (p) REVERT: C 314 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7547 (tm-30) REVERT: C 394 ASN cc_start: 0.8060 (p0) cc_final: 0.7616 (p0) REVERT: C 432 CYS cc_start: 0.5215 (OUTLIER) cc_final: 0.4671 (m) REVERT: C 514 SER cc_start: 0.7824 (p) cc_final: 0.7517 (m) REVERT: C 516 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6498 (mm-30) REVERT: C 546 LEU cc_start: 0.8348 (tp) cc_final: 0.7954 (tt) REVERT: C 555 SER cc_start: 0.8381 (t) cc_final: 0.7910 (m) REVERT: C 574 ASP cc_start: 0.8064 (p0) cc_final: 0.7581 (t0) REVERT: C 596 SER cc_start: 0.8476 (t) cc_final: 0.8111 (p) REVERT: C 606 ASN cc_start: 0.8643 (m-40) cc_final: 0.8313 (m-40) REVERT: C 661 GLU cc_start: 0.7515 (tp30) cc_final: 0.7201 (tp30) REVERT: C 767 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8049 (mp) REVERT: C 773 GLU cc_start: 0.7432 (pt0) cc_final: 0.6883 (tp30) REVERT: C 775 ASP cc_start: 0.7768 (m-30) cc_final: 0.7544 (m-30) REVERT: C 776 LYS cc_start: 0.8663 (tttt) cc_final: 0.8257 (tttp) REVERT: C 804 GLN cc_start: 0.8333 (mt0) cc_final: 0.7902 (mt0) REVERT: C 824 ASN cc_start: 0.8241 (m-40) cc_final: 0.7921 (m-40) REVERT: C 900 MET cc_start: 0.8557 (mmm) cc_final: 0.8326 (mtp) REVERT: C 921 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8219 (mmmm) REVERT: C 935 GLN cc_start: 0.8434 (tt0) cc_final: 0.7965 (tt0) REVERT: C 947 LYS cc_start: 0.8260 (mtpp) cc_final: 0.8023 (mtpp) REVERT: C 957 GLN cc_start: 0.8347 (tt0) cc_final: 0.8075 (tt0) REVERT: C 990 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7492 (mm-30) REVERT: C 1002 GLN cc_start: 0.8300 (tt0) cc_final: 0.8067 (tp40) REVERT: C 1010 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7426 (mm-40) REVERT: C 1019 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7500 (ttp-170) REVERT: C 1073 LYS cc_start: 0.8270 (mttt) cc_final: 0.7979 (mmmm) REVERT: C 1107 ARG cc_start: 0.7735 (mtt90) cc_final: 0.7083 (mtt90) REVERT: C 1132 ILE cc_start: 0.8959 (tt) cc_final: 0.8741 (tt) REVERT: C 1144 GLU cc_start: 0.8381 (tp30) cc_final: 0.8088 (mm-30) REVERT: E 63 ASN cc_start: 0.7830 (m-40) cc_final: 0.7584 (m-40) REVERT: E 72 PHE cc_start: 0.7975 (t80) cc_final: 0.7479 (t80) REVERT: E 180 TYR cc_start: 0.3768 (t80) cc_final: 0.2596 (t80) REVERT: E 269 ASP cc_start: 0.4607 (t0) cc_final: 0.2965 (m-30) REVERT: E 308 PHE cc_start: 0.8878 (m-80) cc_final: 0.7915 (m-80) REVERT: E 309 LYS cc_start: 0.8276 (pttm) cc_final: 0.7455 (pttm) REVERT: E 312 GLU cc_start: 0.8994 (tt0) cc_final: 0.8541 (mt-10) REVERT: E 314 PHE cc_start: 0.8182 (t80) cc_final: 0.7960 (t80) REVERT: E 329 GLU cc_start: 0.8381 (pt0) cc_final: 0.7941 (pp20) REVERT: E 393 ARG cc_start: 0.7270 (ptp-110) cc_final: 0.6991 (ptp-110) REVERT: E 455 MET cc_start: 0.8545 (ppp) cc_final: 0.8109 (ppp) REVERT: E 480 MET cc_start: 0.7746 (mtp) cc_final: 0.7220 (mtp) REVERT: E 510 TYR cc_start: 0.7112 (m-80) cc_final: 0.6741 (m-80) REVERT: E 555 PHE cc_start: 0.8115 (t80) cc_final: 0.7601 (t80) REVERT: D 144 LEU cc_start: -0.3322 (OUTLIER) cc_final: -0.3722 (tt) REVERT: D 323 MET cc_start: 0.4219 (mmm) cc_final: 0.3465 (tpp) REVERT: D 461 TRP cc_start: 0.3574 (t60) cc_final: 0.2912 (t-100) REVERT: D 476 LYS cc_start: 0.2367 (mmmm) cc_final: 0.1477 (ttmm) REVERT: D 562 LYS cc_start: 0.7514 (mttm) cc_final: 0.7181 (ttmm) REVERT: D 579 MET cc_start: 0.0053 (OUTLIER) cc_final: -0.0959 (tpp) REVERT: B 28 TYR cc_start: 0.8194 (m-80) cc_final: 0.7701 (m-10) REVERT: B 99 ASN cc_start: 0.8406 (m-40) cc_final: 0.8115 (m110) REVERT: B 140 PHE cc_start: 0.8202 (p90) cc_final: 0.7774 (p90) REVERT: B 152 TRP cc_start: 0.5900 (m100) cc_final: 0.5089 (m100) REVERT: B 153 MET cc_start: 0.7420 (ptm) cc_final: 0.7133 (ptm) REVERT: B 216 LEU cc_start: 0.7683 (tp) cc_final: 0.7448 (mt) REVERT: B 220 PHE cc_start: 0.8161 (t80) cc_final: 0.7889 (t80) REVERT: B 244 LEU cc_start: 0.6539 (mt) cc_final: 0.6137 (mt) REVERT: B 365 TYR cc_start: 0.8164 (m-80) cc_final: 0.7808 (m-80) REVERT: B 378 LYS cc_start: 0.8408 (tptt) cc_final: 0.8180 (tmtt) REVERT: B 386 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8572 (ptpt) REVERT: B 542 ASN cc_start: 0.8977 (t0) cc_final: 0.8753 (t0) REVERT: B 551 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8679 (m) REVERT: B 553 THR cc_start: 0.8829 (t) cc_final: 0.8500 (p) REVERT: B 555 SER cc_start: 0.8801 (t) cc_final: 0.8318 (p) REVERT: B 705 VAL cc_start: 0.8694 (t) cc_final: 0.8417 (m) REVERT: B 740 MET cc_start: 0.8505 (tpp) cc_final: 0.8231 (ttm) REVERT: B 755 GLN cc_start: 0.7853 (mt0) cc_final: 0.7523 (pt0) REVERT: B 758 SER cc_start: 0.8972 (m) cc_final: 0.8533 (p) REVERT: B 790 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7668 (mtmm) REVERT: B 820 ASP cc_start: 0.7831 (m-30) cc_final: 0.7462 (t0) REVERT: B 860 VAL cc_start: 