Starting phenix.real_space_refine on Sat Mar 7 07:29:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7edj_31073/03_2026/7edj_31073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7edj_31073/03_2026/7edj_31073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7edj_31073/03_2026/7edj_31073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7edj_31073/03_2026/7edj_31073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7edj_31073/03_2026/7edj_31073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7edj_31073/03_2026/7edj_31073.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.050 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 195 5.16 5 C 25216 2.51 5 N 6455 2.21 5 O 7699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39565 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7992 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 7 Chain: "B" Number of atoms: 7933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7933 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 51, 'TRANS': 964} Chain breaks: 7 Chain: "C" Number of atoms: 7878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7878 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 8 Chain: "I" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "J" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "K" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.14, per 1000 atoms: 0.26 Number of scatterers: 39565 At special positions: 0 Unit cell: (161.7, 181.5, 245.3, 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 195 16.00 O 7699 8.00 N 6455 7.00 C 25216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.04 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 163 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.02 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 163 " distance=2.04 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 Simple disulfide: pdb=" SG CYS I 133 " - pdb=" SG CYS I 141 " distance=2.03 Simple disulfide: pdb=" SG CYS I 344 " - pdb=" SG CYS I 361 " distance=2.04 Simple disulfide: pdb=" SG CYS I 530 " - pdb=" SG CYS I 542 " distance=2.03 Simple disulfide: pdb=" SG CYS J 133 " - pdb=" SG CYS J 141 " distance=2.02 Simple disulfide: pdb=" SG CYS J 344 " - pdb=" SG CYS J 361 " distance=2.03 Simple disulfide: pdb=" SG CYS J 530 " - pdb=" SG CYS J 542 " distance=2.03 Simple disulfide: pdb=" SG CYS K 133 " - pdb=" SG CYS K 141 " distance=2.02 Simple disulfide: pdb=" SG CYS K 344 " - pdb=" SG CYS K 361 " distance=2.03 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 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 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 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 120 " " NAG A2004 " - " ASN A 231 " " NAG A2005 " - " ASN A 600 " " NAG A2006 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 162 " " NAG B2003 " - " ASN B 231 " " NAG B2004 " - " ASN B 340 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 120 " " NAG C2003 " - " ASN C 162 " " NAG C2004 " - " ASN C 231 " " NAG C2005 " - " ASN C 340 " " NAG C2006 " - " ASN C 600 " " NAG C2007 " - " ASN C 654 " " NAG D 1 " - " ASN A 279 " " NAG E 1 " - " ASN A 328 " " NAG F 1 " - " ASN A 340 " " NAG G 1 " - " ASN A 613 " " NAG H 1 " - " ASN A 706 " " NAG I1001 " - " ASN I 53 " " NAG I1002 " - " ASN I 90 " " NAG I1003 " - " ASN I 103 " " NAG I1004 " - " ASN I 322 " " NAG I1005 " - " ASN I 432 " " NAG I1006 " - " ASN I 546 " " NAG J1001 " - " ASN J 53 " " NAG L 1 " - " ASN A 714 " " NAG M 1 " - " ASN A 798 " " NAG N 1 " - " ASN A1071 " " NAG O 1 " - " ASN A1095 " " NAG P 1 " - " ASN A1131 " " NAG Q 1 " - " ASN B 120 " " NAG R 1 " - " ASN B 279 " " NAG S 1 " - " ASN B 328 " " NAG T 1 " - " ASN B 613 " " NAG U 1 " - " ASN B 706 " " NAG V 1 " - " ASN B 714 " " NAG W 1 " - " ASN B 798 " " NAG X 1 " - " ASN B1071 " " NAG Y 1 " - " ASN B1095 " " NAG Z 1 " - " ASN B1131 " " NAG a 1 " - " ASN C 279 " " NAG b 1 " - " ASN C 328 " " NAG c 1 " - " ASN C 613 " " NAG d 1 " - " ASN C 706 " " NAG e 1 " - " ASN C 714 " " NAG f 1 " - " ASN C 798 " " NAG g 1 " - " ASN C1071 " " NAG h 1 " - " ASN C1095 " " NAG i 1 " - " ASN C1131 " Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.7 seconds 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9094 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 59 sheets defined 36.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.646A pdb=" N ASP A 386 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 383 through 387' Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.785A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.919A pdb=" N TYR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 419' Processing helix chain 'A' and resid 540 through 543 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.588A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 752 removed outlier: 3.873A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.631A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.049A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 888' Processing helix chain 'A' and resid 894 through 904 Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.604A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.571A pdb=" N ILE A 920 " --> pdb=" O ASN A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.535A pdb=" N ASN A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.689A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 3.916A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N THR A 995 " --> pdb=" O ASP A 991 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.722A pdb=" N GLU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.680A pdb=" N VAL B 338 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.708A pdb=" N LEU B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 540 through 543 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 757 through 780 removed outlier: 3.816A pdb=" N PHE B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.600A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.762A pdb=" N GLN B 898 " --> pdb=" O PRO B 894 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.661A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.813A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 938 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 3.576A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 973 through 981 removed outlier: 4.105A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 981 " --> pdb=" O ILE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.019A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B1030 " --> pdb=" O MET B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1143 removed outlier: 4.282A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B1143 " --> pdb=" O GLN B1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 removed outlier: 3.700A pdb=" N GLU C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 540 through 543 Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.707A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.843A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 894 through 904 Processing helix chain 'C' and resid 910 through 915 removed outlier: 3.985A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 910 through 915' Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.587A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.636A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 1029 removed outlier: 3.921A pdb=" N ILE C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing helix chain 'I' and resid 22 through 53 removed outlier: 3.572A pdb=" N LYS I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS I 34 " --> pdb=" O ASP I 30 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP I 38 " --> pdb=" O HIS I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'I' and resid 58 through 80 removed outlier: 4.263A pdb=" N MET I 62 " --> pdb=" O ASN I 58 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN I 63 " --> pdb=" O VAL I 59 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU I 75 " --> pdb=" O ALA I 71 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA I 80 " --> pdb=" O GLN I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 99 removed outlier: 3.600A pdb=" N ALA I 99 " --> pdb=" O LEU I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 128 removed outlier: 3.748A pdb=" N ARG I 115 " --> pdb=" O ASP I 111 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR I 127 " --> pdb=" O MET I 123 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER I 128 " --> pdb=" O SER I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 154 Processing helix chain 'I' and resid 159 through 172 removed outlier: 3.548A pdb=" N TRP I 163 " --> pdb=" O ASN I 159 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA I 164 " --> pdb=" O GLU I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 193 removed outlier: 3.522A pdb=" N ARG I 177 " --> pdb=" O GLY I 173 " (cutoff:3.500A) Proline residue: I 178 - end of helix removed outlier: 3.673A pdb=" N GLU I 182 " --> pdb=" O PRO I 178 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL I 185 " --> pdb=" O GLU I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 204 removed outlier: 3.537A pdb=" N TRP I 203 " --> pdb=" O TYR I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 229 removed outlier: 3.859A pdb=" N LEU I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE I 223 " --> pdb=" O ARG I 219 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU I 224 " --> pdb=" O GLY I 220 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU I 227 " --> pdb=" O ILE I 223 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR I 229 " --> pdb=" O ASP I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 250 removed outlier: 3.515A pdb=" N ASN I 250 " --> pdb=" O ALA I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 279 removed outlier: 3.559A pdb=" N TYR I 279 " --> pdb=" O THR I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 300 removed outlier: 3.746A pdb=" N MET I 297 " --> pdb=" O VAL I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 319 removed outlier: 3.585A pdb=" N PHE I 308 " --> pdb=" O ALA I 304 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS I 313 " --> pdb=" O LYS I 309 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE I 314 " --> pdb=" O GLU I 310 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 315 " --> pdb=" O ALA I 311 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL I 316 " --> pdb=" O GLU I 312 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL I 318 " --> pdb=" O PHE I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 331 Processing helix chain 'I' and resid 365 through 385 removed outlier: 3.738A pdb=" N TYR I 385 " --> pdb=" O TYR I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 393 removed outlier: 3.800A pdb=" N ARG I 393 " --> pdb=" O PHE I 390 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 411 removed outlier: 3.977A pdb=" N MET I 408 " --> pdb=" O VAL I 404 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER I 409 " --> pdb=" O GLY I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 422 Processing helix chain 'I' and resid 431 through 447 removed outlier: 3.632A pdb=" N GLU I 435 " --> pdb=" O ASP I 431 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS I 441 " --> pdb=" O ASN I 437 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR I 445 " --> pdb=" O LYS I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 453 Processing helix chain 'I' and resid 454 through 466 removed outlier: 3.688A pdb=" N LYS I 458 " --> pdb=" O TYR I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 485 removed outlier: 3.615A pdb=" N TRP I 477 " --> pdb=" O TRP I 473 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG I 482 " --> pdb=" O TRP I 478 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU I 483 " --> pdb=" O GLU I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 503 through 507 removed outlier: 3.532A pdb=" N VAL I 506 " --> pdb=" O LEU I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 530 removed outlier: 4.172A pdb=" N THR I 519 " --> pdb=" O TYR I 515 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU I 520 " --> pdb=" O TYR I 516 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE I 523 " --> pdb=" O THR I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 559 removed outlier: 3.639A pdb=" N GLY I 551 " --> pdb=" O SER I 547 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS I 553 " --> pdb=" O GLU I 549 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET I 557 " --> pdb=" O LYS I 553 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG I 559 " --> pdb=" O PHE I 555 " (cutoff:3.500A) Processing helix chain 'I' and resid 565 through 570 Processing helix chain 'I' and resid 583 through 588 removed outlier: 3.712A pdb=" N PHE I 588 " --> pdb=" O LEU I 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 588 through 596 removed outlier: 3.536A pdb=" N PHE I 592 " --> pdb=" O PHE I 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 53 removed outlier: 4.074A pdb=" N THR J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU J 35 " --> pdb=" O LYS J 31 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP J 38 " --> pdb=" O HIS J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 58 Processing helix chain 'J' and resid 59 through 79 removed outlier: 3.543A pdb=" N ASN J 63 " --> pdb=" O VAL J 59 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU J 75 " --> pdb=" O ALA J 71 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU J 79 " --> pdb=" O GLU J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 102 removed outlier: 3.632A pdb=" N LYS J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA J 99 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU J 100 " --> pdb=" O GLN J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 128 removed outlier: 3.604A pdb=" N ARG J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER J 128 " --> pdb=" O SER J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 154 removed outlier: 3.587A pdb=" N ILE J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 171 removed outlier: 3.634A pdb=" N GLU J 171 " --> pdb=" O SER J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 193 removed outlier: 3.518A pdb=" N LEU J 176 " --> pdb=" O VAL J 172 " (cutoff:3.500A) Proline residue: J 178 - end of helix removed outlier: 3.693A pdb=" N GLU J 182 " --> pdb=" O PRO J 178 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL J 185 " --> pdb=" O GLU J 181 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 204 removed outlier: 3.606A pdb=" N TRP J 203 " --> pdb=" O TYR J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 226 removed outlier: 4.008A pdb=" N LEU J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE J 223 " --> pdb=" O ARG J 219 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU J 224 " --> pdb=" O GLY J 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 232 No H-bonds generated for 'chain 'J' and resid 230 through 232' Processing helix chain 'J' and resid 233 through 250 Processing helix chain 'J' and resid 275 through 279 removed outlier: 3.625A pdb=" N TYR J 279 " --> pdb=" O THR J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 300 removed outlier: 3.717A pdb=" N GLN J 300 " --> pdb=" O ALA J 296 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 313 removed outlier: 3.774A pdb=" N LYS J 313 " --> pdb=" O LYS J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 318 removed outlier: 3.965A pdb=" N VAL J 318 " --> pdb=" O PHE J 314 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 331 removed outlier: 3.511A pdb=" N SER J 331 " --> pdb=" O PHE J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 385 removed outlier: 3.957A pdb=" N TYR J 385 " --> pdb=" O TYR J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 393 Processing helix chain 'J' and resid 399 through 411 removed outlier: 4.236A pdb=" N ALA J 403 " --> pdb=" O GLY J 399 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N MET J 408 " --> pdb=" O VAL J 404 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER J 409 " --> pdb=" O GLY J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 422 Processing helix chain 'J' and resid 431 through 447 removed outlier: 3.502A pdb=" N GLU J 435 " --> pdb=" O ASP J 431 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE J 438 " --> pdb=" O THR J 434 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN J 442 " --> pdb=" O PHE J 438 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR J 445 " --> pdb=" O LYS J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 466 Processing helix chain 'J' and resid 473 through 484 removed outlier: 4.182A pdb=" N TRP J 477 " --> pdb=" O TRP J 473 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP J 478 " --> pdb=" O MET J 474 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU J 483 " --> pdb=" O GLU J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 503 through 508 removed outlier: 3.951A pdb=" N SER J 507 " --> pdb=" O LEU J 503 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN J 508 " --> pdb=" O PHE J 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 503 through 508' Processing helix chain 'J' and resid 516 through 532 removed outlier: 3.930A pdb=" N LEU J 520 " --> pdb=" O TYR J 516 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA J 532 " --> pdb=" O ALA J 528 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 559 removed outlier: 3.975A pdb=" N LYS J 