Starting phenix.real_space_refine on Fri Mar 6 12:24:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7czw_30519/03_2026/7czw_30519.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czw_30519/03_2026/7czw_30519.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7czw_30519/03_2026/7czw_30519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czw_30519/03_2026/7czw_30519.map" model { file = "/net/cci-nas-00/data/ceres_data/7czw_30519/03_2026/7czw_30519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czw_30519/03_2026/7czw_30519.cif" } 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 19667 2.51 5 N 5060 2.21 5 O 6148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 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: 31004 Number of models: 1 Model: "" Number of chains: 31 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: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1727 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1579 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 14, 'TRANS': 199} Chain: "J" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1727 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1579 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 14, 'TRANS': 199} 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "B" 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: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.66, per 1000 atoms: 0.25 Number of scatterers: 31004 At special positions: 0 Unit cell: (134.788, 169.572, 250.01, 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 129 16.00 O 6148 8.00 N 5060 7.00 C 19667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.33 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.36 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 112 " distance=2.19 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 97 " distance=2.04 Simple disulfide: pdb=" SG CYS J 102 " - pdb=" SG CYS J 112 " distance=2.19 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 211 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 139 " - pdb=" SG CYS N 198 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1410 " - " NAG B1411 " " 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 I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 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 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " 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 B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG B1410 " - " 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 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " 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: 2.58 Conformation dependent library (CDL) restraints added in 923.5 milliseconds 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7244 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 64 sheets defined 19.5% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A 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: 3.860A 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: 3.631A 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: 3.771A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A 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: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.633A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.538A 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: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.575A 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: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.647A 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: 4.632A 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: 3.647A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A 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 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.640A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.543A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A 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: 3.846A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A 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: 3.704A 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: 4.372A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A 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: 3.582A 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: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.625A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.861A 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 616 through 620 removed outlier: 3.582A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A 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: 3.721A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A 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: 3.590A 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: 3.712A 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: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.554A 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: 3.755A 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: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A 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 88 through 92 removed outlier: 3.947A pdb=" N ASP H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 92' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 186 through 193 Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.947A pdb=" N ASP J 91 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR J 92 " --> pdb=" O ALA J 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 88 through 92' 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 126 through 132 Processing helix chain 'N' and resid 186 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A 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: 4.437A 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 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A 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: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A 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: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) 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 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A 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) removed outlier: 6.949A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A 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=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, 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: 6.830A 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: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.969A 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=AB5, 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: 6.830A 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: 3.978A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.728A 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: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, 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=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, 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=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.538A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.649A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.421A 