0.8710 (t) cc_final: 0.8408 (m) REVERT: B 904 TYR cc_start: 0.7840 (m-10) cc_final: 0.7423 (m-10) REVERT: B 934 ILE cc_start: 0.8440 (tt) cc_final: 0.8180 (tt) REVERT: B 979 ASP cc_start: 0.8121 (m-30) cc_final: 0.7828 (t0) REVERT: B 1005 GLN cc_start: 0.8264 (mm-40) cc_final: 0.8010 (mm-40) REVERT: B 1073 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7895 (ttmm) REVERT: B 1142 GLN cc_start: 0.8337 (tp40) cc_final: 0.7499 (tp40) REVERT: A 52 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 96 GLU cc_start: 0.7245 (mp0) cc_final: 0.6636 (mt-10) REVERT: A 113 LYS cc_start: 0.8497 (mptp) cc_final: 0.8180 (mptp) REVERT: A 138 ASP cc_start: 0.8099 (m-30) cc_final: 0.7585 (t0) REVERT: A 149 ASN cc_start: 0.6006 (OUTLIER) cc_final: 0.5611 (p0) REVERT: A 154 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 190 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7944 (mtt90) REVERT: A 203 ILE cc_start: 0.8516 (mt) cc_final: 0.8177 (tt) REVERT: A 276 LEU cc_start: 0.8744 (tp) cc_final: 0.8447 (tt) REVERT: A 294 ASP cc_start: 0.7671 (p0) cc_final: 0.7440 (p0) REVERT: A 323 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8237 (p) REVERT: A 346 ARG cc_start: 0.7252 (mmm160) cc_final: 0.6721 (mmm160) REVERT: A 362 VAL cc_start: 0.6861 (OUTLIER) cc_final: 0.6653 (p) REVERT: A 539 VAL cc_start: 0.8320 (m) cc_final: 0.8057 (p) REVERT: A 574 ASP cc_start: 0.7928 (p0) cc_final: 0.7558 (t0) REVERT: A 654 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 673 SER cc_start: 0.8901 (t) cc_final: 0.8420 (m) REVERT: A 725 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7303 (tt0) REVERT: A 735 SER cc_start: 0.8426 (t) cc_final: 0.8097 (p) REVERT: A 736 VAL cc_start: 0.8588 (t) cc_final: 0.8313 (p) REVERT: A 878 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8552 (tp) REVERT: A 933 LYS cc_start: 0.8335 (mtmm) cc_final: 0.7984 (mttm) REVERT: A 949 GLN cc_start: 0.8534 (tp40) cc_final: 0.8154 (mm-40) REVERT: A 950 ASP cc_start: 0.7725 (t70) cc_final: 0.7316 (t0) REVERT: A 955 ASN cc_start: 0.8035 (t0) cc_final: 0.7681 (m-40) REVERT: A 957 GLN cc_start: 0.8510 (tt0) cc_final: 0.8304 (tt0) REVERT: A 963 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8802 (t) REVERT: A 981 LEU cc_start: 0.8792 (mt) cc_final: 0.8569 (mt) REVERT: A 988 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7355 (mt-10) REVERT: A 1019 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.7419 (ttp80) REVERT: A 1038 LYS cc_start: 0.8765 (mttt) cc_final: 0.8409 (mttm) REVERT: A 1086 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7929 (mtmm) REVERT: A 1122 VAL cc_start: 0.8885 (m) cc_final: 0.8604 (p) REVERT: A 1123 SER cc_start: 0.8560 (t) cc_final: 0.8087 (p) outliers start: 133 outliers final: 99 residues processed: 826 average time/residue: 0.2570 time to fit residues: 335.0019 Evaluate side-chains 841 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 730 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 369 PHE Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1004 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 51 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 197 optimal weight: 0.0270 chunk 262 optimal weight: 1.9990 chunk 438 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN E 42 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 183 GLN B 487 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.198111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.148647 restraints weight = 63849.635| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.84 r_work: 0.3599 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37070 Z= 0.139 Angle : 0.606 16.354 50581 Z= 0.298 Chirality : 0.044 0.340 5802 Planarity : 0.004 0.075 6393 Dihedral : 5.328 55.461 6497 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.00 % Allowed : 14.75 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.13), residues: 4382 helix: 1.85 (0.14), residues: 1375 sheet: -0.37 (0.18), residues: 763 loop : -1.33 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 273 TYR 0.059 0.001 TYR D 385 PHE 0.037 0.002 PHE C 32 TRP 0.043 0.001 TRP D 473 HIS 0.010 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00314 (36940) covalent geometry : angle 0.58785 (50239) SS BOND : bond 0.00371 ( 48) SS BOND : angle 2.04970 ( 96) hydrogen bonds : bond 0.03619 ( 1468) hydrogen bonds : angle 4.87070 ( 4188) link_BETA1-4 : bond 0.00819 ( 28) link_BETA1-4 : angle 2.26698 ( 84) link_NAG-ASN : bond 0.00229 ( 54) link_NAG-ASN : angle 1.55145 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 727 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 PHE cc_start: 0.8302 (m-10) cc_final: 0.8074 (m-10) REVERT: C 116 SER cc_start: 0.7120 (m) cc_final: 0.6622 (p) REVERT: C 120 VAL cc_start: 0.8306 (t) cc_final: 0.7942 (m) REVERT: C 129 LYS cc_start: 0.8019 (ttmt) cc_final: 0.7501 (tptp) REVERT: C 196 ASN cc_start: 0.7901 (t0) cc_final: 0.7647 (t0) REVERT: C 218 GLN cc_start: 0.7807 (tp40) cc_final: 0.7100 (tp40) REVERT: C 308 VAL cc_start: 0.8448 (t) cc_final: 0.8013 (p) REVERT: C 341 VAL cc_start: 0.8616 (m) cc_final: 0.8415 (p) REVERT: C 394 ASN cc_start: 0.7923 (p0) cc_final: 0.7575 (p0) REVERT: C 432 CYS cc_start: 0.5128 (OUTLIER) cc_final: 0.4570 (m) REVERT: C 514 SER cc_start: 0.7851 (p) cc_final: 0.7517 (m) REVERT: C 530 SER cc_start: 0.8344 (m) cc_final: 0.7861 (t) REVERT: C 546 LEU cc_start: 0.8344 (tp) cc_final: 0.7969 (tt) REVERT: C 555 SER cc_start: 0.8368 (t) cc_final: 0.7857 (m) REVERT: C 558 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7726 (mmmm) REVERT: C 574 ASP cc_start: 0.8060 (p0) cc_final: 0.7595 (t0) REVERT: C 588 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 596 SER cc_start: 0.8452 (t) cc_final: 0.8113 (p) REVERT: C 661 GLU cc_start: 0.7520 (tp30) cc_final: 0.7231 (tp30) REVERT: C 767 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 773 GLU cc_start: 0.7420 (pt0) cc_final: 0.6902 (tp30) REVERT: C 776 LYS cc_start: 0.8660 (tttt) cc_final: 0.8286 (tttp) REVERT: C 803 SER cc_start: 0.8583 (t) cc_final: 0.8013 (p) REVERT: C 804 GLN cc_start: 0.8267 (mt0) cc_final: 0.7800 (mt0) REVERT: C 824 ASN cc_start: 0.8246 (m-40) cc_final: 0.7922 (m-40) REVERT: C 900 MET cc_start: 0.8544 (mmm) cc_final: 0.8305 (mtp) REVERT: C 921 LYS cc_start: 0.8540 (mmtp) cc_final: 0.8236 (mmmm) REVERT: C 935 GLN cc_start: 0.8422 (tt0) cc_final: 0.7916 (tt0) REVERT: C 947 LYS cc_start: 0.8209 (mtpp) cc_final: 0.7984 (mtpp) REVERT: C 990 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 1002 GLN cc_start: 0.8273 (tt0) cc_final: 0.8044 (tp40) REVERT: C 1019 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7516 (ttp-170) REVERT: C 1038 LYS cc_start: 0.8640 (mttt) cc_final: 0.8249 (mttt) REVERT: C 1073 LYS cc_start: 0.8264 (mttt) cc_final: 0.8001 (mmmm) REVERT: C 1107 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7067 (mtt90) REVERT: C 1132 ILE cc_start: 0.8938 (tt) cc_final: 0.8729 (tt) REVERT: C 1144 GLU cc_start: 0.8345 (tp30) cc_final: 0.8075 (mm-30) REVERT: E 26 LYS cc_start: 0.6718 (mmmm) cc_final: 0.5560 (mttm) REVERT: E 63 ASN cc_start: 0.7782 (m-40) cc_final: 0.7547 (m-40) REVERT: E 72 PHE cc_start: 0.7940 (t80) cc_final: 0.7443 (t80) REVERT: E 308 PHE cc_start: 0.8955 (m-80) cc_final: 0.7952 (m-80) REVERT: E 309 LYS cc_start: 0.8289 (pttm) cc_final: 0.7454 (pttm) REVERT: E 312 GLU cc_start: 0.8993 (tt0) cc_final: 0.8459 (mt-10) REVERT: E 315 PHE cc_start: 0.6955 (m-80) cc_final: 0.6119 (m-80) REVERT: E 329 GLU cc_start: 0.8386 (pt0) cc_final: 0.7947 (pp20) REVERT: E 360 MET cc_start: -0.0439 (ttt) cc_final: -0.0905 (ttt) REVERT: E 455 MET cc_start: 0.8512 (ppp) cc_final: 0.8092 (ppp) REVERT: E 480 MET cc_start: 0.7733 (mtp) cc_final: 0.7204 (mtp) REVERT: E 510 TYR cc_start: 0.7125 (m-80) cc_final: 0.6724 (m-80) REVERT: E 555 PHE cc_start: 0.8016 (t80) cc_final: 0.7507 (t80) REVERT: D 144 LEU cc_start: -0.3254 (OUTLIER) cc_final: -0.3737 (tt) REVERT: D 190 MET cc_start: 0.9289 (ppp) cc_final: 0.9074 (ppp) REVERT: D 323 MET cc_start: 0.4119 (mmm) cc_final: 0.3649 (tpp) REVERT: D 461 TRP cc_start: 0.3434 (t60) cc_final: 0.2735 (t-100) REVERT: D 476 LYS cc_start: 0.2306 (mmmm) cc_final: 0.1547 (ttmm) REVERT: D 481 LYS cc_start: 0.0475 (tmtt) cc_final: 0.0108 (tttt) REVERT: D 562 LYS cc_start: 0.7450 (mttm) cc_final: 0.7119 (ttmm) REVERT: D 579 MET cc_start: 0.0100 (OUTLIER) cc_final: -0.0849 (tpp) REVERT: B 99 ASN cc_start: 0.8399 (m-40) cc_final: 0.8130 (m110) REVERT: B 140 PHE cc_start: 0.8183 (p90) cc_final: 0.7781 (p90) REVERT: B 152 TRP cc_start: 0.5878 (m100) cc_final: 0.5073 (m100) REVERT: B 153 MET cc_start: 0.7457 (ptm) cc_final: 0.7159 (ptm) REVERT: B 220 PHE cc_start: 0.8213 (t80) cc_final: 0.7878 (t80) REVERT: B 244 LEU cc_start: 0.6522 (mt) cc_final: 0.6140 (mt) REVERT: B 365 TYR cc_start: 0.8121 (m-80) cc_final: 0.7805 (m-80) REVERT: B 378 LYS cc_start: 0.8436 (tptt) cc_final: 0.8200 (tmtt) REVERT: B 386 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8575 (ptpt) REVERT: B 542 ASN cc_start: 0.8984 (t0) cc_final: 0.8769 (t0) REVERT: B 551 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8698 (m) REVERT: B 553 THR cc_start: 0.8835 (t) cc_final: 0.8533 (p) REVERT: B 555 SER cc_start: 0.8768 (t) cc_final: 0.8309 (p) REVERT: B 705 VAL cc_start: 0.8681 (t) cc_final: 0.8408 (m) REVERT: B 740 MET cc_start: 0.8436 (tpp) cc_final: 0.8128 (ttm) REVERT: B 758 SER cc_start: 0.8966 (m) cc_final: 0.8533 (p) REVERT: B 775 ASP cc_start: 0.7882 (t0) cc_final: 0.7533 (m-30) REVERT: B 790 LYS cc_start: 0.8022 (mtpp) cc_final: 0.7659 (mtmm) REVERT: B 820 ASP cc_start: 0.7814 (m-30) cc_final: 0.7444 (t0) REVERT: B 860 VAL cc_start: 0.8702 (t) cc_final: 0.8393 (m) REVERT: B 904 TYR cc_start: 0.7830 (m-10) cc_final: 0.7430 (m-10) REVERT: B 921 LYS cc_start: 0.8383 (mmtp) cc_final: 0.8162 (mmtp) REVERT: B 934 ILE cc_start: 0.8450 (tt) cc_final: 0.8099 (tt) REVERT: B 979 ASP cc_start: 0.8081 (m-30) cc_final: 0.7849 (t0) REVERT: B 1005 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7992 (mm-40) REVERT: B 1073 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7935 (ttmm) REVERT: B 1142 GLN cc_start: 0.8362 (tp40) cc_final: 0.7533 (tp40) REVERT: A 41 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7922 (mmmm) REVERT: A 52 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 68 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7507 (mt) REVERT: A 96 GLU cc_start: 0.7272 (mp0) cc_final: 0.6651 (mt-10) REVERT: A 113 LYS cc_start: 0.8508 (mptp) cc_final: 0.8188 (mptp) REVERT: A 138 ASP cc_start: 0.8084 (m-30) cc_final: 0.7580 (t0) REVERT: A 149 ASN cc_start: 0.5999 (OUTLIER) cc_final: 0.5640 (p0) REVERT: A 154 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7980 (tm-30) REVERT: A 203 ILE cc_start: 0.8498 (mt) cc_final: 0.8164 (tt) REVERT: A 276 LEU cc_start: 0.8725 (tp) cc_final: 0.8430 (tt) REVERT: A 294 ASP cc_start: 0.7618 (p0) cc_final: 0.7388 (p0) REVERT: A 323 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 346 ARG cc_start: 0.7225 (mmm160) cc_final: 0.6711 (mmm160) REVERT: A 362 VAL cc_start: 0.6910 (OUTLIER) cc_final: 0.6706 (p) REVERT: A 539 VAL cc_start: 0.8316 (m) cc_final: 0.8060 (p) REVERT: A 574 ASP cc_start: 0.7890 (p0) cc_final: 0.7532 (t0) REVERT: A 654 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7429 (mt-10) REVERT: A 673 SER cc_start: 0.8900 (t) cc_final: 0.8410 (m) REVERT: A 725 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7344 (tt0) REVERT: A 735 SER cc_start: 0.8396 (t) cc_final: 0.8068 (p) REVERT: A 736 VAL cc_start: 0.8578 (t) cc_final: 0.8296 (p) REVERT: A 878 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8569 (tp) REVERT: A 933 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7991 (mttm) REVERT: A 949 GLN cc_start: 0.8531 (tp40) cc_final: 0.8163 (mm-40) REVERT: A 950 ASP cc_start: 0.7698 (t70) cc_final: 0.7306 (t0) REVERT: A 955 ASN cc_start: 0.7981 (t0) cc_final: 0.7638 (m-40) REVERT: A 957 GLN cc_start: 0.8508 (tt0) cc_final: 0.8289 (tt0) REVERT: A 963 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8795 (t) REVERT: A 988 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7307 (mt-10) REVERT: A 1019 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7405 (ttp80) REVERT: A 1038 LYS cc_start: 0.8789 (mttt) cc_final: 0.8416 (mttm) REVERT: A 1086 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7944 (mtmm) REVERT: A 1122 VAL cc_start: 0.8876 (m) cc_final: 0.8588 (p) REVERT: A 1123 SER cc_start: 0.8519 (t) cc_final: 0.8063 (p) outliers start: 116 outliers final: 91 residues processed: 804 average time/residue: 0.2674 time to fit residues: 337.3879 Evaluate side-chains 821 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 718 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1004 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 147 optimal weight: 20.0000 chunk 372 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 171 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 402 optimal weight: 0.8980 chunk 388 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN E 42 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.196941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147389 restraints weight = 63950.320| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.83 r_work: 0.3580 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37070 Z= 0.187 Angle : 0.631 16.665 50581 Z= 0.312 Chirality : 0.045 0.348 5802 Planarity : 0.004 0.071 6393 Dihedral : 5.337 51.973 6497 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.02 % Allowed : 15.03 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.19 (0.13), residues: 4382 helix: 1.84 (0.14), residues: 1375 sheet: -0.37 (0.18), residues: 756 loop : -1.34 (0.12), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 273 TYR 0.048 0.001 TYR D 385 PHE 0.032 0.002 PHE C 140 TRP 0.041 0.002 TRP D 473 HIS 0.005 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00424 (36940) covalent geometry : angle 0.61268 (50239) SS BOND : bond 0.00398 ( 48) SS BOND : angle 2.17301 ( 96) hydrogen bonds : bond 0.03808 ( 1468) hydrogen bonds : angle 4.91764 ( 4188) link_BETA1-4 : bond 0.00868 ( 28) link_BETA1-4 : angle 2.29171 ( 84) link_NAG-ASN : bond 0.00265 ( 54) link_NAG-ASN : angle 1.59896 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 746 