553 " --> pdb=" O GLU J 549 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU J 554 " --> pdb=" O ALA J 550 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE J 555 " --> pdb=" O GLY J 551 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN J 556 " --> pdb=" O GLN J 552 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET J 557 " --> pdb=" O LYS J 553 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG J 559 " --> pdb=" O PHE J 555 " (cutoff:3.500A) Processing helix chain 'J' and resid 565 through 570 Processing helix chain 'J' and resid 583 through 588 removed outlier: 3.908A pdb=" N PHE J 588 " --> pdb=" O LEU J 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 596 Processing helix chain 'K' and resid 22 through 53 removed outlier: 3.757A pdb=" N LYS K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS K 31 " --> pdb=" O THR K 27 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE K 32 " --> pdb=" O PHE K 28 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS K 34 " --> pdb=" O ASP K 30 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU K 35 " --> pdb=" O LYS K 31 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP K 38 " --> pdb=" O HIS K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 58 Processing helix chain 'K' and resid 59 through 80 removed outlier: 3.501A pdb=" N ASN K 63 " --> pdb=" O VAL K 59 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA K 71 " --> pdb=" O ASP K 67 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA K 80 " --> pdb=" O GLN K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 102 removed outlier: 3.521A pdb=" N LEU K 100 " --> pdb=" O GLN K 96 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN K 102 " --> pdb=" O GLN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 128 removed outlier: 4.148A pdb=" N LYS K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG K 115 " --> pdb=" O ASP K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 152 removed outlier: 3.547A pdb=" N MET K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 172 removed outlier: 3.905A pdb=" N TRP K 163 " --> pdb=" O ASN K 159 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA K 164 " --> pdb=" O GLU K 160 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 193 removed outlier: 4.433A pdb=" N LEU K 179 " --> pdb=" O GLN K 175 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU K 182 " --> pdb=" O PRO K 178 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL K 185 " --> pdb=" O GLU K 181 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA K 193 " --> pdb=" O GLU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 204 Processing helix chain 'K' and resid 220 through 229 removed outlier: 4.105A pdb=" N GLU K 224 " --> pdb=" O GLY K 220 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU K 227 " --> pdb=" O ILE K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 230 through 232 No H-bonds generated for 'chain 'K' and resid 230 through 232' Processing helix chain 'K' and resid 233 through 252 removed outlier: 3.908A pdb=" N MET K 249 " --> pdb=" O ARG K 245 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN K 250 " --> pdb=" O ALA K 246 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA K 251 " --> pdb=" O LYS K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 279 removed outlier: 3.664A pdb=" N TYR K 279 " --> pdb=" O THR K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 299 removed outlier: 3.953A pdb=" N MET K 297 " --> pdb=" O VAL K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 318 removed outlier: 3.868A pdb=" N LYS K 313 " --> pdb=" O LYS K 309 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE K 314 " --> pdb=" O GLU K 310 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE K 315 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL K 318 " --> pdb=" O PHE K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 331 Processing helix chain 'K' and resid 365 through 385 removed outlier: 3.739A pdb=" N TYR K 385 " --> pdb=" O TYR K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 389 through 393 removed outlier: 3.728A pdb=" N ARG K 393 " --> pdb=" O PHE K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 399 through 411 removed outlier: 3.972A pdb=" N ALA K 403 " --> pdb=" O GLY K 399 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET K 408 " --> pdb=" O VAL K 404 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER K 409 " --> pdb=" O GLY K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 422 removed outlier: 3.645A pdb=" N SER K 420 " --> pdb=" O LYS K 416 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE K 421 " --> pdb=" O HIS K 417 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY K 422 " --> pdb=" O LEU K 418 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 447 removed outlier: 3.799A pdb=" N PHE K 438 " --> pdb=" O THR K 434 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA K 443 " --> pdb=" O LEU K 439 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR K 445 " --> pdb=" O LYS K 441 " (cutoff:3.500A) Processing helix chain 'K' and resid 450 through 466 removed outlier: 4.038A pdb=" N MET K 455 " --> pdb=" O PRO K 451 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU K 456 " --> pdb=" O PHE K 452 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU K 457 " --> pdb=" O THR K 453 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 458 " --> pdb=" O TYR K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 473 through 485 removed outlier: 3.643A pdb=" N GLU K 483 " --> pdb=" O GLU K 479 " (cutoff:3.500A) Processing helix chain 'K' and resid 503 through 507 removed outlier: 3.759A pdb=" N VAL K 506 " --> pdb=" O LEU K 503 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER K 507 " --> pdb=" O PHE K 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 503 through 507' Processing helix chain 'K' and resid 513 through 530 removed outlier: 4.229A pdb=" N THR K 519 " --> pdb=" O TYR K 515 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU K 520 " --> pdb=" O TYR K 516 " (cutoff:3.500A) Processing helix chain 'K' and resid 549 through 554 removed outlier: 4.207A pdb=" N LYS K 553 " --> pdb=" O GLU K 549 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU K 554 " --> pdb=" O ALA K 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 549 through 554' Processing helix chain 'K' and resid 554 through 559 removed outlier: 3.648A pdb=" N ARG K 559 " --> pdb=" O PHE K 555 " (cutoff:3.500A) Processing helix chain 'K' and resid 565 through 570 Processing helix chain 'K' and resid 583 through 588 Processing helix chain 'K' and resid 588 through 596 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.280A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.897A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA6, first strand: chain 'A' and resid 88 through 89 removed outlier: 3.635A pdb=" N VAL A 88 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 191 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.620A pdb=" N ARG A 187 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA9, first strand: chain 'A' and resid 124 through 125 removed outlier: 4.055A pdb=" N VAL A 124 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER A 169 " --> pdb=" O VAL A 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.619A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 321 through 323 removed outlier: 4.114A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 351 through 355 removed outlier: 4.115A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.788A pdb=" N ILE A 399 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB6, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB7, first strand: chain 'A' and resid 562 through 563 removed outlier: 7.275A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 651 through 657 removed outlier: 3.520A pdb=" N VAL A 653 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR A 693 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 655 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AC1, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.661A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AC3, first strand: chain 'A' and resid 1117 through 1119 removed outlier: 3.587A pdb=" N ILE A1078 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.916A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.744A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AC8, first strand: chain 'B' and resid 88 through 91 removed outlier: 3.646A pdb=" N VAL B 190 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE B 200 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 224 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 116 through 117 removed outlier: 4.098A pdb=" N LYS B 127 