Starting phenix.real_space_refine on Mon Jul 6 08:53:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dx8_30899/07_2026/7dx8_30899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dx8_30899/07_2026/7dx8_30899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dx8_30899/07_2026/7dx8_30899.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dx8_30899/07_2026/7dx8_30899.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dx8_30899/07_2026/7dx8_30899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dx8_30899/07_2026/7dx8_30899.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dx8_30899/07_2026/7dx8_30899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dx8_30899/07_2026/7dx8_30899.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 21850 2.51 5 N 5582 2.21 5 O 6742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34338 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 8 Chain: "B" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "C" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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 chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.98, per 1000 atoms: 0.23 Number of scatterers: 34338 At special positions: 0 Unit cell: (135.875, 193.486, 248.923, 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 164 16.00 O 6742 8.00 N 5582 7.00 C 21850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.17 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=2.11 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=1.93 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.17 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=2.10 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.15 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.17 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=2.11 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=2.13 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.17 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.17 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1409 " - " NAG B1410 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 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 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " 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 901 " - " ASN D 322 " " NAG E 901 " - " ASN E 322 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 331 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 331 " " NAG U 1 " - " ASN C 343 " " NAG V 1 " - " ASN C 709 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " " NAG b 1 " - " ASN D 53 " " NAG c 1 " - " ASN D 90 " " NAG d 1 " - " ASN D 103 " " NAG e 1 " - " ASN D 432 " " NAG f 1 " - " ASN D 546 " " NAG g 1 " - " ASN E 53 " " NAG h 1 " - " ASN E 90 " " NAG i 1 " - " ASN E 103 " " NAG j 1 " - " ASN E 432 " " NAG k 1 " - " ASN E 546 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7848 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 49 sheets defined 35.8% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 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: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A 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: 3.559A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A 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: 3.646A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A 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: 3.677A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.631A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.648A 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: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.648A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.694A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.965A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A 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: 3.722A 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: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A 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: 3.673A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.506A 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: 4.258A 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: 3.622A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.739A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.716A 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: 3.559A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.634A 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: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A 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: 4.354A 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: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.222A 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: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.791A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.755A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.641A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.687A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.528A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.549A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.834A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.564A pdb=" N GLU D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.308A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.760A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.637A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.550A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.551A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.598A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.751A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.593A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.878A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.395A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.674A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.578A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.575A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 53 removed outlier: 3.791A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 81 removed outlier: 3.754A pdb=" N ASN E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.641A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 130 removed outlier: 3.688A pdb=" N LYS E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.527A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.549A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.834A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 205 through 208 removed outlier: 3.564A pdb=" N GLU E 208 " --> pdb=" O GLY E 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 205 through 208' Processing helix chain 'E' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 3.594A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 4.308A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.760A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 383 removed outlier: 3.637A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.550A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.551A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 412 " --> pdb=" O MET E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 removed outlier: 3.598A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE E 436 " --> pdb=" O ASN E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 465 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.750A pdb=" N TRP E 478 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.593A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.879A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 548 through 559 removed outlier: 4.396A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG E 559 " --> pdb=" O PHE E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.674A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.579A