Starting phenix.real_space_refine on Fri Mar 6 21:42:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7czx_30520/03_2026/7czx_30520.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czx_30520/03_2026/7czx_30520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7czx_30520/03_2026/7czx_30520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czx_30520/03_2026/7czx_30520.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7czx_30520/03_2026/7czx_30520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czx_30520/03_2026/7czx_30520.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 138 5.16 5 C 22132 2.51 5 N 5680 2.21 5 O 6929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34879 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "C" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "H" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1732 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Chain: "K" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "I" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1732 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Chain: "M" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "J" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1732 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Chain: "N" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: "M" 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 Time building chain proxies: 8.35, per 1000 atoms: 0.24 Number of scatterers: 34879 At special positions: 0 Unit cell: (139.136, 216.313, 241.314, 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 138 16.00 O 6929 8.00 N 5680 7.00 C 22132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.45 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.16 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=1.56 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.33 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.29 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.17 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=1.56 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.30 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.51 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.65 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.56 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.85 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 94 " distance=1.93 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 200 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=1.93 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 200 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 211 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 94 " distance=1.93 Simple disulfide: pdb=" SG CYS N 140 " - pdb=" SG CYS N 200 " 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 A1406 " - " NAG A1407 " " NAG B1406 " - " NAG B1407 " " NAG B1411 " - " NAG B1412 " " NAG C1406 " - " NAG M 301 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 343 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 343 " " NAG B1408 " - " ASN B 603 " " NAG B1409 " - " ASN B 616 " " NAG B1410 " - " ASN B 657 " " NAG B1411 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 343 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 709 " " 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 C 331 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 73 sheets defined 17.7% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.075A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A 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 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.635A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.648A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.633A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.018A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.695A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.546A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.012A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.247A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.075A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.718A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.589A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'K' and resid 127 through 134 Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'M' and resid 127 through 134 Processing helix chain 'M' and resid 189 through 193 Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'N' and resid 127 through 134 Processing helix chain 'N' and resid 189 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.605A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.539A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.791A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.689A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.096A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.480A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.686A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.539A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.250A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 removed outlier: 4.197A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 318 through 319 removed outlier: 3.687A pdb=" N PHE C 318 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.133A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.539A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.246A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.581A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.521A pdb=" N ASN H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.521A pdb=" N ASN H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA H 152 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 199 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 154 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER H 195 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 158 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 193 " --> pdb=" O LYS H 158 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA H 152 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 199 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 154 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER H 195 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 158 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 193 " --> pdb=" O LYS H 158 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 165 through 169 Processing sheet with id=AF5, first strand: chain 'K' and resid 20 through 23 removed outlier: 3.913A pdb=" N ILE K 21 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU K 79 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE K 77 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR K 78 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 51 through 54 removed outlier: 6.386A pdb=" N TRP K 41 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 120 through 124 Processing sheet with id=AF8, first strand: chain 'K' and resid 159 through 160 Processing sheet with id=AF9, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.581A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN I 5 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE I 78 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER I 79 " --> pdb=" O SER I 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.521A pdb=" N ASN I 58 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.521A pdb=" N ASN I 58 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA I 152 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL I 199 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 154 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 197 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 156 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER I 195 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS I 158 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 193 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA I 152 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL I 199 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 154 " --> pdb=" O VAL I 197 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 197 