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 308 through 316 removed outlier: 3.728A pdb=" N THR B 312 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 321 through 323 Processing sheet with id=AD3, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.562A pdb=" N ILE B 399 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD5, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.504A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.548A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR B 692 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 699 through 700 removed outlier: 5.581A pdb=" N ILE C 785 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 714 through 719 removed outlier: 3.678A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 722 through 725 Processing sheet with id=AE1, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AE2, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.861A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AE4, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.959A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.630A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AE7, first strand: chain 'C' and resid 221 through 227 removed outlier: 5.923A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL C 190 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.394A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 321 through 323 Processing sheet with id=AF1, first strand: chain 'C' and resid 351 through 356 removed outlier: 4.259A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 396 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 399 " --> pdb=" O TYR C 505 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.799A pdb=" N TYR C 486 " --> pdb=" O TYR C 470 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.341A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 709 through 710 removed outlier: 4.020A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 714 through 725 removed outlier: 3.519A pdb=" N PHE C1049 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 730 through 732 removed outlier: 4.589A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF9, first strand: chain 'I' and resid 132 through 134 removed outlier: 3.740A pdb=" N VAL I 132 " --> pdb=" O LEU I 142 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN I 134 " --> pdb=" O GLU I 140 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU I 140 " --> pdb=" O ASN I 134 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 347 through 352 removed outlier: 5.924A pdb=" N ASP I 355 " --> pdb=" O LEU I 351 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 132 through 134 removed outlier: 5.358A pdb=" N GLU J 140 " --> pdb=" O ASN J 134 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 347 through 352 removed outlier: 5.984A pdb=" N ASP J 355 " --> pdb=" O LEU J 351 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 132 through 134 removed outlier: 5.592A pdb=" N GLU K 140 " --> pdb=" O ASN K 134 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 347 through 352 removed outlier: 5.986A pdb=" N ASP K 355 " --> pdb=" O LEU K 351 " (cutoff:3.500A) 1363 hydrogen bonds defined for protein. 3822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.08 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12557 1.34 - 1.47: 10324 1.47 - 1.59: 17352 1.59 - 1.72: 0 1.72 - 1.84: 282 Bond restraints: 40515 Sorted by residual: bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C HIS A1085 " pdb=" N PHE A1086 " ideal model delta sigma weight residual 1.327 1.243 0.084 2.86e-02 1.22e+03 8.67e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.95e+00 ... (remaining 40510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 53842 2.05 - 4.10: 1110 4.10 - 6.14: 114 6.14 - 8.19: 20 8.19 - 10.24: 5 Bond angle restraints: 55091 Sorted by residual: angle pdb=" N VAL I 506 " pdb=" CA VAL I 506 " pdb=" C VAL I 506 " ideal model delta sigma weight residual 113.71 106.20 7.51 9.50e-01 1.11e+00 6.25e+01 angle pdb=" N ASP C 568 " pdb=" CA ASP C 568 " pdb=" C ASP C 568 " ideal model delta sigma weight residual 111.28 117.56 -6.28 1.35e+00 5.49e-01 2.16e+01 angle pdb=" N ILE K 21 " pdb=" CA ILE K 21 " pdb=" C ILE K 21 " ideal model delta sigma weight residual 112.96 108.81 4.15 1.00e+00 1.00e+00 1.73e+01 angle pdb=" CA GLN A 170 " pdb=" CB GLN A 170 " pdb=" CG GLN A 170 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 angle pdb=" C SER A 169 " pdb=" N GLN A 170 " pdb=" CA GLN A 170 " ideal model delta sigma weight residual 121.80 130.58 -8.78 2.44e+00 1.68e-01 1.29e+01 ... (remaining 55086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.40: 23569 24.40 - 48.79: 1332 48.79 - 73.19: 154 73.19 - 97.58: 51 97.58 - 121.98: 42 Dihedral angle restraints: 25148 sinusoidal: 11027 harmonic: 14121 Sorted by residual: dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual 93.00 178.89 -85.89 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 298 " pdb=" CB CYS B 298 " ideal model delta sinusoidal sigma weight residual 93.00 177.33 -84.33 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual -86.00 -169.76 83.76 1 1.00e+01 1.00e-02 8.56e+01 ... (remaining 25145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 6137 0.110 - 0.220: 166 0.220 - 0.330: 8 0.330 - 0.440: 2 0.440 - 0.550: 2 Chirality restraints: 6315 Sorted by residual: chirality pdb=" C1 NAG A2006 " pdb=" ND2 ASN A 654 " pdb=" C2 NAG A2006 " pdb=" O5 NAG A2006 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN B 706 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.47e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A1131 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 6312 not shown) Planarity restraints: 7073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 798 " 0.001 2.00e-02 2.50e+03 3.76e-02 1.77e+01 pdb=" CG ASN B 798 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 798 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B 798 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.025 2.00e-02 2.50e+03 2.26e-02 6.41e+00 pdb=" CG ASN A 61 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.023 2.00e-02 2.50e+03 pdb=" C1 NAG A2001 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 82 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 83 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 83 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 83 " -0.035 5.00e-02 4.00e+02 ... (remaining 7070 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 534 2.65 - 3.21: 35976 3.21 - 3.77: 56748 3.77 - 4.34: 75458 4.34 - 4.90: 126756 Nonbonded interactions: 295472 Sorted by model distance: nonbonded pdb=" OE1 GLN A 801 " pdb=" O6 NAG M 1 " model vdw 2.085 3.040 nonbonded pdb=" OG SER B 732 " pdb=" OG1 THR B 856 " model vdw 2.109 3.040 nonbonded pdb=" OH TYR K 180 " pdb=" NH1 ARG K 460 " model vdw 2.180 3.120 nonbonded pdb=" OE2 GLU C 722 " pdb=" NE2 HIS C1061 " model vdw 2.182 3.120 nonbonded pdb=" O VAL C 324 " pdb=" OG1 THR C 528 " model vdw 2.206 3.040 ... (remaining 295467 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 139 or resid 152 through 208 or resid 214 throu \ gh 240 or resid 261 through 618 or resid 638 through 672 or resid 688 through 11 \ 43 or resid 2001 through 2006)) selection = (chain 'B' and (resid 27 through 139 or resid 152 through 208 or resid 214 throu \ gh 618 or resid 638 through 2006)) selection = (chain 'C' and (resid 27 through 824 or resid 842 through 1143 or resid 2002 thr \ ough 2007)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' 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' } ncs_group { reference = (chain 'I' and resid 19 through 614) selection = (chain 'J' and resid 19 through 614) 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: 4.090 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: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 38.360 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.006 0.084 40645 Z= 0.250 Angle : 0.732 15.584 55434 Z= 0.375 Chirality : 0.049 0.550 6315 Planarity : 0.005 0.063 7019 Dihedral : 15.382 121.975 15913 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.95 % Favored : 91.88 % Rotamer: Outliers : 0.09 % Allowed : 0.47 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.64 (0.12), residues: 4780 helix: 0.46 (0.14), residues: 1479 sheet: -1.04 (0.20), residues: 638 loop : -2.10 (0.11), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1036 TYR 0.019 0.001 TYR B 262 PHE 0.028 0.002 PHE A1118 TRP 0.019 0.001 TRP J 459 HIS 0.008 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00571 (40515) covalent geometry : angle 0.69761 (55091) SS BOND : bond 0.00456 ( 47) SS BOND : angle 1.61882 ( 94) hydrogen bonds : bond 0.17206 ( 1363) hydrogen bonds : angle 5.87462 ( 3822) link_BETA1-4 : bond 0.00632 ( 29) link_BETA1-4 : angle 3.13332 ( 87) link_NAG-ASN : bond 0.00421 ( 54) link_NAG-ASN : angle 3.34787 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 199 time to evaluate : 1.429 Fit side-chains REVERT: J 82 MET cc_start: -0.0087 (ptt) cc_final: -0.0514 (ptm) REVERT: J 270 MET cc_start: 0.4871 (mmt) cc_final: 0.4553 (mmm) REVERT: K 152 MET cc_start: 0.2261 (mtm) cc_final: 0.1037 (ppp) REVERT: K 270 MET cc_start: 0.3632 (ttm) cc_final: 0.2988 (tpp) outliers start: 4 outliers final: 0 residues processed: 202 average time/residue: 0.2323 time to fit residues: 80.1725 Evaluate side-chains 160 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 40.