Starting phenix.real_space_refine on Sat Mar 7 08:08:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7z_31784/03_2026/7v7z_31784.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7z_31784/03_2026/7v7z_31784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7z_31784/03_2026/7v7z_31784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7z_31784/03_2026/7v7z_31784.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7z_31784/03_2026/7v7z_31784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7z_31784/03_2026/7v7z_31784.cif" } resolution = 3.1 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= -0.002 sd= 0.048 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 198 5.16 5 C 25400 2.51 5 N 6505 2.21 5 O 7748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 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: 39851 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8053 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8053 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8053 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.67, per 1000 atoms: 0.27 Number of scatterers: 39851 At special positions: 0 Unit cell: (185.9, 173.8, 238.7, 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 198 16.00 O 7748 8.00 N 6505 7.00 C 25400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.03 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 535 " - pdb=" SG CYS A 587 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 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=1, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 600 " " NAG A2004 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 340 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 234 " " NAG C2004 " - " ASN C 340 " " NAG C2005 " - " ASN C 600 " " NAG C2006 " - " ASN C 654 " " NAG D 901 " - " ASN D 322 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 279 " " NAG I 1 " - " ASN A 328 " " NAG J 1 " - " ASN A 340 " " NAG K 1 " - " ASN A 613 " " NAG L 1 " - " ASN A 706 " " NAG M 1 " - " ASN A 714 " " NAG N 1 " - " ASN A 798 " " NAG O 1 " - " ASN A1071 " " NAG P 1 " - " ASN A1095 " " NAG Q 1 " - " ASN A1131 " " NAG R 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 279 " " NAG T 1 " - " ASN B 328 " " NAG U 1 " - " ASN B 613 " " NAG V 1 " - " ASN B 706 " " NAG W 1 " - " ASN B 714 " " NAG X 1 " - " ASN B 798 " " NAG Y 1 " - " ASN B1071 " " NAG Z 1 " - " ASN B1095 " " NAG a 1 " - " ASN B1131 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 279 " " NAG d 1 " - " ASN C 328 " " NAG e 1 " - " ASN C 613 " " NAG f 1 " - " ASN C 706 " " NAG g 1 " - " ASN C 714 " " NAG h 1 " - " ASN C 798 " " NAG i 1 " - " ASN C1071 " " NAG j 1 " - " ASN C1095 " " NAG k 1 " - " ASN C1131 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9168 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 63 sheets defined 37.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.907A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.746A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 401 through 407 removed outlier: 3.993A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.843A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.608A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.570A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 895 through 905 removed outlier: 3.865A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 904 " --> pdb=" O ALA A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.686A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.605A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 980 removed outlier: 4.133A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.050A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.931A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 3.915A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 387 removed outlier: 3.986A pdb=" N ASN B 385 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.700A pdb=" N SER B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.604A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 780 removed outlier: 3.555A pdb=" N LEU B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 895 through 904 removed outlier: 4.327A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 915 removed outlier: 3.681A pdb=" N VAL B 912 " --> pdb=" O THR B 909 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 914 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.625A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 962 " --> pdb=" O THR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 980 removed outlier: 3.635A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.708A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1142 removed outlier: 3.681A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 4.154A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.858A pdb=" N LEU C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 407 removed outlier: 3.546A pdb=" N VAL C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 407' Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.858A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 780 removed outlier: 3.703A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.576A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 removed outlier: 3.611A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 904 " --> pdb=" O ALA C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.664A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 937 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.522A pdb=" N GLN C 962 " --> pdb=" O THR C 958 " (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 979 removed outlier: 3.894A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.078A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 