pdb=" N TYR E 587 " --> pdb=" O PRO E 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.575A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) 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: 3.680A 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 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A 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=AA5, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.122A pdb=" N LYS A 310 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY A 601 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.259A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=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: 4.784A 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 654 through 655 removed outlier: 6.522A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A 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: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A 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: 6.243A 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: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A 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=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.506A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.105A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.145A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A 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: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A 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: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A 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=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.067A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.338A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=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: 5.863A 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: 4.784A 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 654 through 655 removed outlier: 6.482A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.592A 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=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: 6.843A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A 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: 4.689A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.030A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.583A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF3, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.030A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'E' and resid 347 through 352 removed outlier: 3.582A pdb=" N LEU E 351 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1327 hydrogen bonds defined for protein. 3690 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: 7.31 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7404 1.33 - 1.45: 9031 1.45 - 1.58: 18463 1.58 - 1.70: 0 1.70 - 1.83: 233 Bond restraints: 35131 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.29e+01 bond pdb=" N PRO E 426 " pdb=" CD PRO E 426 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.81e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.068 1.59e-02 3.96e+03 1.81e+01 bond pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.79e+01 bond pdb=" N PRO E 346 " pdb=" CD PRO E 346 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 ... (remaining 35126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 46532 2.65 - 5.30: 1134 5.30 - 7.95: 84 7.95 - 10.60: 12 10.60 - 13.25: 5 Bond angle restraints: 47767 Sorted by residual: angle pdb=" N CYS B 538 " pdb=" CA CYS B 538 " pdb=" C CYS B 538 " ideal model delta sigma weight residual 110.24 100.89 9.35 1.47e+00 4.63e-01 4.05e+01 angle pdb=" N CYS C 538 " pdb=" CA CYS C 538 " pdb=" C CYS C 538 " ideal model delta sigma weight residual 110.10 100.85 9.25 1.49e+00 4.50e-01 3.85e+01 angle pdb=" N THR D 362 " pdb=" CA THR D 362 " pdb=" C THR D 362 " ideal model delta sigma weight residual 109.76 119.33 -9.57 1.59e+00 3.96e-01 3.62e+01 angle pdb=" N THR E 362 " pdb=" CA THR E 362 " pdb=" C THR E 362 " ideal model delta sigma weight residual 109.76 119.32 -9.56 1.59e+00 3.96e-01 3.61e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 ... (remaining 47762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17457 17.93 - 35.87: 1918 35.87 - 53.80: 553 53.80 - 71.74: 154 71.74 - 89.67: 58 Dihedral angle restraints: 20140 sinusoidal: 7962 harmonic: 12178 Sorted by residual: 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 21.06 71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.08 71.92 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 20137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 5564 0.329 - 0.659: 5 0.659 - 0.988: 5 0.988 - 1.318: 1 1.318 - 1.647: 2 Chirality restraints: 5577 Sorted by residual: chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " 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 a 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.04 -1.36 2.00e-01 2.50e+01 4.59e+01 ... (remaining 5574 not shown) Planarity restraints: 6117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.354 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG i 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 2 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG d 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG d 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG d 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG d 2 " 0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " -0.285 2.00e-02 2.50e+03 2.39e-01 7.16e+02 pdb=" C7 NAG i 1 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " 0.406 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " -0.010 2.00e-02 2.50e+03 ... (remaining 6114 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 285 2.53 - 3.12: 24848 3.12 - 3.71: 49519 3.71 - 4.31: 74616 4.31 - 4.90: 122829 Nonbonded interactions: 272097 Sorted by model distance: nonbonded pdb=" O SER D 105 " pdb=" OG SER D 106 " model vdw 1.932 3.040 nonbonded pdb=" O SER E 105 " pdb=" OG SER E 106 " model vdw 1.932 3.040 nonbonded pdb=" O PHE B 559 " pdb=" O LEU B 560 " model vdw 1.951 3.040 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 3.120 ... (remaining 272092 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 455 or resid 491 through 939 or resid 944 throu \ gh 1408)) selection = (chain 'B' and resid 27 through 1408) selection = (chain 'C' and (resid 27 through 455 or resid 491 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } 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: 2.410 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: 0.050 Extract box with map and model: 0.750 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 31.580 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 0.194 35268 Z= 0.488 Angle : 1.372 71.324 48134 Z= 0.698 Chirality : 0.076 1.647 5577 Planarity : 0.010 0.306 6057 Dihedral : 17.485 89.673 12160 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 1.99 % Allowed : 8.29 % Favored : 89.72 % Rotamer: Outliers : 9.61 % Allowed : 14.69 % Favored : 75.70 % 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: -4.47 (0.10), residues: 4114 helix: -3.32 (0.09), residues: 1338 sheet: -1.91 (0.17), residues: 763 loop : -3.12 (0.11), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.028 0.003 TYR B1067 PHE 0.026 0.003 PHE A 898 TRP 0.025 0.002 TRP C 104 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01074 / 0.47 (35131) covalent geometry : angle 0.99326 / 0.57 (47767) SS BOND : bond 0.06089 / 4.05 ( 44) SS BOND : angle 16.65372 / 10.90 ( 88) hydrogen bonds : bond 0.24675 / 16.36 ( 1291) hydrogen bonds : angle 8.30057 / 5.65 ( 3690) link_BETA1-4 : bond 0.03487 / 1.70 ( 33) link_BETA1-4 : angle 4.19356 / 2.69 ( 99) link_NAG-ASN : bond 0.01802 / 