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN C 85 ASN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.193113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.137042 restraints weight = 76557.740| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 5.01 r_work: 0.3311 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40645 Z= 0.144 Angle : 0.628 11.554 55434 Z= 0.309 Chirality : 0.045 0.450 6315 Planarity : 0.004 0.054 7019 Dihedral : 10.174 108.754 6946 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.03 % Favored : 92.80 % Rotamer: Outliers : 0.31 % Allowed : 5.64 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.12), residues: 4780 helix: 0.80 (0.14), residues: 1533 sheet: -0.86 (0.20), residues: 676 loop : -2.03 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 460 TYR 0.016 0.001 TYR A1064 PHE 0.020 0.001 PHE C 90 TRP 0.011 0.001 TRP K 473 HIS 0.007 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00329 (40515) covalent geometry : angle 0.60709 (55091) SS BOND : bond 0.00452 ( 47) SS BOND : angle 1.16346 ( 94) hydrogen bonds : bond 0.05350 ( 1363) hydrogen bonds : angle 4.54612 ( 3822) link_BETA1-4 : bond 0.00626 ( 29) link_BETA1-4 : angle 2.42973 ( 87) link_NAG-ASN : bond 0.00320 ( 54) link_NAG-ASN : angle 2.38664 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: C 172 PHE cc_start: 0.7272 (p90) cc_final: 0.6975 (p90) REVERT: I 408 MET cc_start: 0.8027 (mpp) cc_final: 0.7767 (mpp) REVERT: J 82 MET cc_start: 0.1043 (ptt) cc_final: 0.0515 (ptm) REVERT: K 152 MET cc_start: 0.2606 (mtm) cc_final: 0.1407 (ppp) REVERT: K 270 MET cc_start: 0.2785 (ttm) cc_final: 0.1943 (tpp) outliers start: 13 outliers final: 6 residues processed: 182 average time/residue: 0.2148 time to fit residues: 69.1720 Evaluate side-chains 161 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain J residue 110 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 434 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 384 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 453 optimal weight: 40.0000 chunk 80 optimal weight: 0.5980 chunk 307 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 409 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 85 ASN C 123 ASN C 268 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN I 552 GLN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** 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 = 0.4656 r_free = 0.4656 target = 0.189957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.134605 restraints weight = 76402.004| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 5.32 r_work: 0.3225 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 40645 Z= 0.292 Angle : 0.727 11.183 55434 Z= 0.361 Chirality : 0.049 0.450 6315 Planarity : 0.005 0.071 7019 Dihedral : 9.731 113.430 6946 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.72 % Favored : 91.11 % Rotamer: Outliers : 0.90 % Allowed : 10.03 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.12), residues: 4780 helix: 0.64 (0.14), residues: 1547 sheet: -1.09 (0.20), residues: 661 loop : -2.13 (0.11), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1036 TYR 0.023 0.002 TYR B 262 PHE 0.036 0.002 PHE A1118 TRP 0.020 0.001 TRP B 883 HIS 0.009 0.001 HIS B1055 Details of bonding type rmsd covalent geometry : bond 0.00710 (40515) covalent geometry : angle 0.70258 (55091) SS BOND : bond 0.00483 ( 47) SS BOND : angle 1.77878 ( 94) hydrogen bonds : bond 0.06643 ( 1363) hydrogen bonds : angle 4.63433 ( 3822) link_BETA1-4 : bond 0.00536 ( 29) link_BETA1-4 : angle 2.53444 ( 87) link_NAG-ASN : bond 0.00442 ( 54) link_NAG-ASN : angle 2.78058 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 1.540 Fit side-chains REVERT: A 846 LEU cc_start: 0.7296 (pp) cc_final: 0.7069 (mt) REVERT: B 155 ARG cc_start: 0.6087 (ptt-90) cc_final: 0.5750 (mmp-170) REVERT: B 187 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7669 (mtm-85) REVERT: B 875 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8119 (tt) REVERT: C 268 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: C 295 GLU cc_start: 0.8023 (pm20) cc_final: 0.7797 (pm20) REVERT: I 82 MET cc_start: 0.8177 (ppp) cc_final: 0.7539 (ppp) REVERT: I 361 CYS cc_start: 0.6635 (t) cc_final: 0.6238 (t) REVERT: I 474 MET cc_start: 0.2873 (ttp) cc_final: 0.2514 (ptm) REVERT: J 82 MET cc_start: 0.1198 (ptt) cc_final: 0.0666 (ptm) REVERT: J 270 MET cc_start: 0.2521 (mmm) cc_final: 0.2013 (mmp) REVERT: K 152 MET cc_start: 0.2664 (mtm) cc_final: 0.1410 (ppp) REVERT: K 262 LEU cc_start: 0.5508 (OUTLIER) cc_final: 0.5064 (mp) REVERT: K 270 MET cc_start: 0.2836 (ttm) cc_final: 0.1983 (tpp) REVERT: K 579 MET cc_start: -0.3807 (mmm) cc_final: -0.4263 (mtp) outliers start: 38 outliers final: 21 residues processed: 197 average time/residue: 0.2143 time to fit residues: 74.5404 Evaluate side-chains 180 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 458 optimal weight: 30.0000 chunk 157 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 363 optimal weight: 50.0000 chunk 360 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 459 optimal weight: 50.0000 chunk 105 optimal weight: 1.9990 chunk 419 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 444 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN I 373 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.189652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.132556 restraints weight = 74854.829| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 5.03 r_work: 0.3246 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 40645 Z= 0.233 Angle : 0.675 12.246 55434 Z= 0.331 Chirality : 0.046 0.448 6315 Planarity : 0.004 0.067 7019 Dihedral : 8.929 114.315 6946 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.32 % Rotamer: Outliers : 1.68 % Allowed : 11.90 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.12), residues: 4780 helix: 0.75 (0.14), residues: 1557 sheet: -1.17 (0.20), residues: 650 loop : -2.14 (0.11), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 460 TYR 0.019 0.001 TYR B 262 PHE 0.027 0.002 PHE C 55 TRP 0.015 0.001 TRP A 64 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00564 (40515) covalent geometry : angle 0.64960 (55091) SS BOND : bond 0.00417 ( 47) SS BOND : angle 1.41839 ( 94) hydrogen bonds : bond 0.05956 ( 1363) hydrogen bonds : angle 4.46941 ( 3822) link_BETA1-4 : bond 0.00588 ( 29) link_BETA1-4 : angle 2.54193 ( 87) link_NAG-ASN : bond 0.00350 ( 54) link_NAG-ASN : angle 2.80917 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 169 time to evaluate : 1.338 Fit side-chains REVERT: A 846 LEU cc_start: 0.7409 (pp) cc_final: 0.7198 (mt) REVERT: A 1069 GLU cc_start: 0.8994 (pm20) cc_final: 0.8749 (pm20) REVERT: A 1104 ARG cc_start: 0.8090 (ptp-170) cc_final: 0.7821 (ptt180) REVERT: A 1136 ASP cc_start: 0.8603 (t0) cc_final: 0.8326 (t0) REVERT: B 155 ARG cc_start: 0.6062 (ptt-90) cc_final: 0.5691 (mmp-170) REVERT: B 167 TYR cc_start: 0.8084 (t80) cc_final: 0.7858 (t80) REVERT: B 187 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7587 (mtm-85) REVERT: B 657 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.7704 (m-80) REVERT: B 915 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 197 TYR cc_start: 0.7699 (m-80) cc_final: 0.7225 (m-80) REVERT: I 82 MET cc_start: 0.8237 (ppp) cc_final: 0.7654 (ppp) REVERT: I 408 MET cc_start: 0.7832 (mpp) cc_final: 0.7598 (mpp) REVERT: J 82 MET cc_start: 0.1367 (ptt) cc_final: 0.0824 (ptm) REVERT: J 270 MET cc_start: 0.2570 (mmm) cc_final: 0.2041 (mmp) REVERT: J 364 VAL cc_start: 0.4618 (OUTLIER) cc_final: 0.4395 (p) REVERT: K 152 MET cc_start: 0.2514 (mtm) cc_final: 0.1282 (ppp) REVERT: K 190 MET cc_start: 0.5537 (ptt) cc_final: 0.4785 (ppp) REVERT: K 262 LEU cc_start: 0.5666 (OUTLIER) cc_final: 0.5218 (mp) REVERT: K 270 MET cc_start: 0.2836 (ttm) cc_final: 0.1959 (tpp) REVERT: K 579 MET cc_start: -0.3867 (mmm) cc_final: -0.4309 (mtp) outliers start: 71 outliers final: 40 residues processed: 229 average time/residue: 0.2098 time to fit residues: 84.8513 Evaluate side-chains 200 