Processing helix chain 'D' and resid 21 through 53 removed outlier: 3.719A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.836A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.817A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.814A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 172 removed outlier: 3.532A pdb=" N LEU D 162 " --> pdb=" O TYR D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.644A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 218 through 226 Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 268 removed outlier: 4.092A pdb=" N GLY D 268 " --> pdb=" O HIS D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 4.047A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.796A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 4.074A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.730A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.702A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 474 through 485 removed outlier: 3.782A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 4.393A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 508' Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.720A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS D 530 " --> pdb=" O GLN D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.707A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 583 through 588 removed outlier: 3.749A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.653A pdb=" N PHE D 592 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.657A pdb=" N ALA E 25 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 79 removed outlier: 4.540A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.613A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 147 through 154 removed outlier: 3.608A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 172 Processing helix chain 'E' and resid 176 through 194 removed outlier: 3.548A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 3.560A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 208 Processing helix chain 'E' and resid 218 through 229 removed outlier: 3.579A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 252 removed outlier: 3.934A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.828A pdb=" N LEU E 266 " --> pdb=" O PRO E 263 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 267 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY E 268 " --> pdb=" O HIS E 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 263 through 268' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.866A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.891A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.878A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 399 No H-bonds generated for 'chain 'E' and resid 397 through 399' Processing helix chain 'E' and resid 400 through 412 removed outlier: 4.060A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.549A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 473 through 485 removed outlier: 3.982A pdb=" N TRP E 477 " --> pdb=" O TRP E 473 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU E 483 " --> pdb=" O GLU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 532 removed outlier: 3.583A pdb=" N THR E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.598A pdb=" N GLN E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 583 through 588 removed outlier: 3.937A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 596 Processing helix chain 'F' and resid 21 through 53 removed outlier: 3.603A pdb=" N ALA F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 77 removed outlier: 4.696A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N MET F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F 73 " --> pdb=" O TRP F 69 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 152 removed outlier: 3.650A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 172 Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.692A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 removed outlier: 3.809A pdb=" N TRP F 203 " --> pdb=" O TYR F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 228 removed outlier: 3.544A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.583A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 268 removed outlier: 4.032A pdb=" N GLY F 268 " --> pdb=" O HIS F 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 265 through 268' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.642A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.583A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.684A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.671A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 413 Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.626A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 474 through 485 removed outlier: 3.755A pdb=" N TRP F 478 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.761A pdb=" N VAL F 506 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER F 507 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.593A pdb=" N THR F 517 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 559 removed outlier: 4.037A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 582 through 586 removed outlier: 3.592A pdb=" N LEU F 585 " --> pdb=" O ARG F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.993A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.557A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.000A pdb=" N PHE A 43 " --> pdb=" O ARG C 564 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.829A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.616A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 