0.78 ( 60) link_NAG-ASN : angle 9.80897 / 6.27 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 352 poor density : 554 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7221 (OUTLIER) cc_final: 0.6707 (m-40) REVERT: A 164 ASN cc_start: 0.5360 (OUTLIER) cc_final: 0.4197 (t0) REVERT: A 190 ARG cc_start: 0.6346 (mtt90) cc_final: 0.6127 (mtt-85) REVERT: A 335 LEU cc_start: 0.4702 (OUTLIER) cc_final: 0.4340 (tt) REVERT: A 403 ARG cc_start: 0.3740 (OUTLIER) cc_final: 0.3533 (mmt180) REVERT: A 1039 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.7990 (mtp180) REVERT: A 1074 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8432 (p0) REVERT: B 32 PHE cc_start: 0.7171 (m-80) cc_final: 0.6882 (m-80) REVERT: B 81 ASN cc_start: 0.6460 (OUTLIER) cc_final: 0.5978 (t0) REVERT: B 153 MET cc_start: 0.1964 (mpp) cc_final: -0.0686 (mtm) REVERT: B 190 ARG cc_start: 0.6921 (mtt90) cc_final: 0.6575 (mtt-85) REVERT: B 203 ILE cc_start: 0.7893 (mt) cc_final: 0.7384 (mt) REVERT: B 529 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6471 (mtmm) REVERT: B 725 GLU cc_start: 0.8126 (tt0) cc_final: 0.7866 (tt0) REVERT: B 1050 MET cc_start: 0.8583 (ptm) cc_final: 0.8341 (ptm) REVERT: C 41 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5721 (mmpt) REVERT: C 130 VAL cc_start: 0.6176 (t) cc_final: 0.5937 (t) REVERT: C 153 MET cc_start: 0.0562 (mpp) cc_final: -0.0252 (mtp) REVERT: C 324 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6174 (pt0) REVERT: C 517 LEU cc_start: 0.3251 (OUTLIER) cc_final: 0.2877 (mt) REVERT: C 982 SER cc_start: 0.7635 (p) cc_final: 0.7347 (m) REVERT: D 110 GLU cc_start: 0.5214 (tm-30) cc_final: 0.4639 (tp30) REVERT: D 339 VAL cc_start: 0.3729 (OUTLIER) cc_final: 0.3375 (m) REVERT: D 474 MET cc_start: 0.0419 (mmm) cc_final: -0.0628 (mtt) REVERT: D 480 MET cc_start: 0.1247 (mtp) cc_final: 0.1025 (mmp) REVERT: E 32 PHE cc_start: 0.2983 (t80) cc_final: 0.2734 (t80) REVERT: E 83 TYR cc_start: 0.0344 (m-80) cc_final: 0.0113 (m-80) REVERT: E 127 TYR cc_start: 0.1596 (t80) cc_final: 0.1270 (t80) REVERT: E 249 MET cc_start: 0.2838 (mtp) cc_final: 0.1778 (ptt) REVERT: E 444 LEU cc_start: 0.2521 (mt) cc_final: 0.1940 (pp) outliers start: 352 outliers final: 83 residues processed: 857 average time/residue: 0.5399 time to fit residues: 571.1784 Evaluate side-chains 373 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 278 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 423 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 137 ASN A 188 ASN A 239 GLN A 360 ASN A 422 ASN A 440 ASN A 498 GLN A 644 GLN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 954 GLN A 955 ASN A 969 ASN A 992 GLN A1101 HIS A1125 ASN B 115 GLN B 134 GLN B 137 ASN B 188 ASN B 218 GLN B 317 ASN B 360 ASN B 394 ASN B 422 ASN B 440 ASN B 498 GLN B 540 ASN B 542 ASN B 644 GLN B 655 HIS B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1002 GLN B1054 GLN C 66 HIS C 81 ASN C 115 GLN C 134 GLN C 137 ASN C 188 ASN C 314 GLN C 317 ASN C 440 ASN C 498 GLN C 607 GLN C 613 GLN C 644 GLN C 690 GLN C 703 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 954 GLN C 969 ASN C 992 GLN C1005 GLN C1071 GLN C1101 HIS D 42 GLN D 51 ASN D 96 GLN D 239 HIS D 277 ASN D 417 HIS D 437 ASN D 472 GLN D 505 HIS D 508 ASN D 522 GLN ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN D 599 ASN E 42 GLN E 58 ASN E 64 ASN E 121 ASN E 175 GLN E 239 HIS E 277 ASN E 330 ASN E 437 ASN ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS E 586 ASN Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.224492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.186178 restraints weight = 53264.078| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.04 r_work: 0.3340 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 35268 Z= 0.269 Angle : 0.906 25.549 48134 Z= 0.436 Chirality : 0.055 0.530 5577 Planarity : 0.006 0.064 6057 Dihedral : 8.409 96.394 4620 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.00 % Favored : 92.68 % Rotamer: Outliers : 6.61 % Allowed : 20.09 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.12), residues: 4114 helix: -1.07 (0.13), residues: 1341 sheet: -1.33 (0.18), residues: 718 loop : -2.56 (0.12), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 102 TYR 0.021 0.002 TYR A 265 PHE 0.025 0.002 PHE B1095 TRP 0.018 0.002 TRP D 168 HIS 0.011 0.002 HIS E 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.27 (35131) covalent geometry : angle 0.85632 / 0.42 (47767) SS BOND : bond 0.00741 / 0.46 ( 44) SS BOND : angle 1.96503 / 1.26 ( 88) hydrogen bonds : bond 0.05922 / 3.83 ( 1291) hydrogen bonds : angle 5.56339 / 3.82 ( 3690) link_BETA1-4 : bond 0.00711 / 0.39 ( 33) link_BETA1-4 : angle 2.51414 / 1.62 ( 99) link_NAG-ASN : bond 0.00870 / 0.61 ( 60) link_NAG-ASN : angle 4.43767 / 2.67 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 287 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8217 (m-30) cc_final: 0.7817 (m-30) REVERT: A 153 MET cc_start: 0.0923 (OUTLIER) cc_final: -0.2110 (mpp) REVERT: A 534 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7972 (p) REVERT: A 787 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: A 957 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: A 1039 ARG cc_start: 0.9517 (OUTLIER) cc_final: 0.8882 (mtp180) REVERT: B 140 PHE cc_start: 0.7132 (p90) cc_final: 0.6906 (p90) REVERT: B 205 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8914 (t) REVERT: B 239 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: B 314 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8269 (tp40) REVERT: B 529 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.6747 (mtmm) REVERT: B 535 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6857 (ttpt) REVERT: B 725 GLU cc_start: 0.8749 (tt0) cc_final: 0.8406 (tt0) REVERT: B 779 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: B 1092 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: C 153 MET cc_start: 0.0914 (mpp) cc_final: -0.0012 (mtp) REVERT: C 158 ARG cc_start: 0.5244 (OUTLIER) cc_final: 0.3674 (mmt90) REVERT: C 187 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.5939 (mttp) REVERT: C 347 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.5018 (t80) REVERT: C 585 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7045 (mt) REVERT: C 957 GLN cc_start: 0.8635 (tt0) cc_final: 0.8344 (mt0) REVERT: C 1128 VAL cc_start: 0.9377 (p) cc_final: 0.9144 (t) REVERT: C 1142 GLN cc_start: 0.8100 (mp10) cc_final: 0.7869 (mp10) REVERT: D 110 GLU cc_start: 0.5233 (tm-30) cc_final: 0.4672 (tp30) REVERT: D 249 MET cc_start: 0.0366 (mmt) cc_final: -0.0395 (ptp) REVERT: D 307 ILE cc_start: 0.4217 (OUTLIER) cc_final: 0.3957 (mt) REVERT: D 323 MET cc_start: 0.2675 (mmt) cc_final: 0.2369 (tpt) REVERT: D 325 GLN cc_start: 0.3489 (mp10) cc_final: 0.3262 (mp10) REVERT: D 408 MET cc_start: 0.2424 (OUTLIER) cc_final: 0.2214 (mpt) REVERT: D 465 LYS cc_start: -0.0138 (ptpt) cc_final: -0.0646 (mmtt) REVERT: D 470 LYS cc_start: 0.2917 (mmtt) cc_final: 0.0918 (tppt) REVERT: D 510 TYR cc_start: 0.4101 (OUTLIER) cc_final: 0.2999 (m-10) REVERT: D 557 MET cc_start: 0.2687 (mmm) cc_final: 0.1238 (ptp) REVERT: E 32 PHE cc_start: 0.2722 (t80) cc_final: 0.2289 (t80) REVERT: E 249 MET cc_start: 0.2735 (mtp) cc_final: 0.1622 (ptm) REVERT: E 327 PHE cc_start: 0.1644 (OUTLIER) cc_final: 0.0657 (t80) REVERT: E 444 LEU cc_start: 0.2729 (mt) cc_final: 0.2018 (pp) REVERT: E 516 TYR cc_start: 0.0609 (t80) cc_final: 0.0007 (t80) outliers start: 242 outliers final: 94 residues processed: 489 average time/residue: 0.5504 time to fit residues: 335.9659 Evaluate side-chains 337 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 223 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 967 SER 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 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1077 THR 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 D residue 203 