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: 6.769A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A 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=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A 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: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, 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=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.756A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS C 291 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, 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=AE1, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.865A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.231A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (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: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A 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=AE6, 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: 3.880A 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=AE7, 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=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.444A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 98 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR H 95 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR H 122 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.008A pdb=" N ALA H 152 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.765A 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: 7.048A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.180A 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: 6.573A 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: 5.008A pdb=" N ALA H 152 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.765A 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: 7.048A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.180A 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: 6.573A 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 'L' and resid 9 through 12 removed outlier: 6.973A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET L 49 " --> pdb=" O TRP L 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'L' and resid 119 through 123 Processing sheet with id=AF8, first strand: chain 'L' and resid 119 through 123 Processing sheet with id=AF9, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.441A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'J' and resid 59 through 61 removed outlier: 5.445A pdb=" N TRP J 49 " --> pdb=" O ARG J 40 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG J 40 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY J 51 " --> pdb=" O TRP J 38 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA J 98 " --> pdb=" O SER J 37 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR J 95 " --> pdb=" O THR J 122 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR J 122 " --> pdb=" O TYR J 95 " (cutoff:3.500A) Processing sheet with id=AG3, 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: 6.764A pdb=" N VAL J 199 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 154 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL J 197 " --> pdb=" O GLY J 154 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU J 156 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 195 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 158 " --> pdb=" O LEU J 193 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 193 " --> pdb=" O LYS J 158 " (cutoff:3.500A) Processing sheet with id=AG4, 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: 6.764A pdb=" N VAL J 199 " --> pdb=" O ALA J 152 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 154 " --> pdb=" O VAL J 197 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL J 197 " --> pdb=" O GLY J 154 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU J 156 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 195 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 158 " --> pdb=" O LEU J 193 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 193 " --> pdb=" O LYS J 158 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 165 through 169 Processing sheet with id=AG6, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.972A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET N 49 " --> pdb=" O TRP N 37 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AG8, first strand: chain 'N' and resid 119 through 123 Processing sheet with id=AG9, first strand: chain 'N' and resid 119 through 123 Processing sheet with id=AH1, first strand: chain 'N' and resid 159 through 160 removed outlier: 4.442A pdb=" N TRP N 153 " --> pdb=" O VAL N 160 " (cutoff:3.500A) 1191 hydrogen bonds defined for protein. 3207 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: 7.83 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9615 1.34 - 1.46: 8183 1.46 - 1.59: 13735 1.59 - 1.72: 0 1.72 - 1.84: 158 Bond restraints: 31691 Sorted by residual: bond pdb=" C THR C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.34e-02 5.57e+03 1.82e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.067 1.59e-02 3.96e+03 1.77e+01 bond pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" N PRO L 7 " pdb=" CD PRO L 7 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" N PRO N 7 " pdb=" CD PRO N 7 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 ... (remaining 31686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 42080 2.69 - 5.38: 970 5.38 - 8.07: 73 8.07 - 10.76: 9 10.76 - 13.45: 4 Bond angle restraints: 43136 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.80 -11.26 1.91e+00 2.74e-01 3.48e+01 angle pdb=" N GLU C 156 " pdb=" CA GLU C 156 " pdb=" C GLU C 156 " ideal model delta sigma weight residual 108.45 115.85 -7.40 1.26e+00 6.30e-01 3.45e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 119.78 114.11 5.67 1.03e+00 9.43e-01 3.03e+01 angle pdb=" C LEU B 212 " pdb=" N VAL B 213 " pdb=" CA VAL B 213 " ideal model delta sigma weight residual 123.08 117.63 5.45 1.01e+00 9.80e-01 2.91e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 122.56 115.27 7.29 1.50e+00 4.44e-01 2.36e+01 ... (remaining 43131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17052 17.92 - 35.85: 1940 35.85 - 53.77: 573 53.77 - 71.69: 186 71.69 - 89.61: 59 Dihedral angle restraints: 19810 sinusoidal: 8541 harmonic: 11269 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.11 80.89 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.63 73.37 1 1.00e+01 1.00e-02 6.85e+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 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 19807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 5110 0.329 - 0.658: 3 0.658 - 0.986: 3 0.986 - 1.315: 0 1.315 - 1.644: 1 Chirality restraints: 5117 Sorted by residual: chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.76e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 5114 not shown) Planarity restraints: 5508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 109 " 0.062 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO J 110 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO J 110 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO J 110 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 109 " -0.062 