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: C 116 SER cc_start: 0.7151 (m) cc_final: 0.6689 (p) REVERT: C 120 VAL cc_start: 0.8292 (t) cc_final: 0.7930 (m) REVERT: C 129 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7520 (tptp) REVERT: C 196 ASN cc_start: 0.7925 (t0) cc_final: 0.7671 (t0) REVERT: C 218 GLN cc_start: 0.7708 (tp40) cc_final: 0.7322 (tp40) REVERT: C 308 VAL cc_start: 0.8454 (t) cc_final: 0.8007 (p) REVERT: C 394 ASN cc_start: 0.7928 (p0) cc_final: 0.7573 (p0) REVERT: C 432 CYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4668 (m) REVERT: C 514 SER cc_start: 0.8089 (p) cc_final: 0.7738 (m) REVERT: C 530 SER cc_start: 0.8393 (m) cc_final: 0.7917 (t) REVERT: C 546 LEU cc_start: 0.8349 (tp) cc_final: 0.7975 (tt) REVERT: C 555 SER cc_start: 0.8360 (t) cc_final: 0.7896 (m) REVERT: C 558 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7753 (mmmm) REVERT: C 574 ASP cc_start: 0.8055 (p0) cc_final: 0.7612 (t0) REVERT: C 596 SER cc_start: 0.8475 (t) cc_final: 0.8130 (p) REVERT: C 661 GLU cc_start: 0.7533 (tp30) cc_final: 0.7173 (tp30) REVERT: C 767 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8085 (mp) REVERT: C 773 GLU cc_start: 0.7576 (pt0) cc_final: 0.6987 (tp30) REVERT: C 776 LYS cc_start: 0.8670 (tttt) cc_final: 0.8283 (tttp) REVERT: C 803 SER cc_start: 0.8635 (t) cc_final: 0.8086 (p) REVERT: C 804 GLN cc_start: 0.8314 (mt0) cc_final: 0.7897 (mt0) REVERT: C 824 ASN cc_start: 0.8268 (m-40) cc_final: 0.7951 (m-40) REVERT: C 900 MET cc_start: 0.8560 (mmm) cc_final: 0.8332 (mtp) REVERT: C 921 LYS cc_start: 0.8559 (mmtp) cc_final: 0.8201 (mmmm) REVERT: C 947 LYS cc_start: 0.8242 (mtpp) cc_final: 0.8007 (mtpp) REVERT: C 990 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 1002 GLN cc_start: 0.8294 (tt0) cc_final: 0.8074 (tp40) REVERT: C 1019 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7581 (ttp-170) REVERT: C 1038 LYS cc_start: 0.8635 (mttt) cc_final: 0.8259 (mttt) REVERT: C 1073 LYS cc_start: 0.8288 (mttt) cc_final: 0.8015 (mmmm) REVERT: C 1107 ARG cc_start: 0.7729 (mtt90) cc_final: 0.7101 (mtt90) REVERT: C 1132 ILE cc_start: 0.8954 (tt) cc_final: 0.8746 (tt) REVERT: C 1144 GLU cc_start: 0.8350 (tp30) cc_final: 0.8102 (mm-30) REVERT: E 28 PHE cc_start: 0.7590 (t80) cc_final: 0.7331 (t80) REVERT: E 63 ASN cc_start: 0.7795 (m-40) cc_final: 0.7565 (m-40) REVERT: E 72 PHE cc_start: 0.7919 (t80) cc_final: 0.7426 (t80) REVERT: E 117 ASN cc_start: 0.9044 (m110) cc_final: 0.8781 (m110) REVERT: E 180 TYR cc_start: 0.3945 (t80) cc_final: 0.1613 (t80) REVERT: E 308 PHE cc_start: 0.8972 (m-80) cc_final: 0.8384 (m-80) REVERT: E 329 GLU cc_start: 0.8385 (pt0) cc_final: 0.7900 (pp20) REVERT: E 360 MET cc_start: -0.0294 (ttt) cc_final: -0.0836 (ttt) REVERT: E 455 MET cc_start: 0.8520 (ppp) cc_final: 0.8096 (ppp) REVERT: E 480 MET cc_start: 0.7737 (mtp) cc_final: 0.7208 (mtp) REVERT: E 510 TYR cc_start: 0.6958 (m-80) cc_final: 0.6637 (m-80) REVERT: E 525 PHE cc_start: 0.5826 (m-10) cc_final: 0.5482 (m-10) REVERT: E 555 PHE cc_start: 0.8044 (t80) cc_final: 0.7532 (t80) REVERT: D 79 LEU cc_start: 0.8234 (mt) cc_final: 0.7879 (pp) REVERT: D 144 LEU cc_start: -0.3281 (OUTLIER) cc_final: -0.3727 (tt) REVERT: D 323 MET cc_start: 0.4452 (mmm) cc_final: 0.3799 (tpp) REVERT: D 397 ASN cc_start: 0.4066 (m-40) cc_final: 0.3844 (m110) REVERT: D 461 TRP cc_start: 0.3423 (t60) cc_final: 0.2773 (t-100) REVERT: D 474 MET cc_start: 0.3715 (tpp) cc_final: 0.3005 (tpt) REVERT: D 476 LYS cc_start: 0.2501 (mmmm) cc_final: 0.1814 (ttmm) REVERT: D 579 MET cc_start: 0.0223 (OUTLIER) cc_final: -0.0395 (tpp) REVERT: B 99 ASN cc_start: 0.8477 (m-40) cc_final: 0.8218 (m110) REVERT: B 140 PHE cc_start: 0.8218 (p90) cc_final: 0.7775 (p90) REVERT: B 152 TRP cc_start: 0.5848 (m100) cc_final: 0.5053 (m100) REVERT: B 153 MET cc_start: 0.7443 (ptm) cc_final: 0.7147 (ptm) REVERT: B 220 PHE cc_start: 0.8296 (t80) cc_final: 0.7945 (t80) REVERT: B 244 LEU cc_start: 0.6520 (mt) cc_final: 0.6131 (mt) REVERT: B 365 TYR cc_start: 0.8182 (m-80) cc_final: 0.7825 (m-80) REVERT: B 378 LYS cc_start: 0.8441 (tptt) cc_final: 0.8185 (tmtt) REVERT: B 386 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8581 (ptpt) REVERT: B 542 ASN cc_start: 0.8971 (t0) cc_final: 0.8748 (t0) REVERT: B 551 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8683 (m) REVERT: B 553 THR cc_start: 0.8858 (t) cc_final: 0.8550 (p) REVERT: B 555 SER cc_start: 0.8767 (t) cc_final: 0.8310 (p) REVERT: B 584 ILE cc_start: 0.8378 (mt) cc_final: 0.8160 (mt) REVERT: B 705 VAL cc_start: 0.8689 (t) cc_final: 0.8419 (m) REVERT: B 758 SER cc_start: 0.8999 (m) cc_final: 0.8527 (p) REVERT: B 759 PHE cc_start: 0.8091 (m-10) cc_final: 0.7739 (m-80) REVERT: B 790 LYS cc_start: 0.8027 (mtpp) cc_final: 0.7681 (mtmm) REVERT: B 820 ASP cc_start: 0.7890 (m-30) cc_final: 0.7529 (t0) REVERT: B 860 VAL cc_start: 0.8708 (t) cc_final: 0.8390 (m) REVERT: B 904 TYR cc_start: 0.7852 (m-10) cc_final: 0.7450 (m-10) REVERT: B 934 ILE cc_start: 0.8458 (tt) cc_final: 0.8195 (tt) REVERT: B 957 GLN cc_start: 0.8437 (tt0) cc_final: 0.7968 (tt0) REVERT: B 964 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8475 (tttm) REVERT: B 979 ASP cc_start: 0.8091 (m-30) cc_final: 0.7885 (t0) REVERT: B 1005 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7966 (mm-40) REVERT: B 1073 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7946 (ttmm) REVERT: B 1142 GLN cc_start: 0.8360 (tp40) cc_final: 0.7546 (tp40) REVERT: A 52 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 96 GLU cc_start: 0.7265 (mp0) cc_final: 0.6723 (mt-10) REVERT: A 113 LYS cc_start: 0.8543 (mptp) cc_final: 0.8224 (mptp) REVERT: A 138 ASP cc_start: 0.8083 (m-30) cc_final: 0.7584 (t0) REVERT: A 149 ASN cc_start: 0.6002 (OUTLIER) cc_final: 0.5591 (p0) REVERT: A 203 ILE cc_start: 0.8510 (mt) cc_final: 0.8184 (tt) REVERT: A 276 LEU cc_start: 0.8774 (tp) cc_final: 0.8454 (tt) REVERT: A 294 ASP cc_start: 0.7681 (p0) cc_final: 0.7452 (p0) REVERT: A 346 ARG cc_start: 0.7263 (mmm160) cc_final: 0.6741 (mmm160) REVERT: A 362 VAL cc_start: 0.6941 (OUTLIER) cc_final: 0.6694 (p) REVERT: A 539 VAL cc_start: 0.8343 (m) cc_final: 0.8075 (p) REVERT: A 574 ASP cc_start: 0.7916 (p0) cc_final: 0.7548 (t0) REVERT: A 654 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 663 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: A 673 SER cc_start: 0.8905 (t) cc_final: 0.8409 (m) REVERT: A 735 SER cc_start: 0.8420 (t) cc_final: 0.8067 (p) REVERT: A 736 VAL cc_start: 0.8591 (t) cc_final: 0.8301 (p) REVERT: A 878 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8580 (tp) REVERT: A 918 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7602 (mt-10) REVERT: A 933 LYS cc_start: 0.8376 (mtmm) cc_final: 0.8036 (mttm) REVERT: A 949 GLN cc_start: 0.8545 (tp40) cc_final: 0.8172 (mm-40) REVERT: A 950 ASP cc_start: 0.7736 (t70) cc_final: 0.7339 (t0) REVERT: A 955 ASN cc_start: 0.7999 (t0) cc_final: 0.7690 (m-40) REVERT: A 957 GLN cc_start: 0.8532 (tt0) cc_final: 0.8323 (tt0) REVERT: A 963 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8793 (t) REVERT: A 988 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 1019 ARG cc_start: 0.7716 (ttp-110) cc_final: 0.7471 (ttp80) REVERT: A 1031 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7346 (mp0) REVERT: A 1038 LYS cc_start: 0.8782 (mttt) cc_final: 0.8407 (mttm) REVERT: A 1072 GLU cc_start: 0.8156 (pm20) cc_final: 0.7921 (pm20) REVERT: A 1086 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7933 (mtmm) REVERT: A 1122 VAL cc_start: 0.8888 (m) cc_final: 0.8365 (p) REVERT: A 1123 SER cc_start: 0.8557 (t) cc_final: 0.8317 (m) outliers start: 117 outliers final: 91 residues processed: 824 average time/residue: 0.2589 time to fit residues: 335.3776 Evaluate side-chains 833 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 732 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1004 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 296 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 369 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 256 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN E 42 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.197340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147886 restraints weight = 63868.988| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.83 r_work: 0.3588 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 37070 Z= 0.170 Angle : 0.645 16.417 50581 Z= 0.321 Chirality : 0.045 0.342 5802 Planarity : 0.004 0.075 6393 Dihedral : 5.291 52.056 6496 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.92 % Allowed : 15.42 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -0.16 (0.13), residues: 4382 helix: 1.85 (0.14), residues: 1371 sheet: -0.38 (0.18), residues: 773 loop : -1.30 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 273 TYR 0.046 0.001 TYR D 385 PHE 0.032 0.002 PHE E 369 TRP 0.044 0.002 TRP D 473 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00389 (36940) covalent geometry : angle 0.62592 (50239) SS BOND : bond 0.00406 ( 48) SS BOND : angle 2.31239 ( 96) hydrogen bonds : bond 0.03754 ( 1468) hydrogen bonds : angle 4.90832 ( 4188) link_BETA1-4 : bond 0.00814 ( 28) link_BETA1-4 : angle 2.25595 ( 84) link_NAG-ASN : bond 0.00243 ( 54) link_NAG-ASN : angle 1.62058 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8764 Ramachandran restraints generated. 