TRP Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 347 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 389 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 258 optimal weight: 0.9980 chunk 399 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 613 GLN A 675 GLN B 125 ASN B 540 ASN B 703 ASN B 804 GLN B1002 GLN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C1005 GLN D 98 GLN D 175 GLN D 417 HIS ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.229979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.192596 restraints weight = 53339.164| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.62 r_work: 0.3471 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35268 Z= 0.146 Angle : 0.749 19.673 48134 Z= 0.355 Chirality : 0.050 0.818 5577 Planarity : 0.005 0.050 6057 Dihedral : 6.818 58.789 4534 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.98 % Favored : 93.87 % Rotamer: Outliers : 5.13 % Allowed : 21.73 % Favored : 73.14 % 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: -1.90 (0.12), residues: 4114 helix: -0.10 (0.14), residues: 1336 sheet: -0.95 (0.18), residues: 718 loop : -2.20 (0.12), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 567 TYR 0.037 0.001 TYR B 453 PHE 0.025 0.001 PHE A1075 TRP 0.023 0.001 TRP E 48 HIS 0.006 0.001 HIS E 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (35131) covalent geometry : angle 0.69876 / 0.34 (47767) SS BOND : bond 0.00550 / 0.36 ( 44) SS BOND : angle 1.85276 / 1.20 ( 88) hydrogen bonds : bond 0.04568 / 2.99 ( 1291) hydrogen bonds : angle 5.10177 / 3.50 ( 3690) link_BETA1-4 : bond 0.00599 / 0.35 ( 33) link_BETA1-4 : angle 2.29877 / 1.49 ( 99) link_NAG-ASN : bond 0.00798 / 0.50 ( 60) link_NAG-ASN : angle 3.96885 / 2.42 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 253 time to evaluate : 1.309 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 88 ASP cc_start: 0.8148 (m-30) cc_final: 0.7689 (m-30) REVERT: A 153 MET cc_start: 0.0085 (ptt) cc_final: -0.2668 (mpp) REVERT: A 539 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7963 (m) REVERT: B 140 PHE cc_start: 0.7357 (p90) cc_final: 0.7044 (p90) REVERT: B 239 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: B 323 THR cc_start: 0.5751 (OUTLIER) cc_final: 0.5497 (m) REVERT: B 332 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.6252 (pp) REVERT: B 529 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6522 (ttmm) REVERT: B 535 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6690 (tttt) REVERT: B 585 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6217 (mt) REVERT: B 725 GLU cc_start: 0.8476 (tt0) cc_final: 0.8127 (tt0) REVERT: B 779 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: B 794 ILE cc_start: 0.6602 (pp) cc_final: 0.6189 (mt) REVERT: B 1010 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: C 88 ASP cc_start: 0.7440 (m-30) cc_final: 0.7212 (m-30) REVERT: C 153 MET cc_start: 0.1304 (mpp) cc_final: 0.0352 (mtp) REVERT: C 190 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7676 (mmt90) REVERT: C 740 MET cc_start: 0.9031 (ttt) cc_final: 0.8755 (tpt) REVERT: C 957 GLN cc_start: 0.8279 (tt0) cc_final: 0.8002 (mt0) REVERT: D 60 GLN cc_start: 0.4948 (tp-100) cc_final: 0.3510 (pt0) REVERT: D 74 LYS cc_start: 0.3851 (tmmt) cc_final: 0.3603 (tptm) REVERT: D 190 MET cc_start: 0.1340 (tpp) cc_final: 0.0338 (pp-130) REVERT: D 233 ILE cc_start: -0.0315 (OUTLIER) cc_final: -0.0767 (pt) REVERT: D 249 MET cc_start: 0.0073 (mmt) cc_final: -0.0297 (ptm) REVERT: D 307 ILE cc_start: 0.4075 (OUTLIER) cc_final: 0.3837 (mt) REVERT: D 323 MET cc_start: 0.2610 (mmt) cc_final: 0.2302 (tpp) REVERT: D 360 MET cc_start: 0.2206 (ptp) cc_final: 0.1017 (tpt) REVERT: D 465 LYS cc_start: 0.0508 (ptpt) cc_final: -0.0140 (mmmt) REVERT: D 510 TYR cc_start: 0.3649 (OUTLIER) cc_final: 0.2505 (m-80) REVERT: E 78 THR cc_start: 0.5752 (p) cc_final: 0.5542 (m) REVERT: E 249 MET cc_start: 0.2459 (mtp) cc_final: 0.1301 (ptm) REVERT: E 327 PHE cc_start: 0.0389 (OUTLIER) cc_final: -0.0142 (t80) REVERT: E 383 MET cc_start: 0.2658 (mtt) cc_final: 0.2138 (ptp) REVERT: E 444 LEU cc_start: 0.2689 (mt) cc_final: 0.2011 (pp) outliers start: 188 outliers final: 78 residues processed: 405 average time/residue: 0.5290 time to fit residues: 271.7662 Evaluate side-chains 310 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 218 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1076 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 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1005 GLN 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 1114 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER 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 D residue 58 ASN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 327 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 249 optimal weight: 0.0010 chunk 373 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 188 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 324 optimal weight: 0.0050 chunk 342 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 856 ASN B 125 ASN B 164 ASN B 540 ASN B1002 GLN B1142 GLN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 690 GLN C1005 GLN D 417 HIS D 552 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.231419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.189996 restraints weight = 53628.909| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 3.03 r_work: 0.3410 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35268 Z= 0.114 Angle : 0.680 19.087 48134 Z= 0.320 Chirality : 0.047 0.547 5577 Planarity : 0.004 0.053 6057 Dihedral : 5.817 59.849 4510 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.57 % Favored : 94.29 % Rotamer: Outliers : 4.42 % Allowed : 22.33 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 4114 helix: 0.39 (0.15), residues: 1362 sheet: -0.56 (0.19), residues: 715 loop : -1.93 (0.12), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 328 TYR 0.026 0.001 TYR D 587 PHE 0.024 0.001 PHE B 32 TRP 0.023 0.001 TRP E 48 HIS 0.006 0.001 HIS D 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (35131) covalent geometry : angle 0.63874 / 0.31 (47767) SS BOND : bond 0.00391 / 0.24 ( 44) SS BOND : angle 1.42973 / 0.90 ( 88) hydrogen bonds : bond 0.03732 / 2.45 ( 1291) hydrogen bonds : angle 4.82155 / 3.31 ( 3690) link_BETA1-4 : bond 0.00706 / 0.40 ( 33) link_BETA1-4 : angle 2.06294 / 1.35 ( 99) link_NAG-ASN : bond 0.00611 / 0.40 ( 60) link_NAG-ASN : angle 3.48842 / 2.07 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 252 time to evaluate : 1.329 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 88 ASP cc_start: 0.8076 (m-30) cc_final: 0.7599 (m-30) REVERT: A 153 MET cc_start: 0.0144 (ptt) cc_final: -0.2530 (mpp) REVERT: A 529 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6156 (mmtm) REVERT: A 787 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: A 957 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: B 99 ASN cc_start: 0.7441 (t0) cc_final: 0.7139 (t0) REVERT: B 323 THR cc_start: 0.5793 (OUTLIER) cc_final: 0.5550 (m) REVERT: B 332 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6406 (pp) REVERT: B 702 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 725 GLU cc_start: 0.8713 (tt0) cc_final: 0.8336 (tt0) REVERT: B 794 ILE cc_start: 0.6622 (pp) cc_final: 0.6371 (mt) REVERT: B 808 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: B 1010 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8024 (mp10) REVERT: C 88 ASP cc_start: 0.7582 (m-30) cc_final: 0.7266 (m-30) REVERT: C 114 THR cc_start: 0.4357 (OUTLIER) cc_final: 0.4156 (p) REVERT: C 153 MET cc_start: 0.1364 (mpp) cc_final: 0.0901 (mtp) REVERT: C 190 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7608 (mmt90) REVERT: C 360 ASN cc_start: 0.3869 (OUTLIER) cc_final: 0.3397 (m-40) REVERT: C 583 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6434 (tp30) REVERT: C 957 GLN