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 156 " --> pdb=" O SER I 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER I 195 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS I 158 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 193 " --> pdb=" O LYS I 158 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 165 through 169 Processing sheet with id=AG6, first strand: chain 'M' and resid 20 through 23 removed outlier: 3.914A pdb=" N ILE M 21 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU M 79 " --> pdb=" O ILE M 21 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE M 77 " --> pdb=" O CYS M 23 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR M 78 " --> pdb=" O SER M 71 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 51 through 54 removed outlier: 6.386A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 120 through 124 Processing sheet with id=AG9, first strand: chain 'M' and resid 159 through 160 Processing sheet with id=AH1, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.581A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN J 5 " --> pdb=" O THR J 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER J 79 " --> pdb=" O SER J 70 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 58 through 59 removed outlier: 3.520A pdb=" N ASN J 58 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 58 through 59 removed outlier: 3.520A pdb=" N ASN J 58 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA J 152 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 199 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 154 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 197 " --> pdb=" O GLY J 154 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 156 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER J 195 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 158 " --> pdb=" O LEU J 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 193 " --> pdb=" O LYS J 158 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.007A pdb=" N ALA J 152 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 199 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 154 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 197 " --> pdb=" O GLY J 154 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 156 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER J 195 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 158 " --> pdb=" O LEU J 193 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 193 " --> pdb=" O LYS J 158 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 165 through 169 Processing sheet with id=AH7, first strand: chain 'N' and resid 20 through 23 removed outlier: 3.914A pdb=" N ILE N 21 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU N 79 " --> pdb=" O ILE N 21 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE N 77 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR N 78 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 51 through 54 removed outlier: 6.385A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 120 through 124 Processing sheet with id=AI1, first strand: chain 'N' and resid 159 through 160 1234 hydrogen bonds defined for protein. 3255 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: 8.81 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7166 1.32 - 1.46: 10991 1.46 - 1.59: 17337 1.59 - 1.72: 0 1.72 - 1.85: 168 Bond restraints: 35662 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.20e-02 6.94e+03 4.45e+01 bond pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.16e-02 7.43e+03 2.91e+01 bond pdb=" CA ILE A 693 " pdb=" CB ILE A 693 " ideal model delta sigma weight residual 1.544 1.472 0.072 1.49e-02 4.50e+03 2.34e+01 bond pdb=" N ILE A 692 " pdb=" CA ILE A 692 " ideal model delta sigma weight residual 1.458 1.403 0.055 1.17e-02 7.31e+03 2.24e+01 bond pdb=" C GLN B 321 " pdb=" N PRO B 322 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.31e-02 5.83e+03 2.05e+01 ... (remaining 35657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 46991 2.68 - 5.35: 1381 5.35 - 8.03: 129 8.03 - 10.70: 33 10.70 - 13.38: 11 Bond angle restraints: 48545 Sorted by residual: angle pdb=" N ILE A 692 " pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 109.55 100.42 9.13 1.38e+00 5.25e-01 4.37e+01 angle pdb=" N ASP H 111 " pdb=" CA ASP H 111 " pdb=" C ASP H 111 " ideal model delta sigma weight residual 114.64 104.59 10.05 1.52e+00 4.33e-01 4.37e+01 angle pdb=" N ASP I 111 " pdb=" CA ASP I 111 " pdb=" C ASP I 111 " ideal model delta sigma weight residual 114.64 104.60 10.04 1.52e+00 4.33e-01 4.36e+01 angle pdb=" N ASP J 111 " pdb=" CA ASP J 111 " pdb=" C ASP J 111 " ideal model delta sigma weight residual 114.64 104.62 10.02 1.52e+00 4.33e-01 4.34e+01 angle pdb=" CA ILE A 692 " pdb=" C ILE A 692 " pdb=" N ILE A 693 " ideal model delta sigma weight residual 115.82 124.84 -9.02 1.52e+00 4.33e-01 3.52e+01 ... (remaining 48540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 19151 17.95 - 35.90: 2127 35.90 - 53.85: 651 53.85 - 71.81: 203 71.81 - 89.76: 65 Dihedral angle restraints: 22197 sinusoidal: 9492 harmonic: 12705 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.03 71.97 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.08 71.92 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 22194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5696 0.328 - 0.657: 9 0.657 - 0.985: 9 0.985 - 1.313: 0 1.313 - 1.642: 1 Chirality restraints: 5715 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-02 2.50e+03 1.78e+03 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-02 2.50e+03 1.48e+03 chirality pdb=" C1 NAG B1412 " pdb=" O4 NAG B1411 " pdb=" C2 NAG B1412 " pdb=" O5 NAG B1412 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 ... (remaining 5712 not shown) Planarity restraints: 6202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.131 2.00e-02 2.50e+03 1.94e-01 4.68e+02 pdb=" CG ASN B 331 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.343 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.089 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" CG ASN B 343 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.187 2.00e-02 2.50e+03 pdb=" C1 NAG B1406 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " -0.089 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" CG ASN C 343 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " 0.187 2.00e-02 2.50e+03 pdb=" C1 NAG C1406 " -0.133 2.00e-02 2.50e+03 ... (remaining 6199 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 366 2.51 - 3.11: 25617 3.11 - 3.71: 50080 3.71 - 4.30: 75525 4.30 - 4.90: 125542 Nonbonded interactions: 277130 Sorted by model distance: nonbonded pdb=" O THR B 523 " pdb=" CG1 VAL B 524 " model vdw 1.913 3.460 nonbonded pdb=" NE2 GLN C 675 " pdb=" OG1 THR C 676 " model vdw 2.017 3.120 nonbonded pdb=" O THR A 523 " pdb=" O VAL A 524 " model vdw 2.036 3.040 nonbonded pdb=" O ASN K 143 " pdb=" O ASN K 144 " model vdw 2.038 3.040 nonbonded pdb=" O ASN N 143 " pdb=" O ASN N 144 " model vdw 2.038 3.040 ... (remaining 277125 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 27 through 939 or resid 944 through 1409)) selection = (chain 'B' and (resid 27 through 826 or resid 855 through 1409)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = (chain 'M' and resid 1 through 220) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.050 Process input model: 33.920 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 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 : 0.013 0.620 35783 Z= 0.610 Angle : 1.374 48.955 48857 Z= 0.726 Chirality : 0.073 1.642 5715 Planarity : 0.007 0.082 6155 Dihedral : 17.551 89.757 13884 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 29.15 Ramachandran Plot: Outliers : 3.46 % Allowed : 11.02 % Favored : 85.52 % Rotamer: Outliers : 11.08 % Allowed : 17.33 % Favored : 71.58 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.11), residues: 4302 helix: -2.32 (0.16), residues: 701 sheet: -1.81 (0.13), residues: 1320 loop : -3.33 (0.11), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.028 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.035 0.003 TRP J 113 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01078 (35662) covalent geometry : angle 1.09520 (48545) SS BOND : bond 0.18810 ( 51) SS BOND : angle 14.22294 ( 102) hydrogen bonds : bond 0.20535 ( 1144) hydrogen bonds : angle 8.43586 ( 3255) link_BETA1-4 : bond 0.06670 ( 23) link_BETA1-4 : angle 8.30825 ( 69) link_NAG-ASN : bond 0.03768 ( 47) link_NAG-ASN : angle 7.83154 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 424 poor density : 444 time to evaluate : 1.095 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: A 389 ASP cc_start: 0.4705 (OUTLIER) cc_final: 0.4203 (t70) REVERT: A 469 SER cc_start: 0.1636 (OUTLIER) cc_final: 0.1426 (t) REVERT: A 528 LYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5354 (mtmm) REVERT: A 935 GLN cc_start: 0.7760 (tt0) cc_final: 0.7546 (tt0) REVERT: A 1039 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8140 (mtp180) REVERT: B 153 MET cc_start: 0.0848 (mpp) cc_final: 0.0352 (mpp) REVERT: B 160 TYR cc_start: 0.4800 (p90) cc_final: 0.4441 (p90) REVERT: B 366 SER cc_start: 0.7414 (t) cc_final: 0.6818 (p) REVERT: B 403 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.5753 (mtt90) REVERT: B 567 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6784 (mtt90) REVERT: C 153 MET cc_start: 0.1054 (mpp) cc_final: -0.2214 (ptt) REVERT: C 158 ARG cc_start: 0.5434 (OUTLIER) cc_final: 0.5177 (tpt-90) REVERT: C 486 PHE cc_start: 0.2573 (OUTLIER) cc_final: 0.1822 (m-80) REVERT: C 488 CYS cc_start: -0.1179 (OUTLIER) cc_final: -0.2310 (m) REVERT: C 517 LEU cc_start: 0.1351 (OUTLIER) cc_final: 0.1007 (tt) REVERT: C 528 LYS cc_start: 0.3986 (OUTLIER) cc_final: 0.2663 (mptt) REVERT: H 53 TYR cc_start: 0.2635 (m-10) cc_final: 0.0751 (t80) REVERT: H 102 TYR cc_start: 0.2998 (t80) cc_final: 0.1399 (m-80) REVERT: H 153 LEU cc_start: 0.2109 (OUTLIER) cc_final: 0.1769 (pp) REVERT: K 111 GLU cc_start: 0.1695 (OUTLIER) cc_final: 0.0086 (tt0) REVERT: K 148 ARG cc_start: 0.4199 (OUTLIER) cc_final: 0.2897 (ptm160) REVERT: M 93 TYR cc_start: 0.3409 (m-80) cc_final: 0.2689 (m-80) REVERT: M 111 GLU cc_start: 0.2122 (OUTLIER) cc_final: 0.1013 (tt0) REVERT: M 165 SER cc_start: -0.1272 (OUTLIER) cc_final: -0.1590 (t) REVERT: J 218 SER cc_start: 0.1219 (OUTLIER) cc_final: 0.0909 (m) outliers start: 424 outliers final: 100 residues processed: 817 average time/residue: 0.5267 time to fit residues: 538.7251 Evaluate side-chains 321 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 204 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 165 SER Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 218 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 30.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 134 GLN A 137 ASN A 188 ASN A 314 GLN A 334 ASN A 360 ASN A 388 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 448 ASN A 450 ASN A 603 ASN A 644 GLN A 658 ASN A 675 GLN A 751 ASN A 762 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 949 GLN A 954 GLN A 955 ASN A 957 GLN A 969 ASN A 992 GLN B 134 GLN B 137 ASN B 188 ASN B 314 GLN B 394 ASN B 422 ASN B 440 ASN B 450 ASN B 498 GLN B 563 GLN B 644 GLN B 655 HIS B 703 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 935 GLN B1002 GLN B1054 GLN C 52 GLN C 125 ASN C 134 GLN C 137 ASN C 188 ASN C 239 GLN C 360 ASN C 394 ASN C 422 ASN C 440 ASN C 450 ASN C 532 ASN C 540 ASN C 644 GLN C 658 ASN C 703 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C1010 GLN C1071 GLN C1101 HIS H 179 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN K 44 GLN I 212 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 22 ASN M 44 GLN J 212 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN N 44 GLN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.232174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.185901 restraints weight = 52159.350| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 3.18 r_work: 0.3353 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35783 Z= 0.172 Angle : 0.863 15.557 48857 Z= 0.423 Chirality : 0.051 0.514 5715 Planarity : 0.006 0.076 6155 Dihedral : 10.002 98.246 6378 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.60 % Favored : 90.93 % Rotamer: Outliers : 6.25 % Allowed : 21.23 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.12), residues: 4302 helix: -0.26 (0.19), residues: 718 sheet: -1.12 (0.14), residues: 1312 loop : -2.78 (0.11), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 346 TYR 0.026 0.002 TYR M 192 PHE 0.026 0.002 PHE C 329 TRP 0.019 0.001 TRP I 113 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00381 (35662) covalent geometry : angle 0.82245 (48545) SS BOND : bond 0.00615 ( 51) SS BOND : angle 2.31568 ( 102) hydrogen bonds : bond 0.04764 ( 1144) hydrogen bonds : angle 6.10484 ( 3255) link_BETA1-4 : bond 0.00739 ( 23) link_BETA1-4 : angle 3.09890 ( 69) link_NAG-ASN : bond 0.00577 ( 47) link_NAG-ASN : angle 4.06889 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 251 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7266 (m110) REVERT: A 100 ILE cc_start: 0.7126 (mm) cc_final: 0.6854 (mm) REVERT: A 102 ARG cc_start: 0.7414 (mmt90) cc_final: 0.6700 (mmm-85) REVERT: A 125 ASN cc_start: 0.5716 (m-40) cc_final: 0.5457 (p0) REVERT: A 195 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7529 (ttpp) REVERT: A 200 TYR cc_start: 0.7353 (m-80) cc_final: 0.6923 (m-80) REVERT: A 324 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: A 729 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8930 (t) REVERT: A 740 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7920 (ttt) REVERT: B 153 MET cc_start: 0.0667 (mpp) cc_final: -0.0432 (mpp) REVERT: B 160 TYR cc_start: 0.5478 (p90) cc_final: 0.4733 (p90) REVERT: B 195 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7969 (ttpt) REVERT: B 228 ASP cc_start: 0.7261 (t0) cc_final: 0.7031 (t0) REVERT: B 366 SER cc_start: 0.8020 (t) cc_final: 0.7750 (p) REVERT: B 382 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8264 (m) REVERT: B 383 SER cc_start: 0.8264 (t) cc_final: 0.8003 (m) REVERT: B 787 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: C 141 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6603 (pp) REVERT: C 153 MET cc_start: 0.0255 (mpp) cc_final: -0.2741 (ptt) REVERT: C 158 ARG cc_start: 0.5563 (OUTLIER) cc_final: 0.4844 (mmm160) REVERT: C 488 CYS cc_start: -0.1204 (OUTLIER) cc_final: -0.1695 (m) REVERT: C 498 GLN cc_start: 0.4627 (OUTLIER) cc_final: 0.3575 (mm-40) REVERT: C 528 LYS cc_start: 0.3450 (OUTLIER) cc_final: 0.3233 (ptpt) REVERT: C 534 VAL cc_start: 0.8015 (m) cc_final: 0.7545 (p) REVERT: C 558 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7036 (mptt) REVERT: C 936 ASP cc_start: 0.8153 (m-30) cc_final: 0.7911 (m-30) REVERT: C 977 LEU cc_start: 0.7817 (tt) cc_final: 0.7551 (mt) REVERT: C 1136 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8580 (t) REVERT: H 53 TYR cc_start: 0.2045 (m-10) cc_final: 0.0474 (t80) REVERT: H 153 LEU cc_start: 0.1353 (OUTLIER) cc_final: 0.1058 (pp) REVERT: K 52 LEU cc_start: 0.0910 (OUTLIER) cc_final: 0.0673 (mt) REVERT: K 114 ARG cc_start: 0.2852 (OUTLIER) cc_final: 0.1556 (ttp80) REVERT: K 178 THR cc_start: 0.1476 (OUTLIER) cc_final: 0.1065 (p) REVERT: M 4 MET cc_start: 0.3909 (mtm) cc_final: 0.3506 (ptm) REVERT: M 27 GLN cc_start: 0.3470 (mt0) cc_final: 0.3253 (pp30) REVERT: M 53 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4759 (tp) REVERT: M 96 GLN cc_start: 0.2763 (pt0) cc_final: 0.2103 (pt0) REVERT: M 98 TYR cc_start: 0.3370 (t80) cc_final: 0.3111 (t80) REVERT: M 114 ARG cc_start: 0.2822 (OUTLIER) cc_final: 0.2586 (mmm-85) REVERT: J 162 PRO cc_start: 0.0877 (Cg_endo) cc_final: 0.0636 (Cg_exo) REVERT: J 185 LEU cc_start: -0.0266 (OUTLIER) cc_final: -0.0618 (pt) outliers start: 239 outliers final: 82 residues processed: 462 average time/residue: 0.4842 time to fit residues: 286.0784 Evaluate side-chains 307 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 203 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 208 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 394 optimal weight: 5.9990 chunk 295 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 316 optimal weight: 30.0000 chunk 412 optimal weight: 20.0000 chunk 393 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 658 ASN A 856 ASN A 955 ASN A1101 HIS B 314 GLN B 501 ASN B 703 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 