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain I residue 555 PHE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 364 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 364 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 343 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 345 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 305 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 270 optimal weight: 0.7980 chunk 281 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN C 85 ASN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN C 962 GLN ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.191282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.133865 restraints weight = 74736.431| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 5.01 r_work: 0.3279 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 40645 Z= 0.135 Angle : 0.605 14.053 55434 Z= 0.293 Chirality : 0.044 0.436 6315 Planarity : 0.004 0.063 7019 Dihedral : 8.090 114.407 6946 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.84 % Favored : 92.99 % Rotamer: Outliers : 1.53 % Allowed : 13.17 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.25 (0.12), residues: 4780 helix: 0.98 (0.14), residues: 1562 sheet: -0.96 (0.20), residues: 637 loop : -2.04 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 460 TYR 0.016 0.001 TYR B1064 PHE 0.017 0.001 PHE C 90 TRP 0.015 0.001 TRP C 102 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00313 (40515) covalent geometry : angle 0.57650 (55091) SS BOND : bond 0.00380 ( 47) SS BOND : angle 1.37761 ( 94) hydrogen bonds : bond 0.04934 ( 1363) hydrogen bonds : angle 4.25620 ( 3822) link_BETA1-4 : bond 0.00588 ( 29) link_BETA1-4 : angle 2.52957 ( 87) link_NAG-ASN : bond 0.00294 ( 54) link_NAG-ASN : angle 2.80364 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 1.471 Fit side-chains REVERT: A 170 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6849 (mp10) REVERT: A 846 LEU cc_start: 0.7435 (pp) cc_final: 0.7221 (mt) REVERT: A 974 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8835 (mp) REVERT: A 1104 ARG cc_start: 0.8021 (ptp-170) cc_final: 0.7738 (ptt180) REVERT: A 1136 ASP cc_start: 0.8565 (t0) cc_final: 0.8313 (t0) REVERT: B 155 ARG cc_start: 0.6050 (ptt-90) cc_final: 0.5692 (mmp-170) REVERT: B 167 TYR cc_start: 0.7817 (t80) cc_final: 0.7575 (t80) REVERT: B 694 MET cc_start: 0.8679 (mtt) cc_final: 0.8361 (mtm) REVERT: B 875 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7854 (tt) REVERT: B 915 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: B 1026 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8835 (ttp) REVERT: C 595 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8489 (mp) REVERT: C 720 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.7994 (p) REVERT: C 928 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8336 (tt) REVERT: C 932 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8471 (tm-30) REVERT: I 82 MET cc_start: 0.8276 (ppp) cc_final: 0.7748 (ppp) REVERT: I 190 MET cc_start: 0.8841 (mmm) cc_final: 0.8581 (mmm) REVERT: I 474 MET cc_start: 0.3214 (ttp) cc_final: 0.2835 (ptm) REVERT: J 82 MET cc_start: 0.1570 (ptt) cc_final: 0.1059 (ptm) REVERT: J 249 MET cc_start: 0.2000 (mmp) cc_final: 0.1740 (tpt) REVERT: J 323 MET cc_start: 0.3921 (tpp) cc_final: 0.3461 (tpp) REVERT: K 152 MET cc_start: 0.2450 (mtm) cc_final: 0.1223 (ppp) REVERT: K 190 MET cc_start: 0.5537 (ptt) cc_final: 0.4812 (ppp) REVERT: K 262 LEU cc_start: 0.5705 (OUTLIER) cc_final: 0.5343 (mp) REVERT: K 270 MET cc_start: 0.2809 (ttm) cc_final: 0.1855 (tpp) REVERT: K 579 MET cc_start: -0.3940 (mmm) cc_final: -0.4390 (mtp) outliers start: 65 outliers final: 38 residues processed: 228 average time/residue: 0.2051 time to fit residues: 83.0915 Evaluate side-chains 208 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain I residue 373 HIS Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 364 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 365 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 394 optimal weight: 6.9990 chunk 408 optimal weight: 4.9990 chunk 303 optimal weight: 20.0000 chunk 206 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 265 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 464 optimal weight: 20.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN C 962 GLN ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.191052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.135758 restraints weight = 75028.075| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 5.11 r_work: 0.3289 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40645 Z= 0.154 Angle : 0.605 10.819 55434 Z= 0.295 Chirality : 0.044 0.430 6315 Planarity : 0.004 0.057 7019 Dihedral : 7.732 114.956 6946 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.03 % Favored : 92.80 % Rotamer: Outliers : 1.56 % Allowed : 13.90 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.19 (0.12), residues: 4780 helix: 1.09 (0.14), residues: 1556 sheet: -0.84 (0.20), residues: 628 loop : -2.06 (0.11), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 460 TYR 0.016 0.001 TYR B 262 PHE 0.021 0.001 PHE A1118 TRP 0.014 0.001 TRP C 102 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00365 (40515) covalent geometry : angle 0.57850 (55091) SS BOND : bond 0.00353 ( 47) SS BOND : angle 1.37364 ( 94) hydrogen bonds : bond 0.05015 ( 1363) hydrogen bonds : angle 4.20316 ( 3822) link_BETA1-4 : bond 0.00597 ( 29) link_BETA1-4 : angle 2.56778 ( 87) link_NAG-ASN : bond 0.00296 ( 54) link_NAG-ASN : angle 2.64279 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 171 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 846 LEU cc_start: 0.7448 (pp) cc_final: 0.7237 (mt) REVERT: A 974 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8859 (mp) REVERT: A 1104 ARG cc_start: 0.8011 (ptp-170) cc_final: 0.7755 (ptt180) REVERT: A 1136 ASP cc_start: 0.8553 (t0) cc_final: 0.8281 (t0) REVERT: B 155 ARG cc_start: 0.6078 (ptt-90) cc_final: 0.5734 (mmp-170) REVERT: B 167 TYR cc_start: 0.7855 (t80) cc_final: 0.7593 (t80) REVERT: B 187 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7632 (mtm180) REVERT: B 657 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: B 694 MET cc_start: 0.8675 (mtt) cc_final: 0.8437 (mtm) REVERT: B 875 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7920 (tt) REVERT: B 915 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: B 1026 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8872 (ttp) REVERT: C 197 TYR cc_start: 0.7655 (m-80) cc_final: 0.7204 (m-80) REVERT: C 595 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8524 (mp) REVERT: I 82 MET cc_start: 0.8276 (ppp) cc_final: 0.7720 (ppp) REVERT: I 474 MET cc_start: 0.3013 (ttp) cc_final: 0.2641 (ptm) REVERT: J 82 MET cc_start: 0.1087 (ptt) cc_final: 0.0496 (ptm) REVERT: J 249 MET cc_start: 0.1839 (mmp) cc_final: 0.1606 (tpt) REVERT: K 152 MET cc_start: 0.2577 (mtm) cc_final: 0.1270 (ppp) REVERT: K 190 MET cc_start: 0.5537 (ptt) cc_final: 0.4789 (ppp) REVERT: K 262 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5441 (mp) REVERT: K 270 MET cc_start: 0.3157 (ttm) cc_final: 0.2148 (tpp) REVERT: K 579 MET cc_start: -0.3880 (mmm) cc_final: -0.4320 (mtp) outliers start: 66 outliers final: 45 residues processed: 228 average time/residue: 0.2174 time to fit residues: 87.0109 Evaluate side-chains 212 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 364 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 155 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 368 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 324 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 423 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 398 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A1098 HIS C 85 ASN C 123 ASN I 524 GLN ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.190666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.134393 restraints weight = 74669.985| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 5.14 r_work: 0.3331 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40645 Z= 0.166 Angle : 0.614 10.752 55434 Z= 0.299 Chirality : 0.044 0.425 6315 Planarity : 0.004 0.058 7019 Dihedral : 7.461 115.835 6946 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.24 % Favored : 92.59 % Rotamer: Outliers : 1.79 % Allowed : 14.42 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.17 (0.12), residues: 4780 helix: 1.15 (0.14), residues: 1553 sheet: -0.95 (0.20), residues: 618 loop : -2.03 (0.11), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 460 TYR 0.017 0.001 TYR B1064 PHE 0.022 0.001 PHE A1118 TRP 0.016 0.001 TRP C 102 HIS 0.007 0.001 HIS I 345 Details of bonding type rmsd covalent geometry : bond 0.00395 (40515) covalent geometry : angle 