cc_start: 0.8492 (tt0) cc_final: 0.8272 (mt0) REVERT: C 1129 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9083 (t) REVERT: D 74 LYS cc_start: 0.4214 (tmmt) cc_final: 0.4007 (tptm) REVERT: D 152 MET cc_start: 0.2089 (OUTLIER) cc_final: 0.0990 (ptp) REVERT: D 190 MET cc_start: 0.1701 (tpp) cc_final: 0.0358 (pp-130) REVERT: D 233 ILE cc_start: -0.0670 (OUTLIER) cc_final: -0.1058 (pt) REVERT: D 360 MET cc_start: 0.1636 (ptp) cc_final: 0.0971 (tpt) REVERT: D 465 LYS cc_start: 0.0266 (ptpt) cc_final: -0.0223 (mmmt) REVERT: D 474 MET cc_start: 0.0205 (mmm) cc_final: -0.0454 (mtt) REVERT: D 480 MET cc_start: 0.1109 (mmp) cc_final: 0.0794 (mmm) REVERT: D 493 HIS cc_start: 0.2796 (m170) cc_final: 0.2249 (m170) REVERT: D 510 TYR cc_start: 0.3569 (OUTLIER) cc_final: 0.2425 (m-80) REVERT: D 557 MET cc_start: 0.2283 (mmm) cc_final: 0.1196 (tpt) REVERT: E 249 MET cc_start: 0.2635 (mtp) cc_final: 0.1423 (ptm) REVERT: E 332 MET cc_start: 0.2587 (tpp) cc_final: 0.1667 (ptm) REVERT: E 360 MET cc_start: 0.1136 (tmm) cc_final: 0.0861 (tmm) REVERT: E 383 MET cc_start: 0.2650 (OUTLIER) cc_final: 0.2329 (ptp) REVERT: E 444 LEU cc_start: 0.2858 (mt) cc_final: 0.2227 (pp) REVERT: E 541 LYS cc_start: 0.1519 (OUTLIER) cc_final: 0.0562 (mmtt) outliers start: 162 outliers final: 61 residues processed: 384 average time/residue: 0.5125 time to fit residues: 248.3839 Evaluate side-chains 301 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 223 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 541 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 13 optimal weight: 4.9990 chunk 342 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 198 optimal weight: 10.0000 chunk 318 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 ASN A 955 ASN B 540 ASN B 703 ASN B1002 GLN B1142 GLN C 613 GLN C 690 GLN C1005 GLN D 24 GLN D 373 HIS D 374 HIS D 417 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.224831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.192048 restraints weight = 53141.932| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.35 r_work: 0.3493 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 35268 Z= 0.250 Angle : 0.797 19.493 48134 Z= 0.378 Chirality : 0.053 0.722 5577 Planarity : 0.005 0.058 6057 Dihedral : 5.982 59.157 4493 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.32 % Favored : 93.53 % Rotamer: Outliers : 4.86 % Allowed : 22.52 % Favored : 72.62 % 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: -1.46 (0.13), residues: 4114 helix: 0.29 (0.15), residues: 1352 sheet: -0.60 (0.19), residues: 713 loop : -2.02 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 567 TYR 0.024 0.002 TYR D 587 PHE 0.026 0.002 PHE B 86 TRP 0.024 0.002 TRP E 566 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.25 (35131) covalent geometry : angle 0.75058 / 0.37 (47767) SS BOND : bond 0.00460 / 0.29 ( 44) SS BOND : angle 1.82636 / 1.13 ( 88) hydrogen bonds : bond 0.05232 / 3.41 ( 1291) hydrogen bonds : angle 5.16924 / 3.52 ( 3690) link_BETA1-4 : bond 0.00441 / 0.25 ( 33) link_BETA1-4 : angle 2.19357 / 1.43 ( 99) link_NAG-ASN : bond 0.00657 / 0.43 ( 60) link_NAG-ASN : angle 4.00926 / 2.37 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 237 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6328 (mmtm) REVERT: A 539 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8176 (m) REVERT: A 702 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6543 (tp30) REVERT: A 787 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: A 856 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8343 (p0) REVERT: B 99 ASN cc_start: 0.7254 (t0) cc_final: 0.7010 (t0) REVERT: B 140 PHE cc_start: 0.7353 (p90) cc_final: 0.7023 (p90) REVERT: B 332 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6447 (pp) REVERT: B 585 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6045 (mt) REVERT: B 725 GLU cc_start: 0.8377 (tt0) cc_final: 0.8047 (tt0) REVERT: B 779 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: B 808 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: B 1010 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: C 88 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: C 153 MET cc_start: 0.1313 (mpp) cc_final: -0.0740 (tmm) REVERT: C 158 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.3850 (mmt90) REVERT: C 360 ASN cc_start: 0.3701 (OUTLIER) cc_final: 0.3405 (m110) REVERT: C 957 GLN cc_start: 0.8275 (tt0) cc_final: 0.7983 (mt0) REVERT: D 152 MET cc_start: 0.2630 (OUTLIER) cc_final: 0.1044 (ptp) REVERT: D 190 MET cc_start: 0.1558 (tpp) cc_final: 0.0529 (pp-130) REVERT: D 233 ILE cc_start: -0.0204 (OUTLIER) cc_final: -0.0802 (pt) REVERT: D 316 VAL cc_start: 0.1917 (OUTLIER) cc_final: 0.1603 (t) REVERT: D 323 MET cc_start: 0.2375 (mmt) cc_final: 0.0317 (mtt) REVERT: D 360 MET cc_start: 0.2507 (ptp) cc_final: 0.1178 (tpt) REVERT: D 465 LYS cc_start: 0.0554 (ptpt) cc_final: -0.0070 (mmtt) REVERT: D 474 MET cc_start: -0.0054 (mmm) cc_final: -0.0653 (mtt) REVERT: D 493 HIS cc_start: 0.2954 (m170) cc_final: 0.2408 (m170) REVERT: D 510 TYR cc_start: 0.3485 (OUTLIER) cc_final: 0.2276 (m-80) REVERT: E 249 MET cc_start: 0.2871 (mtp) cc_final: 0.1711 (ptm) REVERT: E 332 MET cc_start: 0.2584 (tpp) cc_final: 0.1761 (ptm) REVERT: E 383 MET cc_start: 0.2984 (OUTLIER) cc_final: 0.2331 (ptp) REVERT: E 444 LEU cc_start: 0.2383 (mt) cc_final: 0.1836 (pp) REVERT: E 579 MET cc_start: 0.2196 (OUTLIER) cc_final: 0.1982 (tmm) outliers start: 178 outliers final: 92 residues processed: 385 average time/residue: 0.4598 time to fit residues: 224.7953 Evaluate side-chains 320 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 209 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 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 641 ASN Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1076 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 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 383 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 200 optimal weight: 0.9990 chunk 285 optimal weight: 0.9980 chunk 327 optimal weight: 2.9990 chunk 271 optimal weight: 0.9990 chunk 401 optimal weight: 20.0000 chunk 396 optimal weight: 9.9990 chunk 173 optimal weight: 0.8980 chunk 206 optimal weight: 20.0000 chunk 145 optimal weight: 0.0670 chunk 363 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 856 ASN A 955 ASN A1125 ASN B 540 ASN B 703 ASN B1002 GLN B1142 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 690 GLN C1005 GLN D 277 ASN D 417 HIS ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.223039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.185152 restraints weight = 53121.481| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.89 r_work: 0.3407 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35268 Z= 0.116 Angle : 0.681 18.811 48134 Z= 0.319 Chirality : 0.047 0.666 5577 Planarity : 0.004 0.052 6057 Dihedral : 5.510 58.811 4492 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.10 % Favored : 94.73 % Rotamer: Outliers : 3.60 % Allowed : 23.64 % Favored : 72.75 % 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: -1.07 (0.13), residues: 4114 helix: 0.63 (0.15), residues: 1370 sheet: -0.43 (0.19), residues: 728 loop : -1.80 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.027 0.001 TYR D 587 PHE 0.021 0.001 PHE B 32 TRP 0.018 0.001 TRP E 48 HIS 0.004 0.001 HIS E 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (35131) covalent geometry : angle 0.63765 / 0.31 (47767) SS BOND : bond 0.00389 / 0.27 ( 44) SS BOND : angle 1.78822 / 1.13 ( 88) hydrogen bonds : bond 0.03704 / 2.45 ( 1291) hydrogen bonds : angle 4.83843 / 3.31 ( 3690) link_BETA1-4 : bond 0.00595 / 0.36 ( 33) link_BETA1-4 : angle 1.95684 / 1.27 ( 99) link_NAG-ASN : bond 0.00775 / 0.49 ( 60) link_NAG-ASN : angle 3.50429 / 2.09 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 228 time to evaluate : 1.331 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 