89 through 90 removed outlier: 3.616A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 93 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.864A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.573A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.943A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 355 removed outlier: 4.367A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 513 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 573 removed outlier: 3.969A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.009A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 708 through 709 Processing sheet with id=AB7, first strand: chain 'A' and resid 714 through 725 removed outlier: 7.036A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 714 through 725 Processing sheet with id=AB9, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.638A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1078 through 1080 removed outlier: 4.567A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.649A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 49 removed outlier: 7.948A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.822A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.849A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.559A pdb=" N GLY B 308 " --> pdb=" O THR B 596 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.559A pdb=" N GLY B 308 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.697A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.802A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 358 through 359 removed outlier: 7.203A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 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 Processing sheet with id=AD6, first strand: chain 'B' and resid 651 through 656 removed outlier: 5.985A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.556A 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 Processing sheet with id=AD8, first strand: chain 'B' and resid 714 through 719 removed outlier: 5.877A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.792A 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 1078 through 1080 removed outlier: 4.593A 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 50 through 55 removed outlier: 3.674A pdb=" N THR C 51 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.638A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.637A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.777A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL C 430 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS C 375 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 358 through 359 removed outlier: 7.302A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF2, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF3, first strand: chain 'C' and resid 536 through 540 Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 657 removed outlier: 6.103A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N VAL C 653 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AF6, first strand: chain 'C' and resid 714 through 725 removed outlier: 6.951A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 714 through 725 Processing sheet with id=AF8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.700A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1078 through 1080 removed outlier: 4.360A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C1120 " --> pdb=" O ALA C1084 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG2, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.632A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.556A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.937A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 132 through 133 removed outlier: 3.691A pdb=" N VAL E 132 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.010A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 132 through 133 removed outlier: 4.192A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.834A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'F' and resid 347 through 352 removed outlier: 5.855A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1525 hydrogen bonds defined for protein. 4269 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: 10.51 Time building geometry restraints manager: 4.93 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: 12650 1.34 - 1.46: 10122 1.46 - 1.58: 17760 1.58 - 1.70: 0 1.70 - 1.82: 288 Bond restraints: 40820 Sorted by residual: bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C PRO B 983 " pdb=" N PRO B 984 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.97e+00 bond pdb=" C PRO A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.373 0.033 2.00e-02 2.50e+03 2.66e+00 ... (remaining 40815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 53986 1.63 - 3.27: 1317 3.27 - 4.90: 174 4.90 - 6.54: 34 6.54 - 8.17: 14 Bond angle restraints: 55525 Sorted by residual: angle pdb=" N VAL C1125 " pdb=" CA VAL C1125 " pdb=" C VAL C1125 " ideal model delta sigma weight residual 113.71 108.97 4.74 9.50e-01 1.11e+00 2.49e+01 angle pdb=" N ILE E 21 " pdb=" CA ILE E 21 " pdb=" C ILE E 21 " ideal model delta sigma weight residual 112.96 108.88 4.08 1.00e+00 1.00e+00 1.67e+01 angle pdb=" C TRP D 461 " pdb=" N MET D 462 " pdb=" CA MET D 462 " ideal model delta sigma weight residual 121.14 114.72 6.42 1.75e+00 3.27e-01 1.35e+01 angle pdb=" C GLU E 375 " pdb=" N MET E 376 " pdb=" CA MET E 376 " ideal model delta sigma weight residual 121.58 114.56 7.02 1.95e+00 2.63e-01 1.29e+01 angle pdb=" C ASN B 234 " pdb=" N ILE B 235 " pdb=" CA ILE B 235 " ideal model delta sigma weight residual 120.49 125.44 -4.95 1.38e+00 