125 ASN C 360 ASN C 498 GLN C 613 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS H 186 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN M 6 GLN M 48 GLN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.225745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.177298 restraints weight = 50849.343| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 3.46 r_work: 0.3240 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 0.073 35783 Z= 0.189 Angle : 0.795 13.751 48857 Z= 0.387 Chirality : 0.051 0.596 5715 Planarity : 0.005 0.078 6155 Dihedral : 8.526 59.979 6250 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.76 % Favored : 90.91 % Rotamer: Outliers : 6.22 % Allowed : 20.73 % Favored : 73.05 % 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 are not related in a simple way. whole: -2.08 (0.12), residues: 4302 helix: 0.47 (0.20), residues: 699 sheet: -0.73 (0.14), residues: 1309 loop : -2.47 (0.11), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 346 TYR 0.030 0.002 TYR M 31 PHE 0.026 0.002 PHE M 122 TRP 0.015 0.002 TRP I 113 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00449 (35662) covalent geometry : angle 0.76132 (48545) SS BOND : bond 0.00542 ( 51) SS BOND : angle 1.95828 ( 102) hydrogen bonds : bond 0.04881 ( 1144) hydrogen bonds : angle 5.68763 ( 3255) link_BETA1-4 : bond 0.00556 ( 23) link_BETA1-4 : angle 3.17911 ( 69) link_NAG-ASN : bond 0.00669 ( 47) link_NAG-ASN : angle 3.42160 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 238 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7176 (m110) REVERT: A 100 ILE cc_start: 0.7195 (mm) cc_final: 0.6859 (mm) REVERT: A 102 ARG cc_start: 0.7438 (mmt90) cc_final: 0.6678 (mmm-85) REVERT: A 125 ASN cc_start: 0.5791 (m-40) cc_final: 0.5411 (p0) REVERT: A 190 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6478 (mmt90) REVERT: A 324 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6997 (pm20) REVERT: A 729 VAL cc_start: 0.9376 (OUTLIER) cc_final: 0.9103 (t) REVERT: A 740 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8361 (ttm) REVERT: A 1113 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8861 (mp10) REVERT: B 153 MET cc_start: 0.0445 (mpp) cc_final: -0.0429 (mpp) REVERT: B 160 TYR cc_start: 0.5380 (p90) cc_final: 0.4740 (p90) REVERT: B 195 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8040 (ttpt) REVERT: B 226 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8411 (mp) REVERT: B 382 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8449 (t) REVERT: B 392 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 580 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.6228 (mp10) REVERT: B 787 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: C 141 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.6958 (pp) REVERT: C 153 MET cc_start: 0.0116 (mpp) cc_final: -0.3033 (ptt) REVERT: C 158 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5197 (tpt-90) REVERT: C 488 CYS cc_start: -0.1053 (OUTLIER) cc_final: -0.1450 (m) REVERT: C 498 GLN cc_start: 0.4305 (OUTLIER) cc_final: 0.3398 (mm-40) REVERT: C 572 THR cc_start: 0.8245 (p) cc_final: 0.8010 (t) REVERT: C 574 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6384 (t0) REVERT: C 599 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9089 (p) REVERT: C 697 MET cc_start: 0.8775 (ptt) cc_final: 0.8560 (ptt) REVERT: C 778 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9106 (m) REVERT: C 787 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8734 (mt0) REVERT: C 982 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8203 (m) REVERT: H 216 LYS cc_start: 0.2040 (OUTLIER) cc_final: 0.1643 (tttt) REVERT: K 148 ARG cc_start: 0.4435 (OUTLIER) cc_final: 0.2376 (mtp180) REVERT: I 193 LEU cc_start: 0.2922 (OUTLIER) cc_final: 0.2684 (mt) REVERT: M 93 TYR cc_start: 0.3901 (m-80) cc_final: 0.3042 (m-80) REVERT: M 95 GLN cc_start: 0.3184 (tp40) cc_final: 0.2476 (tp-100) REVERT: M 97 TYR cc_start: 0.4192 (p90) cc_final: 0.3715 (p90) REVERT: J 102 TYR cc_start: 0.2217 (t80) cc_final: 0.1615 (p90) REVERT: J 185 LEU cc_start: -0.0089 (OUTLIER) cc_final: -0.0449 (pt) REVERT: J 193 LEU cc_start: 0.1229 (OUTLIER) cc_final: 0.0586 (mp) REVERT: N 111 GLU cc_start: 0.3582 (OUTLIER) cc_final: 0.3054 (mp0) REVERT: N 114 ARG cc_start: 0.2201 (OUTLIER) cc_final: 0.1304 (mmm160) outliers start: 238 outliers final: 105 residues processed: 441 average time/residue: 0.4888 time to fit residues: 273.9493 Evaluate side-chains 314 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 181 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 114 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 165 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 431 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 367 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 275 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 703 ASN A 762 GLN A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 99 ASN B 314 GLN B 703 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 125 ASN C 540 ASN C 613 GLN C 992 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN K 166 GLN M 166 GLN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.222400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.175602 restraints weight = 50000.196| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.13 r_work: 0.3229 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 35783 Z= 0.274 Angle : 0.855 15.747 48857 Z= 0.415 Chirality : 0.054 0.716 5715 Planarity : 0.006 0.068 6155 Dihedral : 8.539 59.515 6233 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.30 % Favored : 91.45 % Rotamer: Outliers : 6.33 % Allowed : 21.25 % Favored : 72.42 % 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 are not related in a simple way. whole: -2.03 (0.12), residues: 4302 helix: 0.33 (0.19), residues: 702 sheet: -0.70 (0.14), residues: 1329 loop : -2.37 (0.11), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 102 TYR 0.028 0.002 TYR M 31 PHE 0.020 0.003 PHE N 122 TRP 0.017 0.002 TRP I 113 HIS 0.009 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00669 (35662) covalent geometry : angle 0.82037 (48545) SS BOND : bond 0.00616 ( 51) SS BOND : angle 2.18196 ( 102) hydrogen bonds : bond 0.05627 ( 1144) hydrogen bonds : angle 5.78024 ( 3255) link_BETA1-4 : bond 0.00632 ( 23) link_BETA1-4 : angle 3.09681 ( 69) link_NAG-ASN : bond 0.00665 ( 47) link_NAG-ASN : angle 3.65704 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 198 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7156 (m110) REVERT: A 102 ARG cc_start: 0.7504 (mmt90) cc_final: 0.6732 (mmm-85) REVERT: A 125 ASN cc_start: 0.6041 (m-40) cc_final: 0.5632 (p0) REVERT: A 169 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 190 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6588 (mmt90) REVERT: A 324 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: A 390 LEU cc_start: 0.3250 (OUTLIER) cc_final: 0.2894 (mt) REVERT: A 452 LEU cc_start: 0.5831 (OUTLIER) cc_final: 0.4867 (tp) REVERT: A 569 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6899 (mm) REVERT: A 740 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8654 (ttm) REVERT: A 916 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9057 (tp) REVERT: B 153 MET cc_start: 0.0914 (mpp) cc_final: -0.0210 (mpp) REVERT: B 160 TYR cc_start: 0.5305 (p90) cc_final: 0.4717 (p90) REVERT: B 226 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 237 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7487 (mtt180) REVERT: B 360 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7755 (m-40) REVERT: B 382 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8502 (t) REVERT: B 392 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: B 580 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.6496 (mp10) REVERT: B 619 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: B 787 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: C 105 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8386 (pt) REVERT: C 141 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7008 (pp) REVERT: C 153 MET cc_start: 0.0184 (mpp) cc_final: -0.3154 (ptt) REVERT: C 158 ARG cc_start: 0.5791 (OUTLIER) cc_final: 0.5151 (tpt-90) REVERT: C 314 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8655 (tm-30) REVERT: C 574 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6526 (t0) REVERT: C 599 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9198 (p) REVERT: C 787 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8707 (mm-40) REVERT: C 790 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8833 (mtpm) REVERT: C 957 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8171 (tp-100) REVERT: H 145 SER cc_start: -0.1774 (OUTLIER) cc_final: -0.2765 (t) REVERT: H 153 LEU cc_start: 0.1023 (OUTLIER) cc_final: 0.0758 (pp) REVERT: H 193 LEU cc_start: 0.2034 (OUTLIER) cc_final: 0.1796 (tp) REVERT: H 216 LYS cc_start: 0.1994 (OUTLIER) cc_final: 0.1580 (tttt) REVERT: K 148 ARG cc_start: 0.4525 (OUTLIER) cc_final: 0.2405 (mtp180) REVERT: I 20 LEU cc_start: 0.3712 (OUTLIER) cc_final: 0.3228 (tt) REVERT: M 4 MET cc_start: 0.3225 (ptm) cc_final: 0.1792 (pp-130) REVERT: M 81 ILE cc_start: 0.0453 (OUTLIER) cc_final: -0.0150 (pt) REVERT: J 102 TYR cc_start: 0.2132 (t80) cc_final: 0.1566 (p90) REVERT: J 139 LEU cc_start: 0.1058 (OUTLIER) cc_final: 0.0762 (tp) REVERT: J 162 PRO cc_start: 0.0916 (Cg_endo) cc_final: 0.0709 (Cg_exo) REVERT: J 185 LEU cc_start: -0.0193 (OUTLIER) cc_final: -0.0604 (tp) REVERT: J 193 LEU cc_start: 0.0949 (OUTLIER) cc_final: 0.0063 (mp) REVERT: N 4 MET cc_start: 0.1600 (mpt) cc_final: 0.1266 (mmt) REVERT: N 111 GLU cc_start: 0.3682 (OUTLIER) cc_final: 0.3114 (mp0) REVERT: N 114 ARG cc_start: 0.2699 (OUTLIER) cc_final: 0.1646 (mmm160) outliers start: 242 outliers final: 121 residues processed: 408 average time/residue: 0.4914 time to fit residues: 255.6263 Evaluate side-chains 318 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 161 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 114 ARG Chi-restraints excluded: chain N residue 208 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 405 optimal weight: 7.9990 chunk 395 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 326 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 957 GLN A1005 GLN B 314 GLN B 498 GLN B 703 ASN B 935 GLN B1002 GLN B1010 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN J 186 GLN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.224108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.175601 restraints weight = 50411.178| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 3.43 r_work: 0.3201 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35783 Z= 0.157 Angle : 0.742 16.014 48857 Z= 0.358 Chirality : 0.049 0.649 5715 Planarity : 0.005 0.062 6155 Dihedral : 8.026 59.843 6227 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.95 % Favored : 91.82 % Rotamer: Outliers : 5.41 % Allowed : 22.35 % Favored : 72.24 % 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 are not related in a simple way. whole: -1.71 (0.12), residues: 4302 helix: 0.70 (0.20), residues: 709 sheet: -0.45 (0.14), residues: 1310 loop : -2.24 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.022 0.001 TYR I 160 PHE 0.021 0.002 PHE A 347 TRP 0.015 0.001 TRP H 113 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00371 (35662) covalent geometry : angle 0.71084 (48545) SS BOND : bond 0.00521 ( 51) SS BOND : angle 1.65832 ( 102) hydrogen bonds : bond 0.04466 ( 1144) hydrogen bonds : angle 5.47752 ( 3255) link_BETA1-4 : bond 0.00537 ( 23) link_BETA1-4 : angle 2.88798 ( 69) link_NAG-ASN : bond 0.00525 ( 47) link_NAG-ASN : angle 3.26477 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 193 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7189 (m110) REVERT: A 102 ARG cc_start: 0.7430 (mmt90) cc_final: 0.6723 (mmm-85) REVERT: A 125 ASN cc_start: 0.5710 (m-40) cc_final: 0.5246 (p0) REVERT: A 169 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 190 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6423 (mmt90) REVERT: A 324 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: A 390 LEU cc_start: 0.3070 (OUTLIER) cc_final: 0.2325 (mt) REVERT: A 452 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5012 (tp) REVERT: A 606 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8296 (t0) REVERT: A 740 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8726 (ttm) REVERT: A 916 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9048 (tp) REVERT: A 1113 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: B 153 MET cc_start: 0.0843 (mpp) cc_final: -0.0126 (mpp) REVERT: B 160 TYR cc_start: 0.5212 (p90) cc_final: 0.4668 (p90) REVERT: B 195 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8002 (ttpt) REVERT: B 237 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7468 (mtt180) REVERT: B 580 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.6469 (mp10) REVERT: B 787 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8402 (mt0) REVERT: C 125 ASN cc_start: 0.4690 (m-40) cc_final: 0.4454 (t0) REVERT: C 141 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.6917 (pp) REVERT: C 153 MET cc_start: 0.0219 (mpp) cc_final: -0.3158 (ptt) REVERT: C 158 ARG cc_start: 0.5866 (OUTLIER) cc_final: 0.5168 (tpt-90) REVERT: C 314 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8692 (tm-30) REVERT: C 574 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6374 (t0) REVERT: C 599 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9206 (p) REVERT: C 778 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9061 (m) REVERT: C 787 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8792 (mt0) REVERT: H 112 TYR cc_start: 0.3957 (OUTLIER) cc_final: 0.2613 (m-80) REVERT: H 145 SER cc_start: -0.1574 (OUTLIER) cc_final: -0.2682 (t) REVERT: H 153 LEU cc_start: 0.1094 (OUTLIER) cc_final: 0.0853 (pp) REVERT: H 193 LEU cc_start: 0.2021 (OUTLIER) cc_final: 0.1798 (tp) REVERT: I 20 LEU cc_start: 0.3603 (OUTLIER) cc_final: 0.3189 (tt) REVERT: I 105 LEU cc_start: 0.2759 (pt) cc_final: 0.1700 (mm) REVERT: I 139 LEU cc_start: 0.0533 (OUTLIER) cc_final: -0.0084 (mm) REVERT: M 81 ILE cc_start: 0.0193 (OUTLIER) cc_final: -0.0400 (pt) REVERT: J 102 TYR cc_start: 0.2108 (t80) cc_final: 0.1541 (p90) REVERT: J 113 TRP cc_start: 0.2512 (OUTLIER) cc_final: 0.1426 (p90) REVERT: J 139 LEU cc_start: 0.0971 (mp) cc_final: 0.0700 (tp) REVERT: J 185 LEU cc_start: -0.0153 (OUTLIER) cc_final: -0.0512 (pt) REVERT: J 193 LEU cc_start: 0.0979 (OUTLIER) cc_final: 0.0039 (mp) REVERT: N 4 MET cc_start: 0.1789 (mpt) cc_final: 0.1440 (mmt) REVERT: N 111 GLU cc_start: 0.3767 (OUTLIER) cc_final: 0.3140 (mp0) outliers start: 207 outliers final: 97 residues processed: 378 average time/residue: 0.4962 time to fit residues: 238.2559 Evaluate side-chains 288 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 161 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 113 TRP Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 208 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 61 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 215 optimal weight: 0.0870 chunk 26 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 423 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 210 optimal weight: 0.4980 chunk 422 optimal weight: 5.