529 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6364 (mmtm) REVERT: A 702 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6746 (tp30) REVERT: A 755 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8301 (mm-40) REVERT: A 787 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: B 99 ASN cc_start: 0.7390 (t0) cc_final: 0.7061 (t0) REVERT: B 305 SER cc_start: 0.8818 (t) cc_final: 0.8606 (p) REVERT: B 332 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6569 (pp) REVERT: B 702 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 794 ILE cc_start: 0.6436 (pp) cc_final: 0.6149 (mt) REVERT: B 808 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: B 1010 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: C 190 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7583 (mmt90) REVERT: C 360 ASN cc_start: 0.3719 (OUTLIER) cc_final: 0.3278 (m-40) REVERT: C 957 GLN cc_start: 0.8517 (tt0) cc_final: 0.8279 (mt0) REVERT: C 1129 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.9061 (t) REVERT: D 152 MET cc_start: 0.2041 (OUTLIER) cc_final: 0.1170 (ptp) REVERT: D 190 MET cc_start: 0.1910 (tpp) cc_final: 0.0752 (pp-130) REVERT: D 233 ILE cc_start: -0.0444 (OUTLIER) cc_final: -0.0895 (pt) REVERT: D 323 MET cc_start: 0.1989 (mmt) cc_final: 0.0448 (mtt) REVERT: D 388 GLN cc_start: 0.4487 (OUTLIER) cc_final: 0.4282 (tp40) REVERT: D 465 LYS cc_start: 0.0379 (ptpt) cc_final: -0.0219 (mmtt) REVERT: D 474 MET cc_start: 0.0316 (mmm) cc_final: -0.0463 (mtt) REVERT: D 493 HIS cc_start: 0.2695 (m170) cc_final: 0.2264 (m170) REVERT: D 510 TYR cc_start: 0.3705 (OUTLIER) cc_final: 0.2719 (m-80) REVERT: E 32 PHE cc_start: 0.1303 (t80) cc_final: 0.0856 (t80) REVERT: E 181 GLU cc_start: -0.0225 (mt-10) cc_final: -0.1527 (tp30) REVERT: E 238 GLU cc_start: 0.3185 (pt0) cc_final: 0.2610 (tp30) REVERT: E 249 MET cc_start: 0.2736 (mtp) cc_final: 0.1531 (ptm) REVERT: E 332 MET cc_start: 0.2814 (tpp) cc_final: 0.2152 (ptm) REVERT: E 360 MET cc_start: 0.1243 (ttt) cc_final: 0.1012 (tmm) REVERT: E 383 MET cc_start: 0.2502 (mtt) cc_final: 0.2208 (ptp) REVERT: E 444 LEU cc_start: 0.2484 (mt) cc_final: 0.1946 (pp) REVERT: E 579 MET cc_start: 0.2544 (OUTLIER) cc_final: 0.2045 (tmm) outliers start: 132 outliers final: 66 residues processed: 340 average time/residue: 0.4895 time to fit residues: 211.3022 Evaluate side-chains 294 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 213 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 935 GLN 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 D residue 58 ASN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 132 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 304 optimal weight: 50.0000 chunk 93 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 367 optimal weight: 10.0000 chunk 256 optimal weight: 0.3980 chunk 257 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN B 125 ASN B 540 ASN B1002 GLN B1142 GLN C 690 GLN C1005 GLN D 535 HIS ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.223824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.186150 restraints weight = 52796.772| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.74 r_work: 0.3411 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 35268 Z= 0.146 Angle : 0.693 18.887 48134 Z= 0.325 Chirality : 0.048 0.630 5577 Planarity : 0.004 0.052 6057 Dihedral : 5.445 59.601 4491 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer: Outliers : 3.74 % Allowed : 23.78 % Favored : 72.48 % 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: -0.99 (0.13), residues: 4114 helix: 0.73 (0.15), residues: 1360 sheet: -0.27 (0.19), residues: 710 loop : -1.82 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.027 0.001 TYR D 587 PHE 0.024 0.001 PHE B 32 TRP 0.016 0.001 TRP E 610 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (35131) covalent geometry : angle 0.65249 / 0.32 (47767) SS BOND : bond 0.00330 / 0.21 ( 44) SS BOND : angle 1.65529 / 1.04 ( 88) hydrogen bonds : bond 0.04022 / 2.64 ( 1291) hydrogen bonds : angle 4.87015 / 3.32 ( 3690) link_BETA1-4 : bond 0.00522 / 0.31 ( 33) link_BETA1-4 : angle 1.97579 / 1.29 ( 99) link_NAG-ASN : bond 0.00662 / 0.43 ( 60) link_NAG-ASN : angle 3.47208 / 2.07 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 223 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7090 (tp30) REVERT: A 529 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6554 (mmtm) REVERT: A 702 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: A 755 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8218 (mm-40) REVERT: A 787 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: B 99 ASN cc_start: 0.7361 (t0) cc_final: 0.7014 (t0) REVERT: B 305 SER cc_start: 0.8780 (t) cc_final: 0.8569 (p) REVERT: B 332 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6575 (pp) REVERT: B 794 ILE cc_start: 0.6574 (pp) cc_final: 0.6263 (mt) REVERT: B 808 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7565 (OUTLIER) REVERT: B 1010 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: C 88 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: C 190 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7581 (mmt90) REVERT: C 360 ASN cc_start: 0.3880 (OUTLIER) cc_final: 0.3469 (m-40) REVERT: C 770 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8397 (pt) REVERT: C 957 GLN cc_start: 0.8459 (tt0) cc_final: 0.8216 (mt0) REVERT: D 190 MET cc_start: 0.1819 (tpp) cc_final: 0.0557 (pp-130) REVERT: D 233 ILE cc_start: -0.0350 (OUTLIER) cc_final: -0.0882 (pt) REVERT: D 316 VAL cc_start: 0.2158 (OUTLIER) cc_final: 0.1842 (t) REVERT: D 323 MET cc_start: 0.2213 (mmt) cc_final: 0.0633 (mtt) REVERT: D 388 GLN cc_start: 0.4503 (OUTLIER) cc_final: 0.4298 (tp40) REVERT: D 465 LYS cc_start: 0.0774 (ptpt) cc_final: 0.0223 (mmtt) REVERT: D 474 MET cc_start: 0.0202 (mmm) cc_final: -0.0849 (mtt) REVERT: D 480 MET cc_start: 0.0587 (mmp) cc_final: 0.0346 (mmp) REVERT: D 493 HIS cc_start: 0.2556 (m170) cc_final: 0.2139 (m170) REVERT: D 510 TYR cc_start: 0.3717 (OUTLIER) cc_final: 0.2632 (m-80) REVERT: E 32 PHE cc_start: 0.1575 (t80) cc_final: 0.1032 (t80) REVERT: E 152 MET cc_start: -0.1837 (mtp) cc_final: -0.2082 (mtp) REVERT: E 189 GLU cc_start: 0.2469 (OUTLIER) cc_final: 0.2194 (tm-30) REVERT: E 238 GLU cc_start: 0.3154 (pt0) cc_final: 0.2606 (tp30) REVERT: E 249 MET cc_start: 0.2964 (mtp) cc_final: 0.1584 (ptm) REVERT: E 360 MET cc_start: 0.1364 (ttt) cc_final: 0.1111 (tmm) REVERT: E 510 TYR cc_start: 0.3216 (OUTLIER) cc_final: 0.2372 (t80) REVERT: E 579 MET cc_start: 0.2560 (OUTLIER) cc_final: 0.2112 (tmm) REVERT: E 610 TRP cc_start: 0.1837 (t60) cc_final: 0.1096 (t60) outliers start: 137 outliers final: 82 residues processed: 341 average time/residue: 0.4877 time to fit residues: 211.1362 Evaluate side-chains 313 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 213 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET 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 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 878 LEU 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 D residue 58 ASN Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 417 HIS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 358 optimal weight: 40.0000 chunk 285 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 181 optimal weight: 0.4980 chunk 334 optimal weight: 20.0000 chunk 139 optimal weight: 0.7980 chunk 267 optimal weight: 0.8980 chunk 283 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN B 540 ASN B 703 ASN B 935 GLN B1002 GLN B1106 GLN B1142 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C1005 GLN D 305 GLN ** E 472 GLN ** 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 = 0.4622 r_free = 0.4622 target = 0.223492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.187167 restraints weight = 53373.693| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.73 r_work: 0.3442 