0.58696 (55091) SS BOND : bond 0.00401 ( 47) SS BOND : angle 1.34911 ( 94) hydrogen bonds : bond 0.05112 ( 1363) hydrogen bonds : angle 4.20396 ( 3822) link_BETA1-4 : bond 0.00616 ( 29) link_BETA1-4 : angle 2.60414 ( 87) link_NAG-ASN : bond 0.00356 ( 54) link_NAG-ASN : angle 2.67795 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 172 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 974 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8846 (mp) REVERT: A 1069 GLU cc_start: 0.8824 (pm20) cc_final: 0.8582 (pm20) REVERT: A 1078 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8197 (pt) REVERT: A 1104 ARG cc_start: 0.8008 (ptp-170) cc_final: 0.7726 (ptt180) REVERT: B 155 ARG cc_start: 0.5892 (ptt-90) cc_final: 0.5624 (mmp-170) REVERT: B 167 TYR cc_start: 0.7814 (t80) cc_final: 0.7540 (t80) REVERT: B 187 ARG cc_start: 0.7902 (ttm-80) cc_final: 0.7613 (mtm180) REVERT: B 583 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7847 (m-30) REVERT: B 657 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: B 694 MET cc_start: 0.8670 (mtt) cc_final: 0.8433 (mtm) REVERT: B 875 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7890 (tt) REVERT: B 915 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: B 1026 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8844 (ttp) REVERT: C 197 TYR cc_start: 0.7576 (m-80) cc_final: 0.7118 (m-80) REVERT: C 595 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8513 (mt) REVERT: C 928 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8383 (tt) REVERT: I 82 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7698 (ppp) REVERT: I 474 MET cc_start: 0.3100 (ttp) cc_final: 0.2279 (ptm) REVERT: I 477 TRP cc_start: 0.4876 (OUTLIER) cc_final: 0.4449 (t-100) REVERT: J 82 MET cc_start: 0.1024 (ptt) cc_final: 0.0432 (ptm) REVERT: J 249 MET cc_start: 0.1919 (mmp) cc_final: 0.1677 (tpt) REVERT: J 323 MET cc_start: 0.3661 (tpp) cc_final: 0.3119 (tpp) REVERT: K 152 MET cc_start: 0.2536 (mtm) cc_final: 0.1292 (ppp) REVERT: K 190 MET cc_start: 0.5938 (ptt) cc_final: 0.5216 (ppp) REVERT: K 262 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5293 (mp) REVERT: K 270 MET cc_start: 0.3124 (ttm) cc_final: 0.2136 (tpp) REVERT: K 297 MET cc_start: -0.0248 (ppp) cc_final: -0.1125 (ptt) REVERT: K 332 MET cc_start: 0.3914 (ptt) cc_final: 0.3637 (ptt) REVERT: K 358 ILE cc_start: -0.0792 (OUTLIER) cc_final: -0.1121 (mt) REVERT: K 364 VAL cc_start: -0.0455 (OUTLIER) cc_final: -0.1294 (p) REVERT: K 579 MET cc_start: -0.3932 (mmm) cc_final: -0.4383 (mtp) outliers start: 76 outliers final: 50 residues processed: 239 average time/residue: 0.2176 time to fit residues: 90.7338 Evaluate side-chains 228 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 164 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 797 PHE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 477 TRP Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 364 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 287 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 424 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 448 optimal weight: 10.0000 chunk 320 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN C 911 ASN C 954 GLN C1103 GLN I 373 HIS ** J 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.191712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.134792 restraints weight = 74835.601| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 5.03 r_work: 0.3363 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 40645 Z= 0.122 Angle : 0.597 12.433 55434 Z= 0.287 Chirality : 0.043 0.417 6315 Planarity : 0.004 0.059 7019 Dihedral : 7.145 115.603 6946 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 1.79 % Allowed : 14.77 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.02 (0.12), residues: 4780 helix: 1.28 (0.14), residues: 1550 sheet: -0.81 (0.20), residues: 620 loop : -1.96 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 460 TYR 0.017 0.001 TYR B1064 PHE 0.021 0.001 PHE B 797 TRP 0.016 0.001 TRP C 102 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00284 (40515) covalent geometry : angle 0.56521 (55091) SS BOND : bond 0.00337 ( 47) SS BOND : angle 1.94976 ( 94) hydrogen bonds : bond 0.04576 ( 1363) hydrogen bonds : angle 4.10186 ( 3822) link_BETA1-4 : bond 0.00611 ( 29) link_BETA1-4 : angle 2.61487 ( 87) link_NAG-ASN : bond 0.00331 ( 54) link_NAG-ASN : angle 2.74325 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 1.754 Fit side-chains revert: symmetry clash REVERT: A 438 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7133 (pt) REVERT: A 974 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8836 (mp) REVERT: A 1078 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8109 (pt) REVERT: A 1104 ARG cc_start: 0.8025 (ptp-170) cc_final: 0.7710 (ptt180) REVERT: B 155 ARG cc_start: 0.5864 (ptt-90) cc_final: 0.5639 (mmp-170) REVERT: B 167 TYR cc_start: 0.7618 (t80) cc_final: 0.7352 (t80) REVERT: B 187 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7588 (mtm180) REVERT: B 583 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7794 (m-30) REVERT: B 640 PHE cc_start: 0.7996 (t80) cc_final: 0.7694 (t80) REVERT: B 657 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: B 694 MET cc_start: 0.8628 (mtt) cc_final: 0.8355 (mtm) REVERT: B 875 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7813 (tt) REVERT: B 915 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: B 1026 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.9008 (ttt) REVERT: C 197 TYR cc_start: 0.7541 (m-80) cc_final: 0.7100 (m-80) REVERT: C 595 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8486 (mp) REVERT: C 820 PHE cc_start: 0.8453 (m-80) cc_final: 0.8253 (m-80) REVERT: C 928 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8335 (tt) REVERT: I 82 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7756 (ppp) REVERT: I 270 MET cc_start: 0.1334 (ttt) cc_final: 0.0938 (tmt) REVERT: I 408 MET cc_start: 0.7885 (mpp) cc_final: 0.7624 (mpp) REVERT: I 462 MET cc_start: 0.6106 (mmp) cc_final: 0.4808 (mtt) REVERT: I 474 MET cc_start: 0.3180 (ttp) cc_final: 0.2322 (ptm) REVERT: I 477 TRP cc_start: 0.4855 (OUTLIER) cc_final: 0.4457 (t-100) REVERT: I 512 PHE cc_start: 0.7620 (m-80) cc_final: 0.7003 (m-80) REVERT: J 82 MET cc_start: 0.1097 (ptt) cc_final: 0.0504 (ptm) REVERT: J 249 MET cc_start: 0.1925 (mmp) cc_final: 0.1719 (tpt) REVERT: K 152 MET cc_start: 0.2469 (mtm) cc_final: 0.1277 (ppp) REVERT: K 190 MET cc_start: 0.5696 (ptt) cc_final: 0.5044 (ppp) REVERT: K 262 LEU cc_start: 0.5681 (OUTLIER) cc_final: 0.5351 (mp) REVERT: K 270 MET cc_start: 0.3046 (ttm) cc_final: 0.2078 (tpp) REVERT: K 297 MET cc_start: -0.0360 (ppp) cc_final: -0.1218 (ptt) REVERT: K 358 ILE cc_start: -0.0861 (OUTLIER) cc_final: -0.1184 (mt) REVERT: K 364 VAL cc_start: -0.0467 (OUTLIER) cc_final: -0.1294 (p) REVERT: K 579 MET cc_start: -0.4001 (mmm) cc_final: -0.4456 (mtp) outliers start: 76 outliers final: 46 residues processed: 238 average time/residue: 0.2087 time to fit residues: 87.2203 Evaluate side-chains 225 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 164 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 797 PHE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 477 TRP Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 364 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 111 optimal weight: 0.2980 chunk 216 optimal weight: 3.9990 chunk 415 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 441 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 442 optimal weight: 9.9990 chunk 290 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 539 ASN C 85 ASN I 340 GLN I 373 HIS ** J 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.190565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.136455 restraints weight = 74695.768| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 5.88 r_work: 0.3257 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 40645 Z= 0.180 Angle : 0.638 11.853 55434 Z= 0.307 Chirality : 0.045 0.415 6315 Planarity : 0.004 0.055 7019 Dihedral : 7.499 115.731 6946 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.34 % Favored : 92.49 % Rotamer: Outliers : 1.75 % Allowed : 15.11 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.06 (0.12), residues: 4780 helix: 1.25 (0.14), residues: 1554 sheet: -0.74 (0.21), residues: 594 loop : -2.01 (0.11), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 460 TYR 0.017 0.001 TYR B1064 PHE 0.025 0.001 PHE A1118 TRP 0.017 0.001 TRP C 102 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00431 (40515) covalent geometry : angle 0.60704 (55091) SS BOND : bond 0.00396 ( 47) SS BOND : angle 1.87711 ( 94) hydrogen bonds : bond 0.05098 ( 1363) hydrogen bonds : angle 4.15460 ( 3822) link_BETA1-4 : bond 