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 957 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 498 GLN B 690 GLN B 703 ASN B 935 GLN B1002 GLN B1010 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.224593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.176774 restraints weight = 50385.483| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 3.43 r_work: 0.3217 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35783 Z= 0.126 Angle : 0.711 14.290 48857 Z= 0.341 Chirality : 0.047 0.573 5715 Planarity : 0.005 0.060 6155 Dihedral : 7.506 59.913 6213 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.48 % Favored : 92.31 % Rotamer: Outliers : 5.25 % Allowed : 22.80 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.12), residues: 4302 helix: 1.04 (0.20), residues: 709 sheet: -0.31 (0.14), residues: 1325 loop : -2.09 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 102 TYR 0.019 0.001 TYR M 31 PHE 0.016 0.001 PHE B 192 TRP 0.027 0.001 TRP H 113 HIS 0.004 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00285 (35662) covalent geometry : angle 0.68292 (48545) SS BOND : bond 0.00431 ( 51) SS BOND : angle 1.43462 ( 102) hydrogen bonds : bond 0.03871 ( 1144) hydrogen bonds : angle 5.23373 ( 3255) link_BETA1-4 : bond 0.00621 ( 23) link_BETA1-4 : angle 2.73725 ( 69) link_NAG-ASN : bond 0.00487 ( 47) link_NAG-ASN : angle 3.05846 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 192 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7157 (m110) REVERT: A 102 ARG cc_start: 0.7341 (mmt90) cc_final: 0.6597 (mmm-85) REVERT: A 125 ASN cc_start: 0.5536 (m-40) cc_final: 0.5102 (p0) REVERT: A 190 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6419 (mmt90) REVERT: A 226 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8029 (mt) REVERT: A 324 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: A 390 LEU cc_start: 0.2884 (OUTLIER) cc_final: 0.2318 (mt) REVERT: A 452 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5036 (tp) REVERT: A 606 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8383 (t0) REVERT: A 729 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9053 (t) REVERT: A 916 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9034 (tp) REVERT: A 1113 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8501 (mt0) REVERT: B 153 MET cc_start: 0.0921 (mpp) cc_final: -0.0137 (mpp) REVERT: B 160 TYR cc_start: 0.5211 (p90) cc_final: 0.4663 (p90) REVERT: B 195 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7999 (ttmt) REVERT: B 226 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8348 (mp) REVERT: B 237 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7389 (mtt180) REVERT: B 580 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.6399 (mp10) REVERT: B 787 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: B 867 ASP cc_start: 0.8226 (p0) cc_final: 0.8004 (m-30) REVERT: C 141 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.6902 (pp) REVERT: C 153 MET cc_start: 0.0100 (OUTLIER) cc_final: -0.3242 (ptt) REVERT: C 158 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5201 (tpt-90) REVERT: C 314 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8736 (tm-30) REVERT: C 558 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.6881 (mptt) REVERT: C 574 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6222 (t0) REVERT: C 581 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8205 (p) REVERT: C 787 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8824 (mt0) REVERT: C 1132 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8811 (tt) REVERT: H 112 TYR cc_start: 0.3904 (OUTLIER) cc_final: 0.2558 (m-80) REVERT: H 145 SER cc_start: -0.1325 (OUTLIER) cc_final: -0.2552 (t) REVERT: H 153 LEU cc_start: 0.1100 (OUTLIER) cc_final: 0.0867 (pp) REVERT: H 193 LEU cc_start: 0.2007 (OUTLIER) cc_final: 0.1766 (tp) REVERT: K 148 ARG cc_start: 0.4324 (OUTLIER) cc_final: 0.2445 (mtp180) REVERT: M 81 ILE cc_start: 0.0101 (OUTLIER) cc_final: -0.0336 (pt) REVERT: J 102 TYR cc_start: 0.2067 (t80) cc_final: 0.1525 (p90) REVERT: J 113 TRP cc_start: 0.2550 (OUTLIER) cc_final: 0.1460 (p90) REVERT: J 139 LEU cc_start: 0.0965 (OUTLIER) cc_final: 0.0689 (tp) REVERT: J 185 LEU cc_start: -0.0134 (OUTLIER) cc_final: -0.0489 (pt) REVERT: J 193 LEU cc_start: 0.1182 (OUTLIER) cc_final: 0.0189 (mp) REVERT: N 4 MET cc_start: 0.1658 (mpt) cc_final: 0.1314 (mmt) REVERT: N 111 GLU cc_start: 0.3456 (OUTLIER) cc_final: 0.3229 (mm-30) outliers start: 201 outliers final: 91 residues processed: 371 average time/residue: 0.4762 time to fit residues: 225.0370 Evaluate side-chains 292 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 167 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 143 ASN Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 113 TRP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 208 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 341 optimal weight: 50.0000 chunk 416 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 239 optimal weight: 10.0000 chunk 386 optimal weight: 30.0000 chunk 392 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 957 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 314 GLN B 422 ASN B 498 GLN B 703 ASN B 935 GLN B1010 GLN C 125 ASN C 422 ASN C1010 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.223149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.174479 restraints weight = 50124.598| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.41 r_work: 0.3191 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35783 Z= 0.169 Angle : 0.750 17.066 48857 Z= 0.357 Chirality : 0.049 0.588 5715 Planarity : 0.005 0.059 6155 Dihedral : 7.497 59.657 6208 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.07 % Favored : 91.72 % Rotamer: Outliers : 4.94 % Allowed : 23.19 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.12), residues: 4302 helix: 0.96 (0.20), residues: 709 sheet: -0.28 (0.14), residues: 1324 loop : -2.09 (0.12), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.022 0.001 TYR C1067 PHE 0.017 0.002 PHE B 86 TRP 0.029 0.001 TRP H 113 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00404 (35662) covalent geometry : angle 0.71831 (48545) SS BOND : bond 0.00461 ( 51) SS BOND : angle 1.63543 ( 102) hydrogen bonds : bond 0.04450 ( 1144) hydrogen bonds : angle 5.25925 ( 3255) link_BETA1-4 : bond 0.00561 ( 23) link_BETA1-4 : angle 2.87220 ( 69) link_NAG-ASN : bond 0.00630 ( 47) link_NAG-ASN : angle 3.36193 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 176 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: A 100 ILE cc_start: 0.6999 (mm) cc_final: 0.6652 (mm) REVERT: A 102 ARG cc_start: 0.7323 (mmt90) cc_final: 0.6594 (mmm-85) REVERT: A 125 ASN cc_start: 0.5644 (m-40) cc_final: 0.5161 (p0) REVERT: A 169 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 190 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6456 (mmt90) REVERT: A 226 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8017 (mt) REVERT: A 324 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7089 (pm20) REVERT: A 390 LEU cc_start: 0.2957 (OUTLIER) cc_final: 0.2406 (mt) REVERT: A 452 LEU cc_start: 0.5896 (OUTLIER) cc_final: 0.5062 (OUTLIER) REVERT: A 606 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8427 (t0) REVERT: A 729 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9073 (t) REVERT: A 916 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9080 (tp) REVERT: A 1001 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9131 (tt) REVERT: A 1113 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8556 (mt0) REVERT: B 153 MET cc_start: 0.1212 (mpp) cc_final: 0.0068 (mpp) REVERT: B 195 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7950 (ttmt) REVERT: B 226 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8379 (mp) REVERT: B 237 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7431 (mtt180) REVERT: B 304 LYS cc_start: 0.8743 (tppt) cc_final: 0.8354 (mmtp) REVERT: B 580 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.6476 (mp10) REVERT: B 787 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8424 (mt0) REVERT: B 867 ASP cc_start: 0.8305 (p0) cc_final: 0.8099 (m-30) REVERT: C 141 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.6900 (pp) REVERT: C 153 MET cc_start: 0.0126 (OUTLIER) cc_final: -0.3237 (ptt) REVERT: C 314 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8791 (tm-30) REVERT: C 324 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6176 (pp20) REVERT: C 558 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6770 (mptt) REVERT: C 574 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6397 (t0) REVERT: C 787 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8841 (mt0) REVERT: C 990 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: H 112 TYR cc_start: 0.3890 (OUTLIER) cc_final: 0.2377 (m-80) REVERT: H 145 SER cc_start: -0.1325 (OUTLIER) cc_final: -0.2549 (t) REVERT: H 153 LEU cc_start: 0.1053 (OUTLIER) cc_final: 0.0806 (pp) REVERT: H 193 LEU cc_start: 0.2163 (OUTLIER) cc_final: 0.1925 (tp) REVERT: K 148 ARG cc_start: 0.4331 (OUTLIER) cc_final: 0.2514 (mtp180) REVERT: I 20 LEU cc_start: 0.3618 (OUTLIER) cc_final: 0.3190 (tt) REVERT: I 31 SER cc_start: 0.4592 (OUTLIER) cc_final: 0.3939 (t) REVERT: I 105 LEU cc_start: 0.2862 (pt) cc_final: 0.1914 (mm) REVERT: M 81 ILE cc_start: 0.0179 (OUTLIER) cc_final: -0.0309 (pt) REVERT: J 