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 35268 Z= 0.113 Angle : 0.668 18.569 48134 Z= 0.312 Chirality : 0.047 0.656 5577 Planarity : 0.004 0.050 6057 Dihedral : 5.175 59.392 4490 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.32 % Favored : 94.53 % Rotamer: Outliers : 3.36 % Allowed : 24.08 % Favored : 72.56 % 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: -0.75 (0.13), residues: 4114 helix: 0.97 (0.15), residues: 1359 sheet: -0.17 (0.19), residues: 723 loop : -1.69 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.031 0.001 TYR D 587 PHE 0.022 0.001 PHE D 274 TRP 0.035 0.001 TRP E 459 HIS 0.005 0.000 HIS E 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (35131) covalent geometry : angle 0.63040 / 0.30 (47767) SS BOND : bond 0.00296 / 0.19 ( 44) SS BOND : angle 1.33275 / 0.85 ( 88) hydrogen bonds : bond 0.03449 / 2.28 ( 1291) hydrogen bonds : angle 4.70660 / 3.22 ( 3690) link_BETA1-4 : bond 0.00543 / 0.31 ( 33) link_BETA1-4 : angle 1.92784 / 1.27 ( 99) link_NAG-ASN : bond 0.00675 / 0.44 ( 60) link_NAG-ASN : angle 3.31319 / 1.99 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 228 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1431 (pmt) cc_final: -0.1996 (mpt) REVERT: A 169 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7004 (tp30) REVERT: A 335 LEU cc_start: 0.4663 (OUTLIER) cc_final: 0.4338 (pp) REVERT: A 529 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6437 (mmtm) REVERT: A 702 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: A 722 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8918 (t) REVERT: A 755 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8205 (mm-40) REVERT: A 787 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: B 99 ASN cc_start: 0.7453 (t0) cc_final: 0.7025 (t0) REVERT: B 153 MET cc_start: 0.2502 (mpp) cc_final: 0.1727 (mpp) REVERT: B 305 SER cc_start: 0.8774 (t) cc_final: 0.8513 (p) REVERT: B 332 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6539 (pp) REVERT: B 794 ILE cc_start: 0.6619 (pp) cc_final: 0.6362 (mt) REVERT: B 808 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7468 (OUTLIER) REVERT: B 1010 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: C 88 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: C 190 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7555 (mmt90) REVERT: C 957 GLN cc_start: 0.8447 (tt0) cc_final: 0.8218 (mt0) REVERT: C 1129 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9095 (t) REVERT: D 39 LEU cc_start: 0.4338 (mt) cc_final: 0.4100 (mm) REVERT: D 190 MET cc_start: 0.1772 (tpp) cc_final: 0.0670 (ppp) REVERT: D 233 ILE cc_start: -0.0367 (OUTLIER) cc_final: -0.0927 (pp) REVERT: D 323 MET cc_start: 0.2307 (mmt) cc_final: 0.0659 (mtt) REVERT: D 388 GLN cc_start: 0.4145 (OUTLIER) cc_final: 0.3933 (tp40) REVERT: D 465 LYS cc_start: 0.0816 (ptpt) cc_final: 0.0210 (mmtt) REVERT: D 474 MET cc_start: 0.0011 (mmm) cc_final: -0.1146 (mtt) REVERT: D 493 HIS cc_start: 0.2510 (m170) cc_final: 0.2143 (m170) REVERT: D 510 TYR cc_start: 0.3786 (OUTLIER) cc_final: 0.2912 (m-80) REVERT: D 549 GLU cc_start: 0.3743 (tp30) cc_final: 0.3456 (mm-30) REVERT: E 85 LEU cc_start: 0.1758 (OUTLIER) cc_final: 0.1477 (tt) REVERT: E 181 GLU cc_start: -0.0222 (mt-10) cc_final: -0.1337 (tp30) REVERT: E 249 MET cc_start: 0.2974 (mtp) cc_final: 0.1582 (ptm) REVERT: E 332 MET cc_start: 0.2748 (tpp) cc_final: 0.1827 (ptm) REVERT: E 444 LEU cc_start: 0.1665 (mt) cc_final: 0.1449 (pp) REVERT: E 541 LYS cc_start: 0.1506 (OUTLIER) cc_final: 0.0409 (mmtt) REVERT: E 579 MET cc_start: 0.2584 (OUTLIER) cc_final: 0.2061 (tmm) REVERT: E 610 TRP cc_start: 0.1938 (t60) cc_final: 0.1278 (t60) outliers start: 123 outliers final: 75 residues processed: 333 average time/residue: 0.5386 time to fit residues: 224.0658 Evaluate side-chains 307 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 214 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET 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 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 878 LEU 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 D residue 58 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 356 optimal weight: 5.9990 chunk 190 optimal weight: 0.5980 chunk 335 optimal weight: 5.9990 chunk 269 optimal weight: 0.1980 chunk 217 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 313 optimal weight: 20.0000 chunk 82 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN B 125 ASN B 394 ASN B 540 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1142 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C1005 GLN D 305 GLN ** E 472 GLN ** 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 = 0.4612 r_free = 0.4612 target = 0.222400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.185148 restraints weight = 52929.685| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.80 r_work: 0.3405 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35268 Z= 0.133 Angle : 0.685 18.578 48134 Z= 0.321 Chirality : 0.049 0.898 5577 Planarity : 0.004 0.052 6057 Dihedral : 5.125 59.322 4487 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 2.98 % Allowed : 24.65 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4114 helix: 0.97 (0.15), residues: 1361 sheet: -0.11 (0.19), residues: 711 loop : -1.68 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.030 0.001 TYR D 587 PHE 0.021 0.001 PHE C 201 TRP 0.037 0.001 TRP E 459 HIS 0.003 0.001 HIS E 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (35131) covalent geometry : angle 0.64667 / 0.31 (47767) SS BOND : bond 0.00318 / 0.20 ( 44) SS BOND : angle 1.35760 / 0.86 ( 88) hydrogen bonds : bond 0.03769 / 2.47 ( 1291) hydrogen bonds : angle 4.73861 / 3.24 ( 3690) link_BETA1-4 : bond 0.00518 / 0.30 ( 33) link_BETA1-4 : angle 1.92637 / 1.26 ( 99) link_NAG-ASN : bond 0.00629 / 0.41 ( 60) link_NAG-ASN : angle 3.42136 / 2.06 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 222 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1345 (pmt) cc_final: -0.1987 (mpt) REVERT: A 169 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7037 (tp30) REVERT: A 335 LEU cc_start: 0.4713 (OUTLIER) cc_final: 0.4400 (pp) REVERT: A 529 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6443 (mmtm) REVERT: A 702 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7046 (tp30) REVERT: A 722 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8871 (t) REVERT: A 755 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8188 (mm-40) REVERT: A 787 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: B 99 ASN cc_start: 0.7575 (t0) cc_final: 0.7132 (t0) REVERT: B 153 MET cc_start: 0.2240 (mpp) cc_final: 0.1750 (mpp) REVERT: B 332 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6544 (pp) REVERT: B 564 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.6044 (tp-100) REVERT: B 794 ILE cc_start: 0.6669 (pp) cc_final: 0.6415 (mt) REVERT: B 808 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7502 (m-30) REVERT: B 1010 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: C 88 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: C 190 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7625 (mmt90) REVERT: C 957 GLN cc_start: 0.8429 (tt0) cc_final: 0.8198 (mt0) REVERT: C 1129 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9027 (t) REVERT: D 39 LEU cc_start: 0.3967 (mt) cc_final: 0.3719 (mm) REVERT: D 190 MET cc_start: 0.1793 (tpp) cc_final: 0.0678 (ppp) REVERT: D 233 ILE cc_start: -0.0341 (OUTLIER) cc_final: -0.0917 (pp) REVERT: D 323 MET cc_start: 0.2507 (mmt) cc_final: 0.0439 (mtt) REVERT: D 388 GLN cc_start: 0.4146 (OUTLIER) cc_final: 0.3856 (tp40) REVERT: D 465 LYS cc_start: 0.0793 (ptpt) cc_final: 0.0145 (mmtt) REVERT: D 474 MET cc_start: -0.0016 (mmm) cc_final: -0.1151 (mtt) REVERT: D 510 TYR cc_start: 0.3865 (OUTLIER) cc_final: 0.2883 (m-80) REVERT: D 549 GLU cc_start: 0.3357 (tp30) cc_final: 0.3086 (mm-30) REVERT: E 181 