5.25e-01 1.29e+01 ... (remaining 55520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 23488 23.25 - 46.50: 1484 46.50 - 69.75: 167 69.75 - 93.01: 63 93.01 - 116.26: 22 Dihedral angle restraints: 25224 sinusoidal: 10971 harmonic: 14253 Sorted by residual: dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 -174.81 88.81 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -0.88 -85.12 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS C 659 " pdb=" SG CYS C 659 " pdb=" SG CYS C 668 " pdb=" CB CYS C 668 " ideal model delta sinusoidal sigma weight residual -86.00 -170.58 84.58 1 1.00e+01 1.00e-02 8.69e+01 ... (remaining 25221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 6328 0.175 - 0.351: 12 0.351 - 0.526: 5 0.526 - 0.701: 1 0.701 - 0.877: 1 Chirality restraints: 6347 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C1 NAG C2006 " pdb=" ND2 ASN C 654 " pdb=" C2 NAG C2006 " pdb=" O5 NAG C2006 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.57e+00 ... (remaining 6344 not shown) Planarity restraints: 7126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.024 2.00e-02 2.50e+03 2.32e-02 6.71e+00 pdb=" CG ASN A 165 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 517 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.34e+00 pdb=" N PRO A 518 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1071 " -0.021 2.00e-02 2.50e+03 1.98e-02 4.88e+00 pdb=" CG ASN B1071 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B1071 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B1071 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.021 2.00e-02 2.50e+03 ... (remaining 7123 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 844 2.68 - 3.23: 38788 3.23 - 3.79: 60712 3.79 - 4.34: 78181 4.34 - 4.90: 129112 Nonbonded interactions: 307637 Sorted by model distance: nonbonded pdb=" OD2 ASP B 575 " pdb=" OG1 THR B 578 " model vdw 2.123 3.040 nonbonded pdb=" OG1 THR A 713 " pdb=" O GLN A1068 " model vdw 2.153 3.040 nonbonded pdb=" OD2 ASP C 575 " pdb=" OG1 THR C 578 " model vdw 2.166 3.040 nonbonded pdb=" OD2 ASP A 575 " pdb=" OG1 THR A 578 " model vdw 2.172 3.040 nonbonded pdb=" OG1 THR A 497 " pdb=" OH TYR D 41 " model vdw 2.173 3.040 ... (remaining 307632 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' selection = (chain 'B' and resid 14 through 2004) selection = (chain 'C' and resid 14 through 2004) } ncs_group { reference = (chain 'D' and resid 19 through 614) selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 41.460 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.170 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.004 0.042 40948 Z= 0.174 Angle : 0.650 17.150 55858 Z= 0.328 Chirality : 0.048 0.877 6347 Planarity : 0.004 0.058 7078 Dihedral : 14.823 116.256 15912 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.12), residues: 4830 helix: 0.96 (0.14), residues: 1566 sheet: -1.16 (0.19), residues: 681 loop : -1.62 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 460 TYR 0.017 0.001 TYR A1064 PHE 0.022 0.001 PHE A 903 TRP 0.016 0.001 TRP E 165 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00354 (40820) covalent geometry : angle 0.61345 (55525) SS BOND : bond 0.00325 ( 48) SS BOND : angle 2.06600 ( 96) hydrogen bonds : bond 0.16398 ( 1497) hydrogen bonds : angle 6.47155 ( 4269) Misc. bond : bond 0.00623 ( 1) link_BETA1-4 : bond 0.00387 ( 31) link_BETA1-4 : angle 1.66260 ( 93) link_NAG-ASN : bond 0.00584 ( 48) link_NAG-ASN : angle 3.76549 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8077 (p90) cc_final: 0.7591 (p90) REVERT: A 153 MET cc_start: 0.5655 (ppp) cc_final: 0.2988 (mmp) REVERT: A 168 PHE cc_start: 0.8132 (t80) cc_final: 0.7829 (t80) REVERT: A 239 GLN cc_start: 0.6088 (tt0) cc_final: 0.5860 (tt0) REVERT: B 52 GLN cc_start: 0.8096 (pp30) cc_final: 0.7735 (pp30) REVERT: B 160 TYR cc_start: 0.8257 (p90) cc_final: 0.8030 (p90) REVERT: C 694 MET cc_start: 0.7637 (mpp) cc_final: 0.7278 (mtp) REVERT: D 455 MET cc_start: 0.4613 (ppp) cc_final: 0.4002 (ppp) REVERT: D 462 MET cc_start: 0.6857 (pmm) cc_final: 0.5256 (mmp) REVERT: D 468 ILE cc_start: 0.0982 (pt) cc_final: -0.1034 (tp) REVERT: D 480 MET cc_start: 0.3727 (tmm) cc_final: 0.3184 (tmm) REVERT: D 579 MET cc_start: -0.1830 (tpt) cc_final: -0.2342 (tpp) REVERT: D 600 LYS cc_start: 0.3358 (mmtm) cc_final: 0.3011 (tmtt) REVERT: E 89 GLN cc_start: 0.4435 (mp10) cc_final: 0.3956 (mm110) REVERT: E 557 MET cc_start: 0.2278 (tmm) cc_final: 0.1696 (ttp) REVERT: E 579 MET cc_start: -0.2554 (mmm) cc_final: -0.3003 (ttt) REVERT: F 62 MET cc_start: 0.2853 (mmm) cc_final: 0.2544 (mmm) REVERT: F 123 MET cc_start: -0.0284 (tmm) cc_final: -0.1244 (mmm) REVERT: F 323 MET cc_start: -0.3144 (tpt) cc_final: -0.3428 (tpt) REVERT: F 383 MET cc_start: -0.0931 (tpp) cc_final: -0.1476 (ttm) REVERT: F 408 MET cc_start: -0.0962 (ptt) cc_final: -0.2561 (ttt) REVERT: F 455 MET cc_start: 0.1697 (ppp) cc_final: 0.1378 (ppp) REVERT: F 474 MET cc_start: -0.1686 (mmp) cc_final: -0.3057 (tpp) REVERT: F 571 GLU cc_start: 0.4563 (mm-30) cc_final: 0.3358 (mt-10) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2250 time to fit residues: 98.0630 Evaluate side-chains 175 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 40.0000 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.0010 chunk 470 optimal weight: 30.0000 overall best weight: 2.