102 TYR cc_start: 0.1965 (t80) cc_final: 0.1283 (p90) REVERT: J 113 TRP cc_start: 0.2192 (OUTLIER) cc_final: 0.1541 (p90) REVERT: J 139 LEU cc_start: 0.0964 (OUTLIER) cc_final: 0.0688 (tp) REVERT: J 185 LEU cc_start: -0.0077 (OUTLIER) cc_final: -0.0481 (tp) REVERT: J 193 LEU cc_start: 0.1233 (OUTLIER) cc_final: 0.0113 (mp) REVERT: N 4 MET cc_start: 0.1970 (OUTLIER) cc_final: 0.1593 (mmt) REVERT: N 111 GLU cc_start: 0.3461 (OUTLIER) cc_final: 0.3204 (mm-30) outliers start: 189 outliers final: 117 residues processed: 345 average time/residue: 0.4674 time to fit residues: 206.6078 Evaluate side-chains 317 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 164 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 113 TRP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 78 optimal weight: 3.9990 chunk 40 optimal weight: 50.0000 chunk 309 optimal weight: 8.9990 chunk 424 optimal weight: 10.0000 chunk 363 optimal weight: 30.0000 chunk 157 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 957 GLN B 207 HIS B 935 GLN B 957 GLN B1010 GLN C 125 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.221795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.174769 restraints weight = 50002.274| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 3.21 r_work: 0.3226 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 35783 Z= 0.228 Angle : 0.803 16.638 48857 Z= 0.385 Chirality : 0.052 0.630 5715 Planarity : 0.005 0.056 6155 Dihedral : 7.739 59.318 6204 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.53 % Favored : 91.26 % Rotamer: Outliers : 5.07 % Allowed : 23.01 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.12), residues: 4302 helix: 0.82 (0.20), residues: 697 sheet: -0.34 (0.14), residues: 1319 loop : -2.14 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 319 TYR 0.025 0.002 TYR C1067 PHE 0.033 0.002 PHE C 168 TRP 0.031 0.002 TRP H 113 HIS 0.007 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00557 (35662) covalent geometry : angle 0.76795 (48545) SS BOND : bond 0.00585 ( 51) SS BOND : angle 2.14977 ( 102) hydrogen bonds : bond 0.05177 ( 1144) hydrogen bonds : angle 5.43825 ( 3255) link_BETA1-4 : bond 0.00560 ( 23) link_BETA1-4 : angle 2.89214 ( 69) link_NAG-ASN : bond 0.00700 ( 47) link_NAG-ASN : angle 3.56324 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 180 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.7925 (m) cc_final: 0.7644 (p) REVERT: A 88 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: A 102 ARG cc_start: 0.7377 (mmt90) cc_final: 0.6695 (mmm-85) REVERT: A 125 ASN cc_start: 0.6017 (m-40) cc_final: 0.5483 (p0) REVERT: A 190 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6570 (mmt90) REVERT: A 237 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7385 (ttt-90) REVERT: A 346 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.4933 (tpm170) REVERT: A 390 LEU cc_start: 0.3022 (OUTLIER) cc_final: 0.2419 (mt) REVERT: A 452 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.4924 (OUTLIER) REVERT: A 571 ASP cc_start: 0.7045 (m-30) cc_final: 0.6831 (m-30) REVERT: A 606 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8344 (t0) REVERT: A 855 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.5278 (m-10) REVERT: A 916 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9060 (tp) REVERT: A 1001 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9061 (tt) REVERT: A 1113 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8573 (mt0) REVERT: B 153 MET cc_start: 0.1916 (mpp) cc_final: 0.0742 (mpp) REVERT: B 237 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7538 (mtt180) REVERT: B 304 LYS cc_start: 0.8720 (tppt) cc_final: 0.8335 (mmtp) REVERT: B 382 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8390 (t) REVERT: B 580 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.6520 (mp10) REVERT: B 787 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: C 141 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.6991 (pp) REVERT: C 153 MET cc_start: 0.0562 (OUTLIER) cc_final: -0.3100 (ptt) REVERT: C 314 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8709 (tm-30) REVERT: C 324 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6230 (pp20) REVERT: C 787 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8684 (mm-40) REVERT: H 112 TYR cc_start: 0.3723 (OUTLIER) cc_final: 0.2122 (m-80) REVERT: H 153 LEU cc_start: 0.0929 (OUTLIER) cc_final: 0.0704 (pp) REVERT: H 193 LEU cc_start: 0.1964 (OUTLIER) cc_final: 0.1556 (tp) REVERT: K 148 ARG cc_start: 0.4433 (OUTLIER) cc_final: 0.2565 (mtp180) REVERT: I 31 SER cc_start: 0.4589 (OUTLIER) cc_final: 0.3949 (t) REVERT: I 105 LEU cc_start: 0.2978 (pt) cc_final: 0.1940 (mm) REVERT: M 81 ILE cc_start: 0.0084 (OUTLIER) cc_final: -0.0428 (mt) REVERT: J 102 TYR cc_start: 0.2135 (t80) cc_final: 0.1747 (p90) REVERT: J 108 GLN cc_start: 0.2100 (OUTLIER) cc_final: 0.1348 (pm20) REVERT: J 113 TRP cc_start: 0.2274 (OUTLIER) cc_final: 0.1502 (p90) REVERT: J 139 LEU cc_start: 0.1089 (OUTLIER) cc_final: 0.0775 (tp) REVERT: J 185 LEU cc_start: -0.0238 (OUTLIER) cc_final: -0.0680 (tp) REVERT: J 193 LEU cc_start: 0.1048 (OUTLIER) cc_final: -0.0105 (mp) REVERT: N 4 MET cc_start: 0.1871 (OUTLIER) cc_final: 0.1583 (mmt) outliers start: 194 outliers final: 135 residues processed: 355 average time/residue: 0.4880 time to fit residues: 220.6724 Evaluate side-chains 323 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 159 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 108 GLN Chi-restraints excluded: chain J residue 113 TRP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 143 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 397 optimal weight: 3.9990 chunk 338 optimal weight: 50.0000 chunk 56 optimal weight: 5.9990 chunk 381 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 957 GLN B 207 HIS B 703 ASN B 935 GLN B1010 GLN C 125 ASN K 6 GLN N 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.222005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.175367 restraints weight = 49895.116| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 3.17 r_work: 0.3246 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 35783 Z= 0.187 Angle : 0.763 17.826 48857 Z= 0.366 Chirality : 0.050 0.596 5715 Planarity : 0.005 0.056 6155 Dihedral : 7.523 59.982 6204 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.00 % Favored : 91.84 % Rotamer: Outliers : 4.55 % Allowed : 23.79 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.12), residues: 4302 helix: 0.91 (0.20), residues: 697 sheet: -0.31 (0.14), residues: 1337 loop : -2.11 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.025 0.002 TYR I 160 PHE 0.017 0.002 PHE B 86 TRP 0.030 0.002 TRP H 113 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00454 (35662) covalent geometry : angle 0.73282 (48545) SS BOND : bond 0.00550 ( 51) SS BOND : angle 1.98570 ( 102) hydrogen bonds : bond 0.04583 ( 1144) hydrogen bonds : angle 5.30770 ( 3255) link_BETA1-4 : bond 0.00493 ( 23) link_BETA1-4 : angle 2.71046 ( 69) link_NAG-ASN : bond 0.00453 ( 47) link_NAG-ASN : angle 3.20737 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 167 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.7848 (m) cc_final: 0.7576 (p) REVERT: A 88 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: A 102 ARG cc_start: 0.7350 (mmt90) cc_final: 0.6709 (mmm-85) REVERT: A 190 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6435 (mmt90) REVERT: A 226 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7922 (mt) REVERT: A 346 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.4827 (tpm170) REVERT: A 390 LEU cc_start: 0.3184 (OUTLIER) cc_final: 0.2622 (mt) REVERT: A 452 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.4895 (OUTLIER) REVERT: A 571 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6867 (m-30) REVERT: A 606 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8275 (t0) REVERT: A 916 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9081 (tp) REVERT: A 1001 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9102 (tt) REVERT: A 1113 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: B 52 GLN cc_start: 0.8224 (tm-30) cc_final: 0.8020 (tp-100) REVERT: B 153 MET cc_start: 0.1924 (mpp) cc_final: 0.0719 (mpp) REVERT: B 