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO H 110 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO H 110 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO H 110 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " -0.022 2.00e-02 2.50e+03 3.13e-02 1.22e+01 pdb=" CG ASN C1134 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.034 2.00e-02 2.50e+03 ... (remaining 5505 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 360 2.56 - 3.15: 24446 3.15 - 3.73: 45311 3.73 - 4.32: 65650 4.32 - 4.90: 109618 Nonbonded interactions: 245385 Sorted by model distance: nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.981 3.120 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.981 3.120 nonbonded pdb=" O ALA C 522 " pdb=" OG1 THR C 523 " model vdw 2.137 3.040 nonbonded pdb=" O ALA A 522 " pdb=" OG1 THR A 523 " model vdw 2.137 3.040 nonbonded pdb=" O SER A 813 " pdb=" OG SER A 813 " model vdw 2.183 3.040 ... (remaining 245380 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 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 620 or resid 641 through 939 or resid 944 through 14 \ 08)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1408)) selection = (chain 'C' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 826 or resid 855 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' 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 'J' } ncs_group { reference = chain 'L' 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: 2.350 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: 0.060 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.750 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 0.011 0.330 31809 Z= 0.496 Angle : 1.180 48.875 43442 Z= 0.620 Chirality : 0.068 1.644 5117 Planarity : 0.007 0.096 5460 Dihedral : 17.561 89.613 12422 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 1.23 % Allowed : 9.99 % Favored : 88.77 % Rotamer: Outliers : 11.42 % Allowed : 19.20 % Favored : 69.38 % 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: -3.75 (0.11), residues: 3812 helix: -2.14 (0.16), residues: 679 sheet: -1.69 (0.14), residues: 1131 loop : -3.17 (0.11), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.026 0.003 TYR B 265 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.003 TRP A 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01066 (31691) covalent geometry : angle 0.99597 (43136) SS BOND : bond 0.07595 ( 48) SS BOND : angle 8.75524 ( 96) hydrogen bonds : bond 0.18978 ( 1109) hydrogen bonds : angle 7.84689 ( 3207) link_BETA1-4 : bond 0.04164 ( 22) link_BETA1-4 : angle 4.32701 ( 66) link_NAG-ASN : bond 0.03397 ( 48) link_NAG-ASN : angle 7.95053 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 386 poor density : 409 time to evaluate : 1.127 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 TARDY: cannot create tardy model for: "SER H 128 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER J 128 " (corrupted residue). Skipping it. REVERT: A 51 THR cc_start: 0.7986 (p) cc_final: 0.7656 (m) REVERT: A 153 MET cc_start: -0.0525 (mpp) cc_final: -0.2254 (ptp) REVERT: A 785 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8147 (m) REVERT: A 1039 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7361 (mtp180) REVERT: B 50 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7857 (t) REVERT: B 95 THR cc_start: 0.4761 (OUTLIER) cc_final: 0.4507 (p) REVERT: B 153 MET cc_start: 0.0535 (ttp) cc_final: 0.0291 (ttp) REVERT: B 278 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8560 (ttmt) REVERT: B 371 SER cc_start: 0.4996 (OUTLIER) cc_final: 0.4706 (p) REVERT: B 430 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6711 (m) REVERT: B 514 SER cc_start: 0.5993 (OUTLIER) cc_final: 0.5506 (m) REVERT: B 581 THR cc_start: 0.7561 (p) cc_final: 0.7330 (t) REVERT: B 878 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8831 (tp) REVERT: B 1029 MET cc_start: 0.9146 (tpp) cc_final: 0.8819 (tpp) REVERT: C 117 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6704 (pt) REVERT: C 306 PHE cc_start: 0.7819 (m-80) cc_final: 0.7486 (m-80) REVERT: C 335 LEU cc_start: 0.4195 (OUTLIER) cc_final: 0.3553 (tp) REVERT: C 382 VAL cc_start: 0.1613 (OUTLIER) cc_final: 0.1383 (t) REVERT: C 486 PHE cc_start: -0.0015 (OUTLIER) cc_final: -0.0263 (t80) REVERT: C 1027 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8513 (m) REVERT: H 34 TYR cc_start: 0.1876 (m-80) cc_final: 0.1089 (m-80) REVERT: H 120 GLN cc_start: 0.2929 (OUTLIER) cc_final: 0.2354 (pt0) REVERT: L 49 MET cc_start: 0.1579 (pmm) cc_final: -0.1091 (mtt) REVERT: L 75 LEU cc_start: -0.0051 (tp) cc_final: -0.0275 (tt) REVERT: L 97 SER cc_start: 0.1828 (OUTLIER) cc_final: 0.1523 (m) REVERT: L 108 LEU cc_start: -0.0723 (tp) cc_final: -0.1000 (pp) REVERT: L 140 LEU cc_start: 0.0911 (mp) cc_final: 0.0457 (tp) REVERT: L 185 LEU cc_start: 0.0079 (OUTLIER) cc_final: -0.0145 (mm) REVERT: J 120 GLN cc_start: 0.2738 (OUTLIER) cc_final: 0.1610 (pt0) REVERT: N 119 SER cc_start: 0.1390 (OUTLIER) cc_final: 0.1128 (p) REVERT: N 185 LEU cc_start: 0.1878 (OUTLIER) cc_final: 0.1230 (mp) outliers start: 386 outliers final: 85 residues processed: 741 average time/residue: 0.4563 time to fit residues: 423.0008 Evaluate side-chains 314 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 209 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1027 THR 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 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain J residue 112 CYS Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 158 SER Chi-restraints excluded: chain N residue 185 LEU Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 188 ASN A 422 ASN A 493 GLN A 498 GLN A 542 ASN A 607 GLN A 644 GLN A 690 GLN A 703 ASN A 755 GLN A 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 969 ASN A 992 GLN A1005 GLN A1011 GLN A1101 HIS A1125 ASN B 115 GLN B 188 ASN B 314 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 563 GLN B 690 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1010 GLN B1054 GLN B1142 GLN C 30 ASN C 66 HIS C 134 GLN C 188 ASN C 321 GLN C 422 ASN C 498 GLN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 926 GLN C 957 GLN C 969 ASN C 992 GLN C1005 GLN C1010 GLN C1071 GLN C1101 HIS H 60 ASN H 186 GLN L 40 GLN L 133 ASN L 193 HIS L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN J 186 GLN N 40 GLN N 193 HIS N 199 GLN ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.226915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.182333 restraints weight = 42524.876| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.52 r_work: 0.3766 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 31809 Z= 0.207 Angle : 0.877 17.328 43442 Z= 0.427 Chirality : 0.053 0.609 5117 Planarity : 0.006 0.069 5460 Dihedral : 9.605 68.946 5760 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.95 % Favored : 92.81 % Rotamer: Outliers : 6.95 % Allowed : 21.83 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.12), residues: 3812 helix: -0.29 (0.19), residues: 697 sheet: -0.81 (0.15), residues: 1076 loop : -2.58 (0.12), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 108 TYR 0.035 0.002 TYR H 104 PHE 0.025 0.002 PHE C 157 TRP 0.017 0.002 TRP J 38 HIS 0.009 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00473 (31691) covalent geometry : angle 0.83171 (43136) SS BOND : bond 0.00864 ( 48) SS