GLU cc_start: -0.0072 (mt-10) cc_final: -0.1358 (tp30) REVERT: E 249 MET cc_start: 0.3048 (mtp) cc_final: 0.1803 (ptt) REVERT: E 332 MET cc_start: 0.2745 (tpp) cc_final: 0.1830 (ptm) REVERT: E 480 MET cc_start: 0.1377 (ttp) cc_final: 0.0641 (mtt) REVERT: E 510 TYR cc_start: 0.3554 (OUTLIER) cc_final: 0.2629 (t80) REVERT: E 541 LYS cc_start: 0.1544 (OUTLIER) cc_final: 0.0450 (mmtt) REVERT: E 579 MET cc_start: 0.2405 (OUTLIER) cc_final: 0.1943 (tmm) REVERT: E 610 TRP cc_start: 0.1921 (t60) cc_final: 0.1262 (t60) outliers start: 109 outliers final: 77 residues processed: 314 average time/residue: 0.5373 time to fit residues: 212.3971 Evaluate side-chains 303 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 206 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1050 MET 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 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 878 LEU 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 D residue 58 ASN Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 69 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 328 optimal weight: 8.9990 chunk 186 optimal weight: 0.0670 chunk 311 optimal weight: 0.9990 chunk 314 optimal weight: 20.0000 chunk 223 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 641 ASN A 856 ASN B 271 GLN B 540 ASN B1002 GLN B1142 GLN C 164 ASN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C1005 GLN D 305 GLN D 493 HIS ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.221903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.185330 restraints weight = 53060.063| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.77 r_work: 0.3397 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35268 Z= 0.145 Angle : 0.698 18.461 48134 Z= 0.328 Chirality : 0.048 0.651 5577 Planarity : 0.004 0.052 6057 Dihedral : 5.149 59.128 4487 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.64 % Favored : 94.21 % Rotamer: Outliers : 3.22 % Allowed : 24.49 % Favored : 72.29 % 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: -0.74 (0.13), residues: 4114 helix: 0.93 (0.15), residues: 1357 sheet: -0.10 (0.19), residues: 711 loop : -1.66 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 306 TYR 0.031 0.001 TYR D 587 PHE 0.020 0.001 PHE D 274 TRP 0.034 0.001 TRP E 48 HIS 0.004 0.001 HIS E 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (35131) covalent geometry : angle 0.66102 / 0.32 (47767) SS BOND : bond 0.00338 / 0.22 ( 44) SS BOND : angle 1.40022 / 0.88 ( 88) hydrogen bonds : bond 0.03919 / 2.56 ( 1291) hydrogen bonds : angle 4.78462 / 3.26 ( 3690) link_BETA1-4 : bond 0.00508 / 0.29 ( 33) link_BETA1-4 : angle 1.91983 / 1.26 ( 99) link_NAG-ASN : bond 0.00621 / 0.40 ( 60) link_NAG-ASN : angle 3.36339 / 2.01 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8228 Ramachandran restraints generated. 4114 Oldfield, 0 Emsley, 4114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 214 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1485 (pmt) cc_final: -0.1838 (mpt) REVERT: A 169 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7068 (tp30) REVERT: A 335 LEU cc_start: 0.4736 (OUTLIER) cc_final: 0.4421 (pp) REVERT: A 529 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6540 (mmtm) REVERT: A 702 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7094 (tp30) REVERT: A 722 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8869 (t) REVERT: A 755 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8205 (mm-40) REVERT: A 787 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: B 99 ASN cc_start: 0.7612 (t0) cc_final: 0.7168 (t0) REVERT: B 153 MET cc_start: 0.2373 (mpp) cc_final: 0.1821 (mpp) REVERT: B 332 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6650 (pp) REVERT: B 564 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.6074 (tp-100) REVERT: B 585 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6233 (mt) REVERT: B 794 ILE cc_start: 0.6642 (pp) cc_final: 0.6406 (mt) REVERT: B 808 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: B 1010 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: C 88 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: C 190 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7622 (mmt90) REVERT: C 957 GLN cc_start: 0.8486 (tt0) cc_final: 0.8249 (mt0) REVERT: D 39 LEU cc_start: 0.3837 (mt) cc_final: 0.3612 (mm) REVERT: D 190 MET cc_start: 0.1543 (tpp) cc_final: 0.0417 (ppp) REVERT: D 233 ILE cc_start: -0.0294 (OUTLIER) cc_final: -0.0732 (pp) REVERT: D 249 MET cc_start: 0.2097 (ptm) cc_final: 0.0180 (mmt) REVERT: D 270 MET cc_start: 0.1707 (OUTLIER) cc_final: 0.0853 (ttp) REVERT: D 323 MET cc_start: 0.2524 (mmt) cc_final: 0.0356 (mtt) REVERT: D 388 GLN cc_start: 0.4182 (OUTLIER) cc_final: 0.3965 (tp40) REVERT: D 465 LYS cc_start: 0.0985 (ptpt) cc_final: 0.0334 (mmtt) REVERT: D 470 LYS cc_start: 0.2622 (mmpt) cc_final: 0.2410 (mmpt) REVERT: D 474 MET cc_start: -0.0439 (mmm) cc_final: -0.1205 (mtt) REVERT: D 510 TYR cc_start: 0.3772 (OUTLIER) cc_final: 0.2801 (m-80) REVERT: E 85 LEU cc_start: 0.1804 (OUTLIER) cc_final: 0.1520 (tt) REVERT: E 249 MET cc_start: 0.3057 (mtp) cc_final: 0.1634 (ptm) REVERT: E 283 VAL cc_start: 0.3062 (p) cc_final: 0.2683 (t) REVERT: E 332 MET cc_start: 0.2758 (tpp) cc_final: 0.1764 (ptm) REVERT: E 366 MET cc_start: 0.2264 (tpt) cc_final: 0.2059 (mmm) REVERT: E 480 MET cc_start: 0.1771 (ttp) cc_final: 0.0949 (mtt) REVERT: E 510 TYR cc_start: 0.3579 (OUTLIER) cc_final: 0.2636 (t80) REVERT: E 541 LYS cc_start: 0.1571 (OUTLIER) cc_final: 0.0467 (mmtt) REVERT: E 579 MET cc_start: 0.2481 (OUTLIER) cc_final: 0.1937 (tmm) REVERT: E 610 TRP cc_start: 0.1906 (t60) cc_final: 0.1145 (t60) outliers start: 118 outliers final: 81 residues processed: 316 average time/residue: 0.5649 time to fit residues: 225.2657 Evaluate side-chains 310 residues out of total 3663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 207 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1050 MET 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 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 878 LEU 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 D residue 58 ASN Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 186 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 375 optimal weight: 50.0000 chunk 321 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 641 ASN B 540 ASN B1002 GLN ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C1005 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.221276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.183980 restraints weight = 52776.004| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.85 r_work: 0.3378 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.305 35268 Z= 0.230 Angle : 0.847 59.200 48134 Z= 0.460 Chirality : 0.050 0.981 5577 Planarity : 0.006 0.217 6057 Dihedral : 5.187 59.096 4487 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.64 % Favored : 94.19 % Rotamer: Outliers : 3.06 % Allowed : 24.76 % Favored : 72.18 % Cbeta Deviations : 0.08 % 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: -0.74 (0.13), residues: 4114 helix: 0.93 (0.15), residues: 1357 sheet: -0.10 (0.19), residues: 711 loop : -1.67 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 357 TYR 0.057 0.001 TYR D 516 PHE 0.048 0.001 PHE D 327 TRP 0.082 0.002 TRP E 48 HIS 0.004 0.001 HIS D 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (35131) covalent geometry : angle 0.81823 / 0.46 (47767) SS BOND : bond 0.00343 / 0.22 ( 44) SS BOND : angle 1.38478 / 0.88 ( 88) hydrogen bonds : bond 0.03939 / 2.57 ( 1291) hydrogen bonds : angle 4.79318 / 3.27 ( 3690) link_BETA1-4 : bond 0.00518 / 0.31 ( 33) link_BETA1-4 : angle 1.93609 / 1.27 ( 99) link_NAG-ASN : bond 0.00634 / 0.41 ( 60) link_NAG-ASN : angle 3.35670 / 2.01 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10894.20 seconds wall clock time: 186 minutes 31.20 seconds (11191.20 seconds total)