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 910 GLN C 87 ASN C 898 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN D 228 HIS ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 GLN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.213751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.150537 restraints weight = 73288.948| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 7.24 r_work: 0.3479 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 40948 Z= 0.243 Angle : 0.687 16.085 55858 Z= 0.339 Chirality : 0.049 0.731 6347 Planarity : 0.004 0.051 7078 Dihedral : 9.437 107.183 6900 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.54 % Allowed : 6.40 % Favored : 93.06 % 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: -0.98 (0.12), residues: 4830 helix: 1.07 (0.13), residues: 1610 sheet: -1.23 (0.19), residues: 723 loop : -1.67 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1036 TYR 0.028 0.002 TYR A1064 PHE 0.035 0.002 PHE B1118 TRP 0.037 0.001 TRP F 461 HIS 0.013 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00588 (40820) covalent geometry : angle 0.65188 (55525) SS BOND : bond 0.00504 ( 48) SS BOND : angle 2.27472 ( 96) hydrogen bonds : bond 0.05305 ( 1497) hydrogen bonds : angle 5.07689 ( 4269) Misc. bond : bond 0.00626 ( 1) link_BETA1-4 : bond 0.00378 ( 31) link_BETA1-4 : angle 1.56744 ( 93) link_NAG-ASN : bond 0.00557 ( 48) link_NAG-ASN : angle 3.79863 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7686 (p90) cc_final: 0.7130 (p90) REVERT: A 153 MET cc_start: 0.5251 (ppp) cc_final: 0.2374 (mmp) REVERT: A 239 GLN cc_start: 0.6666 (tt0) cc_final: 0.6383 (tt0) REVERT: A 362 TYR cc_start: 0.8815 (m-80) cc_final: 0.8204 (m-80) REVERT: A 422 LEU cc_start: 0.9050 (tt) cc_final: 0.8751 (pp) REVERT: A 505 TYR cc_start: 0.7750 (m-10) cc_final: 0.7523 (m-10) REVERT: B 52 GLN cc_start: 0.8571 (pp30) cc_final: 0.7839 (pp30) REVERT: C 694 MET cc_start: 0.8149 (mpp) cc_final: 0.7737 (mtp) REVERT: D 332 MET cc_start: 0.4815 (tmm) cc_final: 0.4611 (tmm) REVERT: D 408 MET cc_start: 0.3933 (tpp) cc_final: 0.3582 (tpp) REVERT: D 455 MET cc_start: 0.4420 (ppp) cc_final: 0.3642 (ppp) REVERT: D 462 MET cc_start: 0.6824 (pmm) cc_final: 0.5696 (mmp) REVERT: D 468 ILE cc_start: 0.3195 (pt) cc_final: 0.0776 (tp) REVERT: D 480 MET cc_start: 0.4008 (tmm) cc_final: 0.3491 (tmm) REVERT: E 89 GLN cc_start: 0.4693 (mp10) cc_final: 0.4191 (mm110) REVERT: E 557 MET cc_start: 0.1565 (tmm) cc_final: 0.1044 (ttp) REVERT: E 579 MET cc_start: -0.2938 (mmm) cc_final: -0.3466 (ttt) REVERT: F 62 MET cc_start: 0.2900 (mmm) cc_final: 0.2593 (mmm) REVERT: F 123 MET cc_start: 0.0374 (tmm) cc_final: -0.0666 (mmm) REVERT: F 323 MET cc_start: -0.2603 (tpt) cc_final: -0.2878 (tpt) REVERT: F 383 MET cc_start: -0.0771 (tpp) cc_final: -0.1290 (ttm) REVERT: F 408 MET cc_start: -0.1164 (ptt) cc_final: -0.2550 (ttt) REVERT: F 474 MET cc_start: -0.2146 (mmp) cc_final: -0.2988 (tpp) REVERT: F 571 GLU cc_start: 0.4203 (mm-30) cc_final: 0.3475 (mt-10) outliers start: 23 outliers final: 17 residues processed: 205 average time/residue: 0.2184 time to fit residues: 78.0463 Evaluate side-chains 189 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 54 optimal weight: 1.9990 chunk 309 optimal weight: 40.0000 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 340 optimal weight: 3.9990 chunk 343 optimal weight: 20.0000 chunk 422 optimal weight: 5.9990 chunk 430 optimal weight: 50.0000 chunk 52 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 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 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN E 599 ASN F 300 GLN ** F 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 = 0.4869 r_free = 0.4869 target = 0.209791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.149175 restraints weight = 73703.227| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 6.54 r_work: 0.3359 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40948 Z= 0.137 Angle : 0.588 14.574 55858 Z= 0.287 Chirality : 0.045 0.508 6347 Planarity : 0.004 0.048 7078 Dihedral : 8.722 108.634 6900 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.96 % Allowed : 9.00 % Favored : 90.04 % 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: -0.79 (0.12), residues: 4830 helix: 1.31 (0.13), residues: 1589 sheet: -1.10 (0.19), residues: 675 loop : -1.60 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 460 TYR 0.022 0.001 TYR A1064 PHE 0.025 0.001 PHE C1086 TRP 0.024 0.001 TRP F 461 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00316 (40820) covalent geometry : angle 0.55653 (55525) SS BOND : bond 0.00348 ( 48) SS BOND : angle 1.79243 ( 96) hydrogen bonds : bond 0.04199 ( 1497) hydrogen bonds : angle 4.72362 ( 4269) Misc. bond : bond 0.00515 ( 1) link_BETA1-4 : bond 0.00397 ( 31) link_BETA1-4 : angle 1.61657 ( 93) link_NAG-ASN : bond 0.00517 ( 48) link_NAG-ASN : angle 3.28587 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7740 (p90) cc_final: 0.7205 (p90) REVERT: A 153 MET cc_start: 0.5327 (ppp) cc_final: 0.2384 (mmp) REVERT: A 168 PHE cc_start: 0.7864 (t80) cc_final: 0.7582 (t80) REVERT: A 204 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6181 (m-10) REVERT: A 339 PHE cc_start: 0.8271 (m-80) cc_final: 0.8063 (m-80) REVERT: A 362 TYR cc_start: 0.8835 (m-80) cc_final: 0.8225 (m-80) REVERT: A 422 LEU cc_start: 0.9145 (tt) cc_final: 0.8677 (pp) REVERT: A 505 TYR cc_start: 0.7795 (m-10) cc_final: 0.7565 (m-10) REVERT: B 52 GLN cc_start: 0.8456 (pp30) cc_final: 0.8010 (pp30) REVERT: C 694 MET cc_start: 0.8186 (mpp) cc_final: 0.7983 (mtp) REVERT: D 190 MET cc_start: 0.5933 (ptm) cc_final: 0.5509 (tmm) REVERT: D 455 MET cc_start: 0.4372 (ppp) cc_final: 0.3599 (ppp) REVERT: D 462 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.5878 (mmt) REVERT: D 480 MET cc_start: 0.4200 (tmm) cc_final: 0.3597 (tmm) REVERT: D 600 LYS cc_start: 0.3534 (mmtm) cc_final: 0.3323 (tmtt) REVERT: E 89 GLN cc_start: 0.4575 (mp10) cc_final: 0.4210 (mm110) REVERT: E 557 MET cc_start: 0.1587 (tmm) cc_final: 0.1082 (ttp) REVERT: E 579 MET cc_start: -0.3035 (mmm) cc_final: -0.3563 (ttt) REVERT: F 62 MET cc_start: 0.2380 (mmm) cc_final: 0.2081 (mmm) REVERT: F 408 MET cc_start: -0.1068 (ptt) cc_final: -0.2458 (ttt) REVERT: F 474 MET cc_start: -0.2106 (mmp) cc_final: -0.2895 (tpp) outliers start: 41 outliers final: 29 residues processed: 213 average time/residue: 0.2142 time to fit residues: 80.2458 Evaluate side-chains 199 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 290 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 375 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 378 optimal weight: 50.0000 chunk 159 optimal weight: 3.9990 chunk 412 optimal weight: 3.9990 chunk 382 optimal weight: 10.0000 chunk 158 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 910 GLN ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4858 r_free = 0.4858 target = 0.208666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.149131 restraints weight = 73276.880| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 7.31 r_work: 0.3302 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 40948 Z= 0.180 Angle : 0.615 13.032 55858 Z= 0.301 Chirality : 0.046 0.484 6347 Planarity : 0.004 0.045 7078 Dihedral : 8.410 107.337 6900 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.45 % Allowed : 11.13 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.12), residues: 4830 helix: 1.28 (0.13), residues: 1589 sheet: -1.13 (0.19), residues: 666 loop : -1.64 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1036 TYR 0.024 0.001 TYR A1064 PHE 0.029 0.002 PHE A1118 TRP 0.018 0.001 TRP F 461 HIS 0.005 0.001 HIS B1055 Details of bonding type rmsd covalent geometry : bond 0.00435 (40820) covalent geometry : angle 0.58461 (55525) SS BOND : bond 0.00449 ( 48) SS BOND : angle 2.07194 ( 96) hydrogen bonds : bond 0.04381 ( 1497) hydrogen bonds : angle 4.67238 ( 4269) Misc. bond : bond 0.00529 ( 1) link_BETA1-4 : bond 0.00424 ( 31) link_BETA1-4 : angle 1.62299 ( 93) link_NAG-ASN : bond 0.00465 ( 48) link_NAG-ASN : angle 3.25393 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7797 (p90) cc_final: 0.7239 (p90) REVERT: A 153 MET cc_start: 0.5438 (ppp) cc_final: 0.2619 (mmp) REVERT: A 204 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: A 339 PHE cc_start: 0.8460 (m-80) cc_final: 0.8191 (m-80) REVERT: A 362 TYR cc_start: 0.8850 (m-80) cc_final: 0.8223 (m-80) REVERT: A 422 LEU cc_start: 0.8912 (tt) cc_final: 0.8673 (pp) REVERT: A 505 TYR cc_start: 0.7734 (m-10) cc_final: 0.7494 (m-10) REVERT: B 52 GLN cc_start: 0.8429 (pp30) cc_final: 0.7998 (pp30) REVERT: C 1026 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8204 (ttm) REVERT: D 190 MET cc_start: 0.5879 (ptm) cc_final: 0.5520 (tmm) REVERT: D 408 MET cc_start: 0.4224 (tpp) cc_final: 0.3799 (tpp) REVERT: D 455 MET cc_start: 0.4235 (ppp) cc_final: 0.3371 (ppp) REVERT: D 462 MET cc_start: 0.6828 (pmm) cc_final: 0.5824 (mmt) REVERT: D 480 MET cc_start: 0.4407 (tmm) cc_final: 0.3818 (tmm) REVERT: E 89 GLN cc_start: 0.4670 (mp10) cc_final: 0.4377 (mm110) REVERT: E 557 MET cc_start: 0.1360 (tmm) cc_final: 0.0905 (ttp) REVERT: E 579 MET cc_start: -0.2727 (mmm) cc_final: -0.3194 (ttt) REVERT: F 62 MET cc_start: 0.2482 (mmm) cc_final: 0.2199 (mmm) REVERT: F 123 MET cc_start: -0.1165 (tmm) cc_final: -0.1975 (mmt) REVERT: F 383 MET cc_start: -0.1024 (mmt) cc_final: -0.2016 (ttm) REVERT: F 408 MET cc_start: -0.0752 (ptt) cc_final: -0.1991 (ttt) REVERT: F 474 MET cc_start: -0.1824 (mmp) cc_final: -0.2597 (tpp) outliers start: 62 outliers final: 44 residues processed: 229 average time/residue: 0.2176 time to fit residues: 87.7941 Evaluate side-chains 217 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 215 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 82 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 469 optimal weight: 50.0000 chunk 322 optimal weight: 0.8980 chunk 454 optimal weight: 30.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN C 318 GLN ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4931 r_free = 0.4931 target = 0.212782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.156763 restraints weight = 74541.000| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 4.35 r_work: 0.3558 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40948 Z= 0.124 Angle : 0.574 12.436 55858 Z= 0.279 Chirality : 0.044 0.472 6347 Planarity : 0.004 0.044 7078 Dihedral : 7.997 105.020 6900 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.38 % Allowed : 12.25 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.12), residues: 4830 helix: 1.37 (0.13), residues: 1598 sheet: -1.03 (0.19), residues: 659 loop : -1.57 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 460 TYR 0.028 0.001 TYR A 393 PHE 0.019 0.001 PHE C1118 TRP 0.014 0.001 TRP F 461 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00288 (40820) covalent geometry : angle 0.54377 (55525) SS BOND : bond 0.00350 ( 48) SS BOND : angle 2.13898 ( 96) hydrogen bonds : bond 0.03856 ( 1497) hydrogen bonds : angle 4.52071 ( 4269) Misc. bond : bond 0.00464 ( 1) link_BETA1-4 : bond 0.00432 ( 31) link_BETA1-4 : angle 1.65624 ( 93) link_NAG-ASN : bond 0.00448 ( 48) link_NAG-ASN : angle 3.02472 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7842 (p90) cc_final: 0.7304 (p90) REVERT: A 153 MET cc_start: 0.5457 (ppp) cc_final: 0.2737 (mmp) REVERT: A 339 PHE cc_start: 0.8427 (m-80) cc_final: 0.8212 (m-80) REVERT: A 362 TYR cc_start: 0.8869 (m-80) cc_final: 0.8286 (m-80) REVERT: A 422 LEU cc_start: 0.9052 (tt) cc_final: 0.8818 (pp) REVERT: A 505 TYR cc_start: 0.7851 (m-10) cc_final: 0.7631 (m-10) REVERT: B 52 GLN cc_start: 0.8371 (pp30) cc_final: 0.7952 (pp30) REVERT: D 190 MET cc_start: 0.6110 (ptm) cc_final: 0.5575 (tmm) REVERT: D 408 MET cc_start: 0.4580 (tpp) cc_final: 