4382 Oldfield, 0 Emsley, 4382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 725 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 TRP cc_start: 0.7674 (m-90) cc_final: 0.6918 (m-90) REVERT: C 116 SER cc_start: 0.7109 (m) cc_final: 0.6644 (p) REVERT: C 120 VAL cc_start: 0.8285 (t) cc_final: 0.7898 (m) REVERT: C 129 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7441 (tptt) REVERT: C 196 ASN cc_start: 0.7926 (t0) cc_final: 0.7671 (t0) REVERT: C 218 GLN cc_start: 0.7699 (tp40) cc_final: 0.7306 (tp40) REVERT: C 308 VAL cc_start: 0.8459 (t) cc_final: 0.8022 (p) REVERT: C 319 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7425 (ttp-110) REVERT: C 394 ASN cc_start: 0.7856 (p0) cc_final: 0.7512 (p0) REVERT: C 432 CYS cc_start: 0.5185 (OUTLIER) cc_final: 0.4603 (m) REVERT: C 514 SER cc_start: 0.8089 (p) cc_final: 0.7732 (m) REVERT: C 530 SER cc_start: 0.8392 (m) cc_final: 0.7908 (t) REVERT: C 546 LEU cc_start: 0.8337 (tp) cc_final: 0.7966 (tt) REVERT: C 555 SER cc_start: 0.8335 (t) cc_final: 0.7760 (m) REVERT: C 558 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7757 (mmmm) REVERT: C 574 ASP cc_start: 0.8006 (p0) cc_final: 0.7581 (t0) REVERT: C 596 SER cc_start: 0.8484 (t) cc_final: 0.8130 (p) REVERT: C 606 ASN cc_start: 0.8538 (m-40) cc_final: 0.8171 (m-40) REVERT: C 661 GLU cc_start: 0.7545 (tp30) cc_final: 0.7176 (tp30) REVERT: C 767 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8055 (mp) REVERT: C 773 GLU cc_start: 0.7442 (pt0) cc_final: 0.6875 (tp30) REVERT: C 775 ASP cc_start: 0.7795 (m-30) cc_final: 0.7579 (m-30) REVERT: C 776 LYS cc_start: 0.8686 (tttt) cc_final: 0.8270 (tttp) REVERT: C 803 SER cc_start: 0.8590 (t) cc_final: 0.8052 (p) REVERT: C 804 GLN cc_start: 0.8308 (mt0) cc_final: 0.7886 (mt0) REVERT: C 824 ASN cc_start: 0.8266 (m-40) cc_final: 0.7955 (m-40) REVERT: C 900 MET cc_start: 0.8550 (mmm) cc_final: 0.8332 (mtp) REVERT: C 921 LYS cc_start: 0.8548 (mmtp) cc_final: 0.8165 (mmmm) REVERT: C 947 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7982 (mtpp) REVERT: C 990 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7534 (mm-30) REVERT: C 1002 GLN cc_start: 0.8269 (tt0) cc_final: 0.8046 (tp40) REVERT: C 1010 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7413 (mm-40) REVERT: C 1019 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7621 (ttp-170) REVERT: C 1038 LYS cc_start: 0.8632 (mttt) cc_final: 0.8244 (mttt) REVERT: C 1073 LYS cc_start: 0.8278 (mttt) cc_final: 0.7989 (mmmm) REVERT: C 1107 ARG cc_start: 0.7728 (mtt90) cc_final: 0.7086 (mtt90) REVERT: C 1132 ILE cc_start: 0.8928 (tt) cc_final: 0.8723 (tt) REVERT: C 1144 GLU cc_start: 0.8331 (tp30) cc_final: 0.8082 (mm-30) REVERT: E 28 PHE cc_start: 0.7554 (t80) cc_final: 0.7299 (t80) REVERT: E 63 ASN cc_start: 0.7801 (m-40) cc_final: 0.7566 (m-40) REVERT: E 72 PHE cc_start: 0.7929 (t80) cc_final: 0.7421 (t80) REVERT: E 114 LYS cc_start: 0.8784 (tptt) cc_final: 0.8544 (tptt) REVERT: E 117 ASN cc_start: 0.9017 (m110) cc_final: 0.8770 (m110) REVERT: E 308 PHE cc_start: 0.8889 (m-80) cc_final: 0.8244 (m-80) REVERT: E 329 GLU cc_start: 0.8361 (pt0) cc_final: 0.7870 (pp20) REVERT: E 360 MET cc_start: -0.0487 (ttt) cc_final: -0.0911 (ttt) REVERT: E 455 MET cc_start: 0.8514 (ppp) cc_final: 0.8082 (ppp) REVERT: E 480 MET cc_start: 0.7740 (mtp) cc_final: 0.7213 (mtp) REVERT: E 510 TYR cc_start: 0.6869 (m-80) cc_final: 0.6578 (m-80) REVERT: E 525 PHE cc_start: 0.5859 (m-10) cc_final: 0.5520 (m-10) REVERT: E 555 PHE cc_start: 0.8028 (t80) cc_final: 0.7519 (t80) REVERT: D 74 LYS cc_start: 0.8648 (tppp) cc_final: 0.8435 (tppp) REVERT: D 79 LEU cc_start: 0.8228 (mt) cc_final: 0.7894 (pp) REVERT: D 144 LEU cc_start: -0.3298 (OUTLIER) cc_final: -0.3741 (tt) REVERT: D 323 MET cc_start: 0.4428 (mmm) cc_final: 0.3835 (tpp) REVERT: D 461 TRP cc_start: 0.3514 (t60) cc_final: 0.2811 (t-100) REVERT: D 474 MET cc_start: 0.3981 (tpp) cc_final: 0.3439 (tpt) REVERT: D 476 LYS cc_start: 0.2636 (mmmm) cc_final: 0.1915 (ttmm) REVERT: D 488 VAL cc_start: 0.7295 (m) cc_final: 0.7067 (m) REVERT: D 579 MET cc_start: 0.0134 (OUTLIER) cc_final: -0.0926 (tpp) REVERT: B 99 ASN cc_start: 0.8461 (m-40) cc_final: 0.8183 (m110) REVERT: B 140 PHE cc_start: 0.8195 (p90) cc_final: 0.7755 (p90) REVERT: B 152 TRP cc_start: 0.5807 (m100) cc_final: 0.5036 (m100) REVERT: B 153 MET cc_start: 0.7437 (ptm) cc_final: 0.7145 (ptm) REVERT: B 220 PHE cc_start: 0.8304 (t80) cc_final: 0.7977 (t80) REVERT: B 244 LEU cc_start: 0.6525 (mt) cc_final: 0.6135 (mt) REVERT: B 365 TYR cc_start: 0.8173 (m-80) cc_final: 0.7834 (m-80) REVERT: B 542 ASN cc_start: 0.8983 (t0) cc_final: 0.8744 (t0) REVERT: B 551 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8679 (m) REVERT: B 553 THR cc_start: 0.8861 (t) cc_final: 0.8548 (p) REVERT: B 555 SER cc_start: 0.8773 (t) cc_final: 0.8304 (p) REVERT: B 705 VAL cc_start: 0.8684 (t) cc_final: 0.8408 (m) REVERT: B 758 SER cc_start: 0.8993 (m) cc_final: 0.8506 (p) REVERT: B 759 PHE cc_start: 0.8099 (m-10) cc_final: 0.7741 (m-80) REVERT: B 790 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7687 (mtmm) REVERT: B 820 ASP cc_start: 0.7846 (m-30) cc_final: 0.7475 (t0) REVERT: B 904 TYR cc_start: 0.7843 (m-10) cc_final: 0.7437 (m-10) REVERT: B 934 ILE cc_start: 0.8454 (tt) cc_final: 0.8186 (tt) REVERT: B 957 GLN cc_start: 0.8214 (tt0) cc_final: 0.7919 (tt0) REVERT: B 1005 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7966 (mm-40) REVERT: B 1073 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7932 (ttmm) REVERT: B 1142 GLN cc_start: 0.8357 (tp40) cc_final: 0.7542 (tp40) REVERT: A 52 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 96 GLU cc_start: 0.7353 (mp0) cc_final: 0.6790 (mt-10) REVERT: A 113 LYS cc_start: 0.8550 (mptp) cc_final: 0.8233 (mptp) REVERT: A 138 ASP cc_start: 0.8085 (m-30) cc_final: 0.7573 (t0) REVERT: A 154 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8185 (tm-30) REVERT: A 203 ILE cc_start: 0.8507 (mt) cc_final: 0.8174 (tt) REVERT: A 276 LEU cc_start: 0.8786 (tp) cc_final: 0.8455 (tt) REVERT: A 294 ASP cc_start: 0.7683 (p0) cc_final: 0.7462 (p0) REVERT: A 323 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8427 (p) REVERT: A 346 ARG cc_start: 0.7270 (mmm160) cc_final: 0.6743 (mmm160) REVERT: A 362 VAL cc_start: 0.6954 (OUTLIER) cc_final: 0.6700 (p) REVERT: A 539 VAL cc_start: 0.8286 (m) cc_final: 0.8030 (p) REVERT: A 574 ASP cc_start: 0.7906 (p0) cc_final: 0.7546 (t0) REVERT: A 654 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7476 (mt-10) REVERT: A 663 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: A 673 SER cc_start: 0.8896 (t) cc_final: 0.8264 (m) REVERT: A 735 SER cc_start: 0.8448 (t) cc_final: 0.8043 (p) REVERT: A 736 VAL cc_start: 0.8605 (t) cc_final: 0.8294 (p) REVERT: A 878 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8555 (tp) REVERT: A 933 LYS cc_start: 0.8353 (mtmm) cc_final: 0.7999 (mttm) REVERT: A 949 GLN cc_start: 0.8532 (tp40) cc_final: 0.8156 (mm-40) REVERT: A 950 ASP cc_start: 0.7729 (t70) cc_final: 0.7319 (t0) REVERT: A 955 ASN cc_start: 0.8010 (t0) cc_final: 0.7696 (m-40) REVERT: A 957 GLN cc_start: 0.8533 (tt0) cc_final: 0.8317 (tt0) REVERT: A 963 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8807 (t) REVERT: A 988 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7306 (mt-10) REVERT: A 1019 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.7475 (ttp80) REVERT: A 1038 LYS cc_start: 0.8771 (mttt) cc_final: 0.8388 (mttm) REVERT: A 1086 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7905 (mtmm) REVERT: A 1122 VAL cc_start: 0.8889 (m) cc_final: 0.8374 (p) REVERT: A 1123 SER cc_start: 0.8557 (t) cc_final: 0.8317 (m) REVERT: A 1144 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7808 (mp0) outliers start: 113 outliers final: 98 residues processed: 804 average time/residue: 0.2620 time to fit residues: 333.6160 Evaluate side-chains 825 residues out of total 3872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 716 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 196 TYR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain D residue 473 TRP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 177 optimal weight: 10.0000 chunk 419 optimal weight: 2.9990 chunk 306 optimal weight: 0.7980 chunk 430 optimal weight: 0.0040 chunk 238 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 379 optimal weight: 9.9990 chunk 325 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.196956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.147587 restraints weight = 63484.053| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.81 r_work: 0.3592 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.690 37070 Z= 0.303 Angle : 0.914 59.096 50581 Z= 0.492 Chirality : 0.047 0.696 5802 Planarity : 0.005 0.140 6393 Dihedral : 5.310 52.060 6495 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 2.87 % Allowed : 15.62 % Favored : 81.51 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.13), residues: 4382 helix: 1.84 (0.14), residues: 1371 sheet: -0.38 (0.18), residues: 773 loop : -1.31 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 192 TYR 0.045 0.002 TYR D 454 PHE 0.029 0.002 PHE C 140 TRP 0.053 0.002 TRP D 271 HIS 0.081 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00746 (36940) covalent geometry : angle 0.82138 (50239) SS BOND : bond 0.03881 ( 48) SS BOND : angle 8.73294 ( 96) hydrogen bonds : bond 0.03861 ( 1468) hydrogen bonds : angle 4.91365 ( 4188) link_BETA1-4 : bond 0.00808 ( 28) link_BETA1-4 : angle 2.27400 ( 84) link_NAG-ASN : bond 0.00409 ( 54) link_NAG-ASN : angle 1.95540 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12213.41 seconds wall clock time: 209 minutes 29.22 seconds (12569.22 seconds total)