BOND : angle 1.99192 ( 96) hydrogen bonds : bond 0.05053 ( 1109) hydrogen bonds : angle 5.86512 ( 3207) link_BETA1-4 : bond 0.00608 ( 22) link_BETA1-4 : angle 2.53081 ( 66) link_NAG-ASN : bond 0.00532 ( 48) link_NAG-ASN : angle 4.36258 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 228 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER H 128 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER J 128 " (corrupted residue). Skipping it. REVERT: A 51 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7749 (m) REVERT: A 153 MET cc_start: -0.0254 (mpp) cc_final: -0.2087 (ptp) REVERT: A 389 ASP cc_start: 0.5416 (OUTLIER) cc_final: 0.4062 (t70) REVERT: A 692 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8417 (mm) REVERT: A 1010 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8112 (mp10) REVERT: A 1084 ASP cc_start: 0.7936 (t70) cc_final: 0.7683 (t0) REVERT: B 125 ASN cc_start: 0.6219 (m-40) cc_final: 0.5972 (m-40) REVERT: B 164 ASN cc_start: 0.5201 (OUTLIER) cc_final: 0.4591 (t0) REVERT: B 360 ASN cc_start: 0.7861 (m-40) cc_final: 0.7584 (m-40) REVERT: B 389 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.6357 (m-30) REVERT: B 430 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.6857 (m) REVERT: B 455 LEU cc_start: 0.2317 (OUTLIER) cc_final: 0.1872 (tp) REVERT: B 731 MET cc_start: 0.8574 (mtm) cc_final: 0.8283 (mtm) REVERT: B 787 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8599 (mt0) REVERT: C 153 MET cc_start: -0.0291 (OUTLIER) cc_final: -0.1106 (mpt) REVERT: C 205 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8483 (t) REVERT: C 306 PHE cc_start: 0.8119 (m-80) cc_final: 0.7724 (m-80) REVERT: C 985 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6818 (p0) REVERT: H 82 LEU cc_start: 0.1358 (OUTLIER) cc_final: 0.0000 (mp) REVERT: H 193 LEU cc_start: -0.1970 (OUTLIER) cc_final: -0.2491 (mp) REVERT: H 204 LEU cc_start: 0.2776 (mt) cc_final: 0.1160 (pt) REVERT: L 49 MET cc_start: 0.1602 (pmm) cc_final: -0.0314 (mtt) REVERT: L 97 SER cc_start: 0.2520 (OUTLIER) cc_final: 0.2125 (m) REVERT: J 123 LEU cc_start: 0.1692 (OUTLIER) cc_final: 0.1368 (mt) REVERT: N 49 MET cc_start: 0.2403 (OUTLIER) cc_final: -0.0482 (ttm) outliers start: 235 outliers final: 87 residues processed: 439 average time/residue: 0.4374 time to fit residues: 242.6986 Evaluate side-chains 285 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 181 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 973 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 36 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 985 ASP 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 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 199 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 252 optimal weight: 8.9990 chunk 52 optimal weight: 0.0870 chunk 231 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 212 optimal weight: 10.0000 chunk 287 optimal weight: 3.9990 chunk 146 optimal weight: 0.2980 chunk 213 optimal weight: 9.9990 chunk 292 optimal weight: 0.6980 chunk 243 optimal weight: 9.9990 chunk 331 optimal weight: 20.0000 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 440 ASN A 450 ASN A 493 GLN A 542 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 957 GLN B 87 ASN B 207 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1142 GLN C 207 HIS C 218 GLN C 556 ASN C 580 GLN C 957 GLN C1005 GLN C1106 GLN L 39 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.225779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.181050 restraints weight = 42380.050| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.58 r_work: 0.3554 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31809 Z= 0.139 Angle : 0.743 13.318 43442 Z= 0.359 Chirality : 0.048 0.271 5117 Planarity : 0.005 0.055 5460 Dihedral : 8.063 59.437 5663 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.69 % Favored : 93.07 % Rotamer: Outliers : 5.12 % Allowed : 23.43 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.13), residues: 3812 helix: 0.64 (0.20), residues: 698 sheet: -0.50 (0.15), residues: 1106 loop : -2.23 (0.12), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.024 0.001 TYR H 104 PHE 0.022 0.001 PHE A 192 TRP 0.012 0.001 TRP H 49 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00310 (31691) covalent geometry : angle 0.70178 (43136) SS BOND : bond 0.00637 ( 48) SS BOND : angle 1.81528 ( 96) hydrogen bonds : bond 0.04362 ( 1109) hydrogen bonds : angle 5.45735 ( 3207) link_BETA1-4 : bond 0.00676 ( 22) link_BETA1-4 : angle 2.48306 ( 66) link_NAG-ASN : bond 0.00559 ( 48) link_NAG-ASN : angle 3.72472 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 201 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7774 (m) REVERT: A 153 MET cc_start: -0.0066 (mpp) cc_final: -0.2297 (ptp) REVERT: B 129 LYS cc_start: 0.6908 (mtpp) cc_final: 0.6428 (mtmm) REVERT: B 164 ASN cc_start: 0.4893 (OUTLIER) cc_final: 0.4271 (t0) REVERT: B 360 ASN cc_start: 0.8047 (m-40) cc_final: 0.7706 (m-40) REVERT: B 414 GLN cc_start: 0.3136 (OUTLIER) cc_final: 0.2038 (mp10) REVERT: B 1029 MET cc_start: 0.9132 (tpp) cc_final: 0.8861 (tpp) REVERT: C 61 ASN cc_start: 0.5580 (OUTLIER) cc_final: 0.5119 (m-40) REVERT: C 86 PHE cc_start: 0.5843 (OUTLIER) cc_final: 0.5221 (t80) REVERT: C 153 MET cc_start: -0.0039 (OUTLIER) cc_final: -0.1136 (mpt) REVERT: C 190 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6711 (mtp85) REVERT: C 205 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8498 (t) REVERT: C 306 PHE cc_start: 0.8206 (m-80) cc_final: 0.7785 (m-80) REVERT: C 558 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.6059 (mttm) REVERT: H 82 LEU cc_start: 0.1565 (OUTLIER) cc_final: 0.0194 (mp) REVERT: L 49 MET cc_start: 0.1777 (pmm) cc_final: -0.0480 (mtt) REVERT: J 190 LEU cc_start: 0.2538 (mt) cc_final: 0.1697 (tt) REVERT: N 49 MET cc_start: 0.2086 (OUTLIER) cc_final: -0.0708 (ttm) outliers start: 173 outliers final: 77 residues processed: 346 average time/residue: 0.4582 time to fit residues: 198.9898 Evaluate side-chains 254 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 166 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR 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 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 856 ASN 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 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 199 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 99 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 363 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 342 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 155 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 354 ASN A 422 ASN A 606 ASN A 856 ASN A1058 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 658 ASN B 935 GLN B1142 GLN C 271 GLN C 957 GLN C1005 GLN L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN N 199 GLN ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.221673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.178737 restraints weight = 41733.823| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.34 r_work: 0.3742 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 31809 Z= 0.228 Angle : 0.831 14.255 43442 Z= 0.403 Chirality : 0.053 0.455 5117 Planarity : 0.005 0.055 5460 Dihedral : 8.103 59.765 5651 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.29 % Favored : 92.42 % Rotamer: Outliers : 6.04 % Allowed : 22.01 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 3812 helix: 0.64 (0.20), residues: 694 sheet: -0.40 (0.15), residues: 1118 loop : -2.12 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 99 TYR 0.027 0.002 TYR A1067 PHE 0.023 0.002 PHE B 43 TRP 0.014 0.002 TRP J 118 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00552 (31691) covalent geometry : angle 0.79158 (43136) SS BOND : bond 0.00541 ( 48) SS BOND : angle 2.05758 ( 96) hydrogen bonds : bond 0.05444 ( 1109) hydrogen bonds : angle 5.64322 ( 3207) link_BETA1-4 : bond 0.00586 ( 22) link_BETA1-4 : angle 2.58067 ( 66) link_NAG-ASN : bond 0.00682 ( 48) link_NAG-ASN : angle 3.83141 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 200 time to evaluate : 1.044 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 153 MET cc_start: 0.0680 (mpp) cc_final: -0.1951 (ptp) REVERT: A 577 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8309 (ptp-110) REVERT: A 692 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8634 (mm) REVERT: A 916 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9081 (tt) REVERT: A 1010 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8328 (mp10) REVERT: B 164 ASN cc_start: 0.5254 (OUTLIER) cc_final: 0.4862 (t0) REVERT: B 360 ASN cc_start: 0.8023 (m-40) cc_final: 0.7806 (m-40) REVERT: B 389 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6620 (m-30) REVERT: B 414 GLN cc_start: 0.3488 (OUTLIER) cc_final: 0.2424 (mp10) REVERT: B 528 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6831 (mtmt) REVERT: B 567 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6171 (ptm160) REVERT: B 1010 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: C 190 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6425 (mtp85) REVERT: C 306 PHE cc_start: 0.8169 (m-80) cc_final: 0.7673 (m-80) REVERT: C 558 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.6059 (mttm) REVERT: H 82 LEU cc_start: 0.1732 (OUTLIER) cc_final: 0.0194 (mp) REVERT: L 49 MET cc_start: 0.1732 (pmm) cc_final: -0.0502 (mtt) REVERT: J 190 LEU cc_start: 0.3273 (mt) cc_final: 0.2120 (pp) REVERT: N 49 MET cc_start: 0.2869 (OUTLIER) cc_final: -0.0316 (ttm) outliers start: 204 outliers final: 101 residues processed: 385 average time/residue: 0.4550 time to fit residues: 220.1324 Evaluate side-chains 282 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 167 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1010 GLN 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 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR 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 1125 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 206 THR Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 199 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 60 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 35 optimal weight: 30.0000 chunk 235 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 358 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 374 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 239 GLN A 544 ASN A 675 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 506 GLN B 542 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C1005 GLN L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN ** N 202 HIS ** 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 = 0.4551 r_free = 0.4551 target = 0.223333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.178906 restraints weight = 41921.815| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.45 r_work: 0.3690 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31809 Z= 0.129 Angle : 0.715 14.764 43442 Z= 0.344 Chirality : 0.047 0.275 5117 Planarity : 0.004 0.055 5460 Dihedral : 7.485 58.677 5647 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.24 % Favored : 93.52 % Rotamer: Outliers : 4.32 % Allowed : 23.85 % Favored : 71.83 % 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: -1.21 (0.13), residues: 3812 helix: 1.21 (0.21), residues: 683 sheet: -0.17 (0.15), residues: 1112 loop : -1.96 (0.12), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 108 TYR 0.019 0.001 TYR B 453 PHE 0.019 0.001 PHE A 192 TRP 0.016 0.001 TRP H 114 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00290 (31691) covalent geometry : angle 0.68202 (43136) SS BOND : bond 0.00456 ( 48) SS BOND : angle 1.80239 ( 96) hydrogen bonds : bond 0.03985 ( 1109) hydrogen bonds : angle 5.30993 ( 3207) link_BETA1-4 : bond 0.00586 ( 22) link_BETA1-4 : angle 2.17414 ( 66) link_NAG-ASN : bond 0.00460 ( 48) link_NAG-ASN : angle 3.23485 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 190 time to evaluate : 0.907 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 116 SER cc_start: 0.6636 (OUTLIER) cc_final: 0.6355 (t) REVERT: A 153 MET cc_start: 0.0659 (mpp) cc_final: -0.2008 (ptp) REVERT: A 673 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7875 (p) REVERT: A 692 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8681 (mm) REVERT: A 964 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8231 (mppt) REVERT: B 164 ASN cc_start: 0.4978 (OUTLIER) cc_final: 0.4562 (t0) REVERT: B 359 SER cc_start: 0.7701 (OUTLIER) cc_final: 0.7309 (m) REVERT: B 360 ASN cc_start: 0.8050 (m-40) cc_final: 0.7809 (m-40) REVERT: B 389 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: B 414 GLN cc_start: 0.3362 (OUTLIER) cc_final: 0.2210 (mp10) REVERT: B 528 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.6837 (mtpt) REVERT: B 564 GLN cc_start: 0.6278 (tp40) cc_final: 0.5880 (tp40) REVERT: B 787 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8750 (mt0) REVERT: B 867 ASP cc_start: 0.8074 (p0) cc_final: 0.7798 (m-30) REVERT: C 153 MET cc_start: 0.1098 (pp-130) cc_final: 0.0877 (pp-130) REVERT: C 190 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6422 (mtp85) REVERT: H 82 LEU cc_start: 0.1672 (OUTLIER) cc_final: 0.0169 (mp) REVERT: H 227 GLU cc_start: 0.1461 (OUTLIER) cc_final: 0.1078 (mp0) REVERT: L 49 MET cc_start: 0.1796 (pmm) cc_final: -0.0557 (mtt) REVERT: L 140 LEU cc_start: 0.1121 (OUTLIER) cc_final: 0.0797 (pp) REVERT: J 11 LEU cc_start: 0.2010 (OUTLIER) cc_final: 0.1807 (mt) REVERT: J 100 GLU cc_start: 0.0805 (OUTLIER) cc_final: 0.0603 (mm-30) REVERT: J 111 ARG cc_start: 0.2774 (OUTLIER) cc_final: 0.2549 (ptp-110) REVERT: J 190 LEU cc_start: 0.3088 (mt) cc_final: 0.1914 (pp) REVERT: N 49 MET cc_start: 0.2523 (OUTLIER) cc_final: -0.0508 (ttm) outliers start: 146 outliers final: 82 residues processed: 321 average time/residue: 0.4710 time to fit residues: 189.2959 Evaluate side-chains 263 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 163 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1045 LYS 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 61 ASN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR 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 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 111 ARG Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 197 SER Chi-restraints excluded: chain N residue 199 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 121 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 291 optimal weight: 0.6980 chunk 352 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 312 optimal weight: 50.0000 chunk 37 optimal weight: 7.9990 chunk 335 optimal weight: 0.0470 