0.4037 (tpp) REVERT: D 455 MET cc_start: 0.4529 (ppp) cc_final: 0.3898 (ppp) REVERT: D 462 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.5627 (mmt) REVERT: D 480 MET cc_start: 0.4015 (tmm) cc_final: 0.3366 (tmm) REVERT: E 89 GLN cc_start: 0.4383 (mp10) cc_final: 0.4017 (mm110) REVERT: E 152 MET cc_start: -0.2870 (OUTLIER) cc_final: -0.3090 (ttp) REVERT: E 557 MET cc_start: 0.2165 (tmm) cc_final: 0.1702 (ttp) REVERT: E 579 MET cc_start: -0.2799 (mmm) cc_final: -0.3355 (ttt) REVERT: F 62 MET cc_start: 0.2121 (mmm) cc_final: 0.1811 (mmm) REVERT: F 408 MET cc_start: -0.1340 (ptt) cc_final: -0.3007 (ttt) REVERT: F 474 MET cc_start: -0.1640 (mmp) cc_final: -0.2733 (tpp) outliers start: 59 outliers final: 38 residues processed: 226 average time/residue: 0.2126 time to fit residues: 84.4459 Evaluate side-chains 208 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 319 optimal weight: 20.0000 chunk 324 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 363 optimal weight: 10.0000 chunk 315 optimal weight: 40.0000 chunk 417 optimal weight: 50.0000 chunk 412 optimal weight: 7.9990 chunk 295 optimal weight: 0.9990 chunk 484 optimal weight: 30.0000 chunk 189 optimal weight: 2.9990 chunk 347 optimal weight: 50.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN A 471 GLN A 541 ASN A 641 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 HIS B 910 GLN C1045 HIS ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS E 586 ASN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.204468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.148393 restraints weight = 73783.721| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 5.01 r_work: 0.3317 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.174 40948 Z= 0.475 Angle : 0.866 14.069 55858 Z= 0.433 Chirality : 0.056 0.461 6347 Planarity : 0.006 0.072 7078 Dihedral : 8.753 108.163 6900 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.31 % Allowed : 13.60 % Favored : 84.08 % 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: -1.36 (0.12), residues: 4830 helix: 0.81 (0.13), residues: 1593 sheet: -1.56 (0.18), residues: 726 loop : -1.88 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1036 TYR 0.057 0.003 TYR B 204 PHE 0.053 0.003 PHE B1118 TRP 0.024 0.002 TRP B 883 HIS 0.014 0.002 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.01153 (40820) covalent geometry : angle 0.83405 (55525) SS BOND : bond 0.00668 ( 48) SS BOND : angle 3.11731 ( 96) hydrogen bonds : bond 0.06173 ( 1497) hydrogen bonds : angle 5.11777 ( 4269) Misc. bond : bond 0.00666 ( 1) link_BETA1-4 : bond 0.00456 ( 31) link_BETA1-4 : angle 1.83038 ( 93) link_NAG-ASN : bond 0.00699 ( 48) link_NAG-ASN : angle 3.71394 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 171 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8055 (p90) cc_final: 0.7491 (p90) REVERT: A 153 MET cc_start: 0.5503 (ppp) cc_final: 0.2605 (mmp) REVERT: A 203 ILE cc_start: 0.8307 (mt) cc_final: 0.8074 (mt) REVERT: A 204 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: A 339 PHE cc_start: 0.8441 (m-80) cc_final: 0.8204 (m-80) REVERT: A 362 TYR cc_start: 0.8932 (m-80) cc_final: 0.8302 (m-80) REVERT: A 422 LEU cc_start: 0.9163 (tt) cc_final: 0.8809 (pp) REVERT: A 505 TYR cc_start: 0.7791 (m-10) cc_final: 0.7556 (m-10) REVERT: A 560 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.5671 (mp10) REVERT: A 956 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8981 (mm) REVERT: B 52 GLN cc_start: 0.8576 (pp30) cc_final: 0.8110 (pp30) REVERT: B 764 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8503 (mm) REVERT: C 204 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8001 (m-10) REVERT: C 560 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.5807 (mp10) REVERT: D 190 MET cc_start: 0.5970 (ptm) cc_final: 0.5380 (tmm) REVERT: D 408 MET cc_start: 0.4553 (tpp) cc_final: 0.4030 (tpp) REVERT: D 455 MET cc_start: 0.4698 (ppp) cc_final: 0.4053 (ppp) REVERT: D 462 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.5209 (mmt) REVERT: D 480 MET cc_start: 0.4191 (tmm) cc_final: 0.3872 (tmm) REVERT: E 89 GLN cc_start: 0.4602 (mp10) cc_final: 0.4132 (mm-40) REVERT: E 557 MET cc_start: 0.2292 (tmm) cc_final: 0.1821 (ttp) REVERT: E 579 MET cc_start: -0.2862 (mmm) cc_final: -0.3373 (ttt) REVERT: F 408 MET cc_start: -0.1142 (ptt) cc_final: -0.2798 (ttt) REVERT: F 474 MET cc_start: -0.1589 (mmp) cc_final: -0.2609 (tpp) outliers start: 99 outliers final: 67 residues processed: 256 average time/residue: 0.2092 time to fit residues: 94.0564 Evaluate side-chains 238 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 164 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 586 ASN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 115 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 327 optimal weight: 50.0000 chunk 217 optimal weight: 20.0000 chunk 365 optimal weight: 1.9990 chunk 406 optimal weight: 50.0000 chunk 168 optimal weight: 2.9990 chunk 370 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN F 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.210701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.150119 restraints weight = 73370.763| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 6.18 r_work: 0.3391 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40948 Z= 0.134 Angle : 0.626 11.777 55858 Z= 0.305 Chirality : 0.045 0.459 6347 Planarity : 0.004 0.063 7078 Dihedral : 8.169 108.157 6900 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.78 % Allowed : 14.63 % Favored : 83.59 % 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: -0.96 (0.12), residues: 4830 helix: 1.24 (0.13), residues: 1582 sheet: -1.34 (0.19), residues: 653 loop : -1.71 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 