0.00723 ( 29) link_BETA1-4 : angle 2.90689 ( 87) link_NAG-ASN : bond 0.00607 ( 54) link_NAG-ASN : angle 2.72325 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 169 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7007 (pt) REVERT: A 1078 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8243 (pt) REVERT: A 1104 ARG cc_start: 0.8070 (ptp-170) cc_final: 0.7759 (ptt180) REVERT: B 155 ARG cc_start: 0.5893 (ptt-90) cc_final: 0.5555 (mmp-170) REVERT: B 167 TYR cc_start: 0.7839 (t80) cc_final: 0.7502 (t80) REVERT: B 187 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7657 (mtm180) REVERT: B 583 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: B 640 PHE cc_start: 0.8075 (t80) cc_final: 0.7781 (t80) REVERT: B 657 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: B 694 MET cc_start: 0.8657 (mtt) cc_final: 0.8401 (mtm) REVERT: B 875 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7871 (tt) REVERT: B 915 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: B 1026 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8936 (ttp) REVERT: C 197 TYR cc_start: 0.7606 (m-80) cc_final: 0.7140 (m-80) REVERT: C 595 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8505 (mt) REVERT: C 928 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8347 (tt) REVERT: I 82 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7838 (ppp) REVERT: I 270 MET cc_start: 0.1223 (ttt) cc_final: 0.0831 (tmt) REVERT: I 408 MET cc_start: 0.7888 (mpp) cc_final: 0.7620 (mpp) REVERT: I 462 MET cc_start: 0.6296 (mmp) cc_final: 0.5180 (mtt) REVERT: I 474 MET cc_start: 0.3124 (ttp) cc_final: 0.2352 (ptm) REVERT: I 477 TRP cc_start: 0.4900 (OUTLIER) cc_final: 0.4483 (t-100) REVERT: I 512 PHE cc_start: 0.7639 (m-80) cc_final: 0.6920 (m-80) REVERT: J 82 MET cc_start: 0.1107 (ptt) cc_final: 0.0528 (ptm) REVERT: K 152 MET cc_start: 0.2487 (mtm) cc_final: 0.1221 (ppp) REVERT: K 190 MET cc_start: 0.5676 (ptt) cc_final: 0.5020 (ppp) REVERT: K 262 LEU cc_start: 0.5712 (OUTLIER) cc_final: 0.5322 (mp) REVERT: K 270 MET cc_start: 0.3193 (ttm) cc_final: 0.2184 (tpp) REVERT: K 297 MET cc_start: -0.0403 (ppp) cc_final: -0.1265 (ptt) REVERT: K 358 ILE cc_start: -0.0892 (OUTLIER) cc_final: -0.1237 (mt) REVERT: K 364 VAL cc_start: -0.0566 (OUTLIER) cc_final: -0.1388 (p) REVERT: K 579 MET cc_start: -0.4037 (mmm) cc_final: -0.4487 (mtp) outliers start: 74 outliers final: 51 residues processed: 233 average time/residue: 0.2054 time to fit residues: 84.4336 Evaluate side-chains 230 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 165 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 477 TRP Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 142 optimal weight: 10.0000 chunk 283 optimal weight: 2.9990 chunk 391 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 400 optimal weight: 50.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN B 801 GLN C1103 GLN I 33 ASN ** J 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN K 33 ASN K 96 GLN ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.192114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.135136 restraints weight = 74429.192| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 4.85 r_work: 0.3322 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 40645 Z= 0.116 Angle : 0.597 19.330 55434 Z= 0.288 Chirality : 0.043 0.407 6315 Planarity : 0.004 0.061 7019 Dihedral : 7.180 114.609 6946 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.17 % Favored : 93.66 % Rotamer: Outliers : 1.46 % Allowed : 15.29 % Favored : 83.24 % 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: -0.93 (0.12), residues: 4780 helix: 1.34 (0.14), residues: 1568 sheet: -0.64 (0.21), residues: 612 loop : -1.96 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 460 TYR 0.017 0.001 TYR B1064 PHE 0.019 0.001 PHE B 799 TRP 0.018 0.001 TRP C 102 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00267 (40515) covalent geometry : angle 0.56651 (55091) SS BOND : bond 0.00415 ( 47) SS BOND : angle 1.99055 ( 94) hydrogen bonds : bond 0.04382 ( 1363) hydrogen bonds : angle 4.05751 ( 3822) link_BETA1-4 : bond 0.00560 ( 29) link_BETA1-4 : angle 2.66586 ( 87) link_NAG-ASN : bond 0.00304 ( 54) link_NAG-ASN : angle 2.61213 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9560 Ramachandran restraints generated. 4780 Oldfield, 0 Emsley, 4780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7098 (pt) REVERT: A 1078 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8086 (pt) REVERT: A 1104 ARG cc_start: 0.7994 (ptp-170) cc_final: 0.7724 (ptt180) REVERT: B 155 ARG cc_start: 0.5867 (ptt-90) cc_final: 0.5621 (mmp-170) REVERT: B 167 TYR cc_start: 0.7565 (t80) cc_final: 0.7221 (t80) REVERT: B 187 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7709 (mtm180) REVERT: B 583 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: B 657 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: B 694 MET cc_start: 0.8691 (mtt) cc_final: 0.8451 (mtm) REVERT: B 875 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7795 (tt) REVERT: B 915 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: C 197 TYR cc_start: 0.7553 (m-80) cc_final: 0.7138 (m-80) REVERT: C 595 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8477 (mp) REVERT: C 928 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8328 (tt) REVERT: I 82 MET cc_start: 0.8340 (ppp) cc_final: 0.7762 (ppp) REVERT: I 270 MET cc_start: 0.1095 (ttt) cc_final: 0.0697 (tmt) REVERT: I 360 MET cc_start: 0.6565 (tpt) cc_final: 0.6252 (tpp) REVERT: I 408 MET cc_start: 0.7946 (mpp) cc_final: 0.7671 (mpp) REVERT: I 462 MET cc_start: 0.6260 (mmp) cc_final: 0.5135 (mtt) REVERT: I 474 MET cc_start: 0.3277 (ttp) cc_final: 0.2514 (ptm) REVERT: I 477 TRP cc_start: 0.4856 (OUTLIER) cc_final: 0.4463 (t-100) REVERT: I 512 PHE cc_start: 0.7661 (m-80) cc_final: 0.6942 (m-80) REVERT: J 82 MET cc_start: 0.1074 (ptt) cc_final: 0.0484 (ptm) REVERT: J 249 MET cc_start: 0.3511 (tpt) cc_final: 0.3234 (mmt) REVERT: K 152 MET cc_start: 0.2434 (mtm) cc_final: 0.1253 (ppp) REVERT: K 190 MET cc_start: 0.5687 (ptt) cc_final: 0.5038 (ppp) REVERT: K 262 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5349 (mp) REVERT: K 270 MET cc_start: 0.3143 (ttm) cc_final: 0.2081 (tpp) REVERT: K 297 MET cc_start: -0.0577 (ppp) cc_final: -0.1430 (ptt) REVERT: K 332 MET cc_start: 0.3014 (ptt) cc_final: 0.2792 (ptt) REVERT: K 358 ILE cc_start: -0.0843 (OUTLIER) cc_final: -0.1219 (mt) REVERT: K 364 VAL cc_start: -0.0374 (OUTLIER) cc_final: -0.1185 (p) REVERT: K 579 MET cc_start: -0.4031 (mmm) cc_final: -0.4485 (mtp) outliers start: 62 outliers final: 45 residues processed: 229 average time/residue: 0.2110 time to fit residues: 85.1447 Evaluate side-chains 221 residues out of total 4237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 657 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain I residue 477 TRP Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain K residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 70 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 331 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 359 optimal weight: 7.9990 chunk 430 optimal weight: 8.9990 chunk 468 optimal weight: 40.0000 chunk 56 optimal weight: 0.7980 chunk 207 optimal weight: 0.0670 chunk 424 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN ** J 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN K 33 ASN K 96 GLN ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.191634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.135420 restraints weight = 75064.611| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 4.93 r_work: 0.3312 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 40645 Z= 0.140 Angle : 0.608 14.535 55434 Z= 0.293 Chirality : 0.044 0.404 6315 Planarity : 0.004 0.051 7019 Dihedral : 7.048 113.911 6946 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.76 % Favored : 93.10 % Rotamer: Outliers : 1.60 % Allowed : 15.32 % Favored : 83.08 % 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: -0.91 (0.12), residues: 4780 helix: 1.38 (0.14), residues: 1559 sheet: -0.64 (0.21), residues: 612 loop : -1.94 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 460 TYR 0.017 0.001 TYR J 613 PHE 0.027 0.001 PHE B 540 TRP 0.017 0.001 TRP C 102 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00332 (40515) covalent geometry : angle 0.57864 (55091) SS BOND : bond 0.00492 ( 47) SS BOND : angle 1.91818 ( 94) hydrogen bonds : bond 0.04643 ( 1363) hydrogen bonds : angle 4.06609 ( 3822) link_BETA1-4 : bond 0.00525 ( 29) link_BETA1-4 : angle 2.65133 ( 87) link_NAG-ASN : bond 0.00317 ( 54) link_NAG-ASN : angle 2.58981 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12675.42 seconds wall clock time: 217 minutes 5.65 seconds (13025.65 seconds total)