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 506 GLN B 542 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 755 GLN C1005 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.222926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.178471 restraints weight = 41817.802| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.33 r_work: 0.3684 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 31809 Z= 0.141 Angle : 0.715 16.161 43442 Z= 0.344 Chirality : 0.048 0.415 5117 Planarity : 0.004 0.082 5460 Dihedral : 7.309 58.814 5646 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.48 % Favored : 93.28 % Rotamer: Outliers : 4.38 % Allowed : 23.79 % Favored : 71.83 % 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: -1.03 (0.13), residues: 3812 helix: 1.35 (0.21), residues: 683 sheet: -0.04 (0.15), residues: 1111 loop : -1.87 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.018 0.001 TYR C1067 PHE 0.015 0.001 PHE B 86 TRP 0.017 0.001 TRP H 114 HIS 0.004 0.001 HIS J 215 Details of bonding type rmsd covalent geometry : bond 0.00329 (31691) covalent geometry : angle 0.68218 (43136) SS BOND : bond 0.00519 ( 48) SS BOND : angle 1.73051 ( 96) hydrogen bonds : bond 0.04063 ( 1109) hydrogen bonds : angle 5.24596 ( 3207) link_BETA1-4 : bond 0.00557 ( 22) link_BETA1-4 : angle 2.14664 ( 66) link_NAG-ASN : bond 0.00436 ( 48) link_NAG-ASN : angle 3.29393 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 172 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.6641 (OUTLIER) cc_final: 0.6367 (t) REVERT: A 153 MET cc_start: 0.0364 (mpp) cc_final: -0.2199 (ptp) REVERT: A 673 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.7923 (p) REVERT: A 692 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8708 (mm) REVERT: A 964 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8183 (mppt) REVERT: B 157 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5545 (t80) REVERT: B 164 ASN cc_start: 0.4944 (OUTLIER) cc_final: 0.4538 (t0) REVERT: B 360 ASN cc_start: 0.7992 (m-40) cc_final: 0.7781 (m-40) REVERT: B 389 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6961 (m-30) REVERT: B 414 GLN cc_start: 0.3202 (OUTLIER) cc_final: 0.2132 (mp10) REVERT: B 473 TYR cc_start: 0.1625 (OUTLIER) cc_final: 0.1346 (m-80) REVERT: B 528 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.6968 (mtpt) REVERT: B 564 GLN cc_start: 0.6246 (tp40) cc_final: 0.5828 (tp40) REVERT: B 787 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8778 (mt0) REVERT: B 867 ASP cc_start: 0.8080 (p0) cc_final: 0.7860 (m-30) REVERT: C 190 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6507 (mtp85) REVERT: H 82 LEU cc_start: 0.1695 (OUTLIER) cc_final: 0.0127 (mp) REVERT: L 49 MET cc_start: 0.1824 (pmm) cc_final: -0.0558 (mtt) REVERT: L 140 LEU cc_start: 0.0937 (OUTLIER) cc_final: 0.0500 (pp) REVERT: J 111 ARG cc_start: 0.2706 (OUTLIER) cc_final: 0.2313 (ptp-110) REVERT: J 190 LEU cc_start: 0.3133 (mt) cc_final: 0.1902 (pp) REVERT: N 49 MET cc_start: 0.2552 (OUTLIER) cc_final: -0.0513 (ttm) outliers start: 148 outliers final: 88 residues processed: 304 average time/residue: 0.4896 time to fit residues: 184.4100 Evaluate side-chains 268 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 164 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1045 LYS 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 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR 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 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 111 ARG Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 197 SER Chi-restraints excluded: chain N residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 48 optimal weight: 0.2980 chunk 171 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 272 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 957 GLN B 207 HIS B 437 ASN B 506 GLN B 542 ASN B 703 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 ASN N 199 GLN ** N 202 HIS ** 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 = 0.4553 r_free = 0.4553 target = 0.223231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.183766 restraints weight = 41968.426| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.10 r_work: 0.3812 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 31809 Z= 0.150 Angle : 0.717 15.018 43442 Z= 0.345 Chirality : 0.048 0.304 5117 Planarity : 0.004 0.075 5460 Dihedral : 7.232 59.098 5644 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.66 % Favored : 93.10 % Rotamer: Outliers : 4.17 % Allowed : 24.08 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 3812 helix: 1.37 (0.21), residues: 685 sheet: 0.13 (0.15), residues: 1094 loop : -1.84 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.020 0.001 TYR A 170 PHE 0.021 0.001 PHE A 140 TRP 0.015 0.001 TRP H 114 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00353 (31691) covalent geometry : angle 0.68724 (43136) SS BOND : bond 0.00493 ( 48) SS BOND : angle 1.68131 ( 96) hydrogen bonds : bond 0.04158 ( 1109) hydrogen bonds : angle 5.20113 ( 3207) link_BETA1-4 : bond 0.00522 ( 22) link_BETA1-4 : angle 2.09994 ( 66) link_NAG-ASN : bond 0.00484 ( 48) link_NAG-ASN : angle 3.14432 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 176 time to evaluate : 1.043 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 116 SER cc_start: 0.6438 (OUTLIER) cc_final: 0.6035 (t) REVERT: A 153 MET cc_start: 0.0353 (OUTLIER) cc_final: -0.2269 (ptp) REVERT: A 517 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.4860 (mp) REVERT: A 577 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8222 (ptp-110) REVERT: A 673 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.7919 (p) REVERT: A 692 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8644 (mm) REVERT: A 964 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8147 (mppt) REVERT: B 164 ASN cc_start: 0.4875 (OUTLIER) cc_final: 0.4450 (t0) REVERT: B 389 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: B 414 GLN cc_start: 0.3211 (OUTLIER) cc_final: 0.2096 (mp10) REVERT: B 473 TYR cc_start: 0.1646 (OUTLIER) cc_final: 0.1028 (m-80) REVERT: B 528 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7011 (mtpt) REVERT: B 564 GLN cc_start: 0.6113 (tp40) cc_final: 0.5695 (tp40) REVERT: B 787 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8681 (mt0) REVERT: B 912 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8636 (m) REVERT: C 306 PHE cc_start: 0.8157 (m-80) cc_final: 0.7705 (m-80) REVERT: H 82 LEU cc_start: 0.1661 (OUTLIER) cc_final: 0.0112 (mp) REVERT: L 35 VAL cc_start: -0.0757 (OUTLIER) cc_final: -0.0965 (m) REVERT: L 49 MET cc_start: 0.1301 (pmm) cc_final: -0.0793 (mtt) REVERT: L 140 LEU cc_start: 0.0915 (OUTLIER) cc_final: 0.0691 (pp) REVERT: J 11 LEU cc_start: 0.2039 (pp) cc_final: 0.0990 (mt) REVERT: J 111 ARG cc_start: 0.2620 (OUTLIER) cc_final: 0.2392 (ptp-110) REVERT: J 190 LEU cc_start: 0.3223 (mt) cc_final: 0.2146 (pp) REVERT: N 49 MET cc_start: 0.2833 (OUTLIER) cc_final: -0.0283 (ttm) outliers start: 141 outliers final: 95 residues processed: 302 average time/residue: 0.4557 time to fit residues: 173.3317 Evaluate side-chains 272 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 158 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1045 LYS 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 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR 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 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 111 ARG Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 197 SER Chi-restraints excluded: chain N residue 199 GLN Chi-restraints excluded: chain N residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 357 optimal weight: 40.0000 chunk 319 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 301 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 361 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 326 optimal weight: 0.0030 chunk 155 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 207 HIS B 437 ASN B 506 GLN B 542 ASN B 935 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 751 ASN L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.223287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.181313 restraints weight = 42061.666| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.23 r_work: 0.3776 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 31809 Z= 0.140 Angle : 0.710 14.364 43442 Z= 0.342 Chirality : 0.048 0.276 5117 Planarity : 0.004 0.068 5460 Dihedral : 7.132 59.582 5644 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.45 % Favored : 93.34 % Rotamer: Outliers : 4.44 % Allowed : 23.88 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 3812 helix: 1.42 (0.21), residues: 685 sheet: 0.20 (0.15), residues: 1092 loop : -1.76 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.024 0.001 TYR H 54 PHE 0.014 0.001 PHE A 140 TRP 0.019 0.001 TRP H 114 HIS 0.004 0.001 HIS J 215 Details of bonding type rmsd covalent geometry : bond 0.00326 (31691) covalent geometry : angle 0.68063 (43136) SS BOND : bond 0.00532 ( 48) SS BOND : angle 1.84057 ( 96) hydrogen bonds : bond 0.04002 ( 1109) hydrogen bonds : angle 5.17913 ( 3207) link_BETA1-4 : bond 0.00551 ( 22) link_BETA1-4 : angle 2.04393 ( 66) link_NAG-ASN : bond 0.00439 ( 48) link_NAG-ASN : angle 3.00746 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 167 time to evaluate : 1.165 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 116 SER cc_start: 0.6458 (OUTLIER) cc_final: 0.6042 (t) REVERT: A 153 MET cc_start: 0.0149 (OUTLIER) cc_final: -0.2316 (ptp) REVERT: A 577 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8241 (ptp-110) REVERT: A 673 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.7924 (p) REVERT: A 692 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8651 (mm) REVERT: A 787 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8295 (mm-40) REVERT: A 964 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8116 (mppt) REVERT: A 1010 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: B 164 ASN cc_start: 0.4890 (OUTLIER) cc_final: 0.4442 (t0) REVERT: B 389 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: B 414 GLN cc_start: 0.3105 (OUTLIER) cc_final: 0.2501 (mp10) REVERT: B 473 TYR cc_start: 0.1760 (OUTLIER) cc_final: 0.1093 (m-80) REVERT: B 528 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7064 (mtpt) REVERT: B 564 GLN cc_start: 0.6142 (tp40) cc_final: 0.5713 (tp40) REVERT: B 787 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8684 (mt0) REVERT: B 900 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8743 (mtm) REVERT: C 190 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6413 (mtp85) REVERT: H 82 LEU cc_start: 0.1850 (OUTLIER) cc_final: 0.0311 (mp) REVERT: L 35 VAL cc_start: -0.0785 (OUTLIER) cc_final: -0.0987 (m) REVERT: L 49 MET cc_start: 0.1339 (pmm) cc_final: -0.0818 (mtt) REVERT: J 111 ARG cc_start: 0.2579 (OUTLIER) cc_final: 0.2358 (ptp-110) REVERT: J 190 LEU cc_start: 0.3190 (mt) cc_final: 0.2128 (pp) REVERT: N 49 MET cc_start: 0.2789 (OUTLIER) cc_final: -0.0312 (ttm) outliers start: 150 outliers final: 92 residues processed: 298 average time/residue: 0.4931 time to fit residues: 182.6456 Evaluate side-chains 271 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 159 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL 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 900 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1045 LYS 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 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 859 THR 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 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 111 ARG Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 199 GLN Chi-restraints excluded: chain N residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 262 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 331 optimal weight: 50.0000 chunk 58 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 263 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 339 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 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 121 ASN A 957 GLN B 49 HIS B 207 HIS B 437 ASN B 506 GLN B 935 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.222426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.180827 restraints weight = 41618.150| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.23 r_work: 0.3783 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31809 Z= 0.154 Angle : 0.725 13.868 43442 Z= 0.349 Chirality : 0.049 0.464 5117 Planarity : 0.005 0.065 5460 Dihedral : 7.144 59.600 5641 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.66 % Favored : 93.13 % Rotamer: Outliers : 4.08 % Allowed : 24.20 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 3812 helix: 1.38 (0.21), residues: 685 sheet: 0.28 (0.15), residues: 1071 loop : -1.74 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 319 TYR 0.020 0.001 TYR A 170 PHE 0.020 0.002 PHE A 194 TRP 0.018 0.001 TRP H 114 HIS 0.004 0.001 HIS J 215 Details of bonding type rmsd covalent geometry : bond 0.00362 (31691) covalent geometry : angle 0.69510 (43136) SS BOND : bond 0.00584 ( 48) SS BOND : angle 1.81655 ( 96) hydrogen bonds : bond 0.04171 ( 1109) hydrogen bonds : angle 5.21339 ( 3207) link_BETA1-4 : bond 0.00530 ( 22) link_BETA1-4 : angle 2.05297 ( 66) link_NAG-ASN : bond 0.00454 ( 48) link_NAG-ASN : angle 3.09698 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 166 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.6481 (OUTLIER) cc_final: 0.6029 (t) REVERT: A 153 MET cc_start: 0.0482 (OUTLIER) cc_final: -0.2104 (ptp) REVERT: A 577 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8250 (ptp-110) REVERT: A 673 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.7940 (p) REVERT: A 692 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8610 (mm) REVERT: A 787 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8299 (mm-40) REVERT: A 964 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8126 (mppt) REVERT: A 1010 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: A 1113 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8045 (mm110) REVERT: B 157 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.5522 (t80) REVERT: B 164 ASN cc_start: 0.5037 (OUTLIER) cc_final: 0.4582 (t0) REVERT: B 241 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6778 (mt) REVERT: B 319 ARG cc_start: 0.7673 (mtp-110) cc_final: 0.7162 (mtp180) REVERT: B 389 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: B 414 GLN cc_start: 0.3122 (OUTLIER) cc_final: 0.1930 (mp10) REVERT: B 473 TYR cc_start: 0.1582 (OUTLIER) cc_final: 0.0829 (m-80) REVERT: B 528 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7076 (mtmt) REVERT: B 787 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8699 (mt0) REVERT: B 900 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8775 (mtm) REVERT: C 190 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6330 (mtp85) REVERT: H 82 LEU cc_start: 0.1839 (OUTLIER) cc_final: 0.0329 (mp) REVERT: L 35 VAL cc_start: -0.0778 (OUTLIER) cc_final: -0.0984 (m) REVERT: L 49 MET cc_start: 0.1384 (pmm) cc_final: -0.0811 (mtt) REVERT: J 111 ARG cc_start: 0.2594 (OUTLIER) cc_final: 0.2380 (ptp-110) REVERT: J 190 LEU cc_start: 0.3090 (mt) cc_final: 0.2046 (pp) REVERT: N 49 MET cc_start: 0.2826 (OUTLIER) cc_final: -0.0294 (ttm) outliers start: 138 outliers final: 98 residues processed: 288 average time/residue: 0.4875 time to fit residues: 175.0784 Evaluate side-chains 281 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 160 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL 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 900 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1045 LYS 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 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 859 THR 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 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 176 LYS Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 111 ARG Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 197 SER Chi-restraints excluded: chain N residue 199 GLN Chi-restraints excluded: chain N residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 319 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 246 optimal weight: 3.9990 chunk 341 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 330 optimal weight: 9.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 207 HIS B 437 ASN B 506 GLN B 935 GLN B 957 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN L 199 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.220914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.178869 restraints weight = 41541.814| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.23 r_work: 0.3737 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 31809 Z= 0.230 Angle : 0.803 15.008 43442 Z= 0.390 Chirality : 0.052 0.415 5117 Planarity : 0.005 0.066 5460 Dihedral : 7.559 59.552 5640 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.37 % Favored : 92.42 % Rotamer: Outliers : 3.91 % Allowed : 24.29 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 3812 helix: 0.98 (0.20), residues: 688 sheet: 0.21 (0.15), residues: 1066 loop : -1.81 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 319 TYR 0.022 0.002 TYR A1067 PHE 0.024 0.002 PHE B 43 TRP 0.017 0.002 TRP H 114 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00560 (31691) covalent geometry : angle 0.76992 (43136) SS BOND : bond 0.00654 ( 48) SS BOND : angle 2.06241 ( 96) hydrogen bonds : bond 0.05110 ( 1109) hydrogen bonds : angle 5.46169 ( 3207) link_BETA1-4 : bond 0.00541 ( 22) link_BETA1-4 : angle 2.25068 ( 66) link_NAG-ASN : bond 0.00508 ( 48) link_NAG-ASN : angle 3.41328 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 166 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0850 (OUTLIER) cc_final: 0.0483 (mmt) REVERT: A 517 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5075 (mp) REVERT: A 577 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8314 (ptp-110) REVERT: A 673 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.7963 (p) REVERT: A 787 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8330 (mm-40) REVERT: A 964 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8142 (mppt) REVERT: A 1010 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: A 1039 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.8890 (mtp180) REVERT: A 1113 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8071 (mm110) REVERT: B 157 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.6237 (t80) REVERT: B 164 ASN cc_start: 0.5202 (OUTLIER) cc_final: 0.4857 (t0) REVERT: B 241 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6885 (mt) REVERT: B 414 GLN cc_start: 0.3230 (OUTLIER) cc_final: 0.2166 (mp10) REVERT: B 473 TYR cc_start: 0.1806 (OUTLIER) cc_final: 0.0485 (m-80) REVERT: B 528 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7171 (mtmt) REVERT: B 787 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8708 (mt0) REVERT: C 153 MET cc_start: 0.2172 (OUTLIER) cc_final: 0.1201 (ppp) REVERT: C 190 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6380 (mtp85) REVERT: C 306 PHE cc_start: 0.8175 (m-80) cc_final: 0.7665 (m-80) REVERT: H 82 LEU cc_start: 0.1661 (OUTLIER) cc_final: 0.0270 (mp) REVERT: L 49 MET cc_start: 0.1610 (pmm) cc_final: -0.0730 (mtt) REVERT: J 190 LEU cc_start: 0.3084 (mt) cc_final: 0.2008 (pp) REVERT: N 49 MET cc_start: 0.2678 (OUTLIER) cc_final: -0.0285 (ttm) outliers start: 132 outliers final: 88 residues processed: 282 average time/residue: 0.4878 time to fit residues: 170.3867 Evaluate side-chains 267 residues out of total 3380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 159 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL 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 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1045 LYS 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 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 859 THR 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 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 230 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain N residue 199 GLN Chi-restraints excluded: chain N residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 164 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 268 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 333 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 87 ASN B 207 HIS B 437 ASN B 506 GLN B 935 GLN B 957 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 540 ASN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 GLN ** N 202 HIS ** 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 = 0.4541 r_free = 0.4541 target = 0.222378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.179691 restraints weight = 41817.022| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.30 r_work: 0.3762 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31809 Z= 0.132 Angle : 0.712 15.555 43442 Z= 0.343 Chirality : 0.048 0.340 5117 Planarity : 0.004 0.060 5460 Dihedral : 7.169 59.959 5640 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.37 % Favored : 93.42 % Rotamer: Outliers : 3.11 % Allowed : 25.09 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 3812 helix: 1.38 (0.21), residues: 683 sheet: 0.30 (0.16), residues: 1062 loop : -1.72 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 319 TYR 0.024 0.001 TYR A 170 PHE 0.024 0.001 PHE A 194 TRP 0.019 0.001 TRP H 114 HIS 0.003 0.001 HIS J 215 Details of bonding type rmsd covalent geometry : bond 0.00303 (31691) covalent geometry : angle 0.68423 (43136) SS BOND : bond 0.00537 ( 48) SS BOND : angle 1.67618 ( 96) hydrogen bonds : bond 0.03884 ( 1109) hydrogen bonds : angle 5.21244 ( 3207) link_BETA1-4 : bond 0.00550 ( 22) link_BETA1-4 : angle 2.02819 ( 66) link_NAG-ASN : bond 0.00444 ( 48) link_NAG-ASN : angle 2.96535 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10611.16 seconds wall clock time: 181 minutes 17.16 seconds (10877.16 seconds total)