195 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8025 (ttmt) REVERT: B 237 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7510 (mtt180) REVERT: B 580 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.6607 (mp10) REVERT: B 787 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8408 (mt0) REVERT: C 141 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.6925 (pp) REVERT: C 153 MET cc_start: 0.0729 (OUTLIER) cc_final: -0.2996 (ptt) REVERT: C 299 THR cc_start: 0.9038 (m) cc_final: 0.8821 (m) REVERT: C 581 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8099 (p) REVERT: C 646 ARG cc_start: 0.8587 (tmt-80) cc_final: 0.8380 (mmm160) REVERT: C 787 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8760 (mt0) REVERT: H 112 TYR cc_start: 0.3930 (OUTLIER) cc_final: 0.2266 (m-80) REVERT: H 193 LEU cc_start: 0.1802 (OUTLIER) cc_final: 0.1411 (tp) REVERT: K 148 ARG cc_start: 0.4292 (OUTLIER) cc_final: 0.2606 (mtp180) REVERT: I 20 LEU cc_start: 0.3860 (OUTLIER) cc_final: 0.3431 (tt) REVERT: I 31 SER cc_start: 0.4478 (OUTLIER) cc_final: 0.3825 (t) REVERT: I 75 LYS cc_start: 0.4441 (mmmm) cc_final: 0.4185 (mmmt) REVERT: I 105 LEU cc_start: 0.2870 (pt) cc_final: 0.2036 (mm) REVERT: M 4 MET cc_start: 0.2181 (ptm) cc_final: 0.1325 (pmm) REVERT: M 81 ILE cc_start: 0.0010 (OUTLIER) cc_final: -0.0563 (mp) REVERT: J 102 TYR cc_start: 0.2260 (t80) cc_final: 0.1844 (p90) REVERT: J 108 GLN cc_start: 0.2220 (OUTLIER) cc_final: 0.1461 (pm20) REVERT: J 113 TRP cc_start: 0.2182 (OUTLIER) cc_final: 0.1445 (p90) REVERT: J 114 TYR cc_start: 0.4075 (p90) cc_final: 0.3872 (p90) REVERT: J 139 LEU cc_start: 0.1079 (OUTLIER) cc_final: 0.0773 (tp) REVERT: J 185 LEU cc_start: -0.0434 (OUTLIER) cc_final: -0.0863 (tp) REVERT: N 4 MET cc_start: 0.1912 (OUTLIER) cc_final: 0.1644 (mmt) outliers start: 174 outliers final: 119 residues processed: 325 average time/residue: 0.4927 time to fit residues: 203.9632 Evaluate side-chains 299 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 152 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 108 GLN Chi-restraints excluded: chain J residue 113 TRP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 31 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 345 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 324 optimal weight: 40.0000 chunk 425 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 415 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 703 ASN B 935 GLN B 957 GLN B1010 GLN C 125 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.222575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.177601 restraints weight = 50257.645| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 3.07 r_work: 0.3344 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 35783 Z= 0.154 Angle : 0.751 23.784 48857 Z= 0.356 Chirality : 0.049 0.584 5715 Planarity : 0.005 0.082 6155 Dihedral : 7.355 58.775 6201 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.83 % Favored : 92.00 % Rotamer: Outliers : 3.97 % Allowed : 24.21 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.12), residues: 4302 helix: 1.02 (0.20), residues: 701 sheet: -0.25 (0.14), residues: 1337 loop : -2.05 (0.12), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 319 TYR 0.021 0.001 TYR C1067 PHE 0.016 0.002 PHE B 192 TRP 0.029 0.001 TRP H 113 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00367 (35662) covalent geometry : angle 0.71233 (48545) SS BOND : bond 0.00515 ( 51) SS BOND : angle 1.89841 ( 102) hydrogen bonds : bond 0.04294 ( 1144) hydrogen bonds : angle 5.23891 ( 3255) link_BETA1-4 : bond 0.00865 ( 23) link_BETA1-4 : angle 2.73955 ( 69) link_NAG-ASN : bond 0.00506 ( 47) link_NAG-ASN : angle 3.79598 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 164 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.7967 (m) cc_final: 0.7678 (p) REVERT: A 88 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: A 102 ARG cc_start: 0.7133 (mmt90) cc_final: 0.6655 (mmm-85) REVERT: A 190 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6519 (mmt90) REVERT: A 226 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7943 (mt) REVERT: A 346 ARG cc_start: 0.6089 (OUTLIER) cc_final: 0.4987 (tpt170) REVERT: A 390 LEU cc_start: 0.3015 (OUTLIER) cc_final: 0.2420 (mt) REVERT: A 452 LEU cc_start: 0.5882 (OUTLIER) cc_final: 0.5153 (OUTLIER) REVERT: A 606 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8324 (t0) REVERT: A 729 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.9006 (t) REVERT: A 916 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9013 (tp) REVERT: A 1113 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: B 153 MET cc_start: 0.1975 (mpp) cc_final: 0.0827 (mpp) REVERT: B 237 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7683 (mtt180) REVERT: B 580 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.6647 (mp10) REVERT: B 787 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8376 (mt0) REVERT: C 141 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7047 (pp) REVERT: C 153 MET cc_start: 0.1104 (OUTLIER) cc_final: -0.2555 (ptt) REVERT: C 581 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8168 (p) REVERT: C 646 ARG cc_start: 0.8617 (tmt-80) cc_final: 0.8391 (mmm160) REVERT: H 112 TYR cc_start: 0.4014 (OUTLIER) cc_final: 0.2076 (m-80) REVERT: H 193 LEU cc_start: 0.2075 (OUTLIER) cc_final: 0.1630 (tp) REVERT: K 55 TYR cc_start: 0.3543 (OUTLIER) cc_final: 0.2690 (m-80) REVERT: K 148 ARG cc_start: 0.4411 (OUTLIER) cc_final: 0.2553 (mtp180) REVERT: I 20 LEU cc_start: 0.4042 (OUTLIER) cc_final: 0.3617 (tt) REVERT: I 31 SER cc_start: 0.4127 (OUTLIER) cc_final: 0.3509 (t) REVERT: I 75 LYS cc_start: 0.4270 (mmmm) cc_final: 0.3984 (mmmt) REVERT: I 105 LEU cc_start: 0.2677 (pt) cc_final: 0.1886 (mm) REVERT: M 4 MET cc_start: 0.1732 (ptm) cc_final: 0.1383 (pmm) REVERT: M 81 ILE cc_start: -0.0082 (OUTLIER) cc_final: -0.0397 (mm) REVERT: J 102 TYR cc_start: 0.2347 (t80) cc_final: 0.2038 (p90) REVERT: J 113 TRP cc_start: 0.1939 (OUTLIER) cc_final: 0.1183 (p90) REVERT: J 139 LEU cc_start: 0.1100 (OUTLIER) cc_final: 0.0898 (tp) REVERT: J 185 LEU cc_start: -0.0490 (OUTLIER) cc_final: -0.0854 (tp) outliers start: 152 outliers final: 112 residues processed: 302 average time/residue: 0.5063 time to fit residues: 193.6327 Evaluate side-chains 292 residues out of total 3825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 156 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain K residue 55 TYR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 81 ILE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 113 TRP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 185 LEU Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 166 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 412 optimal weight: 30.0000 chunk 211 optimal weight: 0.3980 chunk 269 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 414 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.222713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.175953 restraints weight = 49831.706| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.15 r_work: 0.3248 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.210 35783 Z= 0.190 Angle : 0.827 59.168 48857 Z= 0.417 Chirality : 0.050 0.643 5715 Planarity : 0.005 0.079 6155 Dihedral : 7.331 58.788 6196 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.86 % Favored : 91.98 % Rotamer: Outliers : 3.79 % Allowed : 24.37 % Favored : 71.84 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.12), residues: 4302 helix: 1.04 (0.20), residues: 701 sheet: -0.25 (0.14), residues: 1337 loop : -2.05 (0.12), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.021 0.001 TYR C1067 PHE 0.016 0.001 PHE B 192 TRP 0.026 0.001 TRP H 113 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00404 (35662) covalent geometry : angle 0.79263 (48545) SS BOND : bond 0.00515 ( 51) SS BOND : angle 1.88123 ( 102) hydrogen bonds : bond 0.04263 ( 1144) hydrogen bonds : angle 5.25187 ( 3255) link_BETA1-4 : bond 0.00663 ( 23) link_BETA1-4 : angle 2.75141 ( 69) link_NAG-ASN : bond 0.00484 ( 47) link_NAG-ASN : angle 3.78560 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12625.70 seconds wall clock time: 215 minutes 17.40 seconds (12917.40 seconds total)