325 TYR 0.021 0.001 TYR A1064 PHE 0.026 0.001 PHE A 168 TRP 0.021 0.001 TRP C 104 HIS 0.016 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00310 (40820) covalent geometry : angle 0.59498 (55525) SS BOND : bond 0.00377 ( 48) SS BOND : angle 2.29801 ( 96) hydrogen bonds : bond 0.04179 ( 1497) hydrogen bonds : angle 4.69082 ( 4269) Misc. bond : bond 0.00492 ( 1) link_BETA1-4 : bond 0.00415 ( 31) link_BETA1-4 : angle 1.67399 ( 93) link_NAG-ASN : bond 0.00449 ( 48) link_NAG-ASN : angle 3.15494 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 170 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7891 (p90) cc_final: 0.7341 (p90) REVERT: A 153 MET cc_start: 0.5498 (ppp) cc_final: 0.2649 (mmp) REVERT: A 204 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.6244 (m-10) REVERT: A 339 PHE cc_start: 0.8428 (m-80) cc_final: 0.8226 (m-80) REVERT: A 362 TYR cc_start: 0.8837 (m-80) cc_final: 0.8215 (m-80) REVERT: A 422 LEU cc_start: 0.9105 (tt) cc_final: 0.8832 (pp) REVERT: A 505 TYR cc_start: 0.7741 (m-10) cc_final: 0.7503 (m-10) REVERT: A 560 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.5616 (mp10) REVERT: B 52 GLN cc_start: 0.8473 (pp30) cc_final: 0.8013 (pp30) REVERT: D 190 MET cc_start: 0.5954 (ptm) cc_final: 0.5583 (tmm) REVERT: D 408 MET cc_start: 0.4427 (tpp) cc_final: 0.3858 (tpp) REVERT: D 455 MET cc_start: 0.4265 (ppp) cc_final: 0.3475 (ppp) REVERT: D 462 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.5531 (mmt) REVERT: D 480 MET cc_start: 0.4294 (tmm) cc_final: 0.3944 (tmm) REVERT: E 89 GLN cc_start: 0.4803 (mp10) cc_final: 0.4415 (mm-40) REVERT: E 152 MET cc_start: -0.3144 (OUTLIER) cc_final: -0.3393 (ttp) REVERT: E 557 MET cc_start: 0.1561 (tmm) cc_final: 0.1127 (ttp) REVERT: E 579 MET cc_start: -0.3157 (mmm) cc_final: -0.3689 (ttt) REVERT: F 62 MET cc_start: 0.1669 (mmm) cc_final: 0.1309 (mmm) REVERT: F 132 VAL cc_start: -0.1127 (OUTLIER) cc_final: -0.1405 (t) REVERT: F 408 MET cc_start: -0.0973 (ptt) cc_final: -0.2368 (ttp) REVERT: F 474 MET cc_start: -0.2012 (mmp) cc_final: -0.2633 (tpp) outliers start: 76 outliers final: 46 residues processed: 237 average time/residue: 0.2067 time to fit residues: 86.4752 Evaluate side-chains 219 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 24 optimal weight: 1.9990 chunk 272 optimal weight: 0.7980 chunk 337 optimal weight: 30.0000 chunk 355 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 478 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 225 optimal weight: 5.9990 chunk 481 optimal weight: 0.0370 chunk 164 optimal weight: 5.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1045 HIS ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.212292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.150510 restraints weight = 73294.354| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 6.71 r_work: 0.3442 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 40948 Z= 0.108 Angle : 0.582 11.747 55858 Z= 0.281 Chirality : 0.044 0.438 6347 Planarity : 0.004 0.053 7078 Dihedral : 7.429 101.270 6900 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.38 % Allowed : 15.03 % Favored : 83.59 % 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: -0.71 (0.12), residues: 4830 helix: 1.40 (0.13), residues: 1607 sheet: -1.14 (0.19), residues: 656 loop : -1.57 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 460 TYR 0.021 0.001 TYR B1064 PHE 0.033 0.001 PHE A 168 TRP 0.018 0.001 TRP C 104 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00247 (40820) covalent geometry : angle 0.55575 (55525) SS BOND : bond 0.00323 ( 48) SS BOND : angle 1.88213 ( 96) hydrogen bonds : bond 0.03585 ( 1497) hydrogen bonds : angle 4.43396 ( 4269) Misc. bond : bond 0.00409 ( 1) link_BETA1-4 : bond 0.00452 ( 31) link_BETA1-4 : angle 1.75611 ( 93) link_NAG-ASN : bond 0.00464 ( 48) link_NAG-ASN : angle 2.84055 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7650 (p90) cc_final: 0.7142 (p90) REVERT: A 153 MET cc_start: 0.5580 (ppp) cc_final: 0.2842 (mmp) REVERT: A 239 GLN cc_start: 0.6482 (tt0) cc_final: 0.6257 (tt0) REVERT: A 339 PHE cc_start: 0.8457 (m-80) cc_final: 0.8252 (m-80) REVERT: A 362 TYR cc_start: 0.8720 (m-80) cc_final: 0.8245 (m-80) REVERT: A 422 LEU cc_start: 0.9002 (tt) cc_final: 0.8759 (pp) REVERT: A 505 TYR cc_start: 0.7639 (m-10) cc_final: 0.7402 (m-10) REVERT: A 560 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: B 52 GLN cc_start: 0.8443 (pp30) cc_final: 0.7935 (pp30) REVERT: C 1026 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7928 (ttm) REVERT: D 152 MET cc_start: -0.1435 (ppp) cc_final: -0.2999 (pmm) REVERT: D 190 MET cc_start: 0.6005 (ptm) cc_final: 0.5609 (tmm) REVERT: D 366 MET cc_start: 0.6647 (tmm) cc_final: 0.6245 (ppp) REVERT: D 408 MET cc_start: 0.4512 (tpp) cc_final: 0.3956 (tpp) REVERT: D 455 MET cc_start: 0.4358 (ppp) cc_final: 0.3626 (ppp) REVERT: D 462 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.5427 (mmt) REVERT: D 480 MET cc_start: 0.4131 (tmm) cc_final: 0.3773 (tmm) REVERT: E 89 GLN cc_start: 0.4419 (mp10) cc_final: 0.4028 (mm-40) REVERT: E 152 MET cc_start: -0.3272 (OUTLIER) cc_final: -0.3524 (ttp) REVERT: E 557 MET cc_start: 0.1702 (tmm) cc_final: 0.1127 (ttp) REVERT: E 579 MET cc_start: -0.3488 (mmm) cc_final: -0.3997 (ttt) REVERT: F 62 MET cc_start: 0.1898 (mmm) cc_final: 0.1565 (mmm) REVERT: F 132 VAL cc_start: -0.1733 (OUTLIER) cc_final: -0.2018 (t) REVERT: F 249 MET cc_start: 0.1892 (mpp) cc_final: 0.0299 (tpp) REVERT: F 408 MET cc_start: -0.1063 (ptt) cc_final: -0.2495 (ttp) REVERT: F 474 MET cc_start: -0.2266 (mmp) cc_final: -0.2973 (tpp) outliers start: 59 outliers final: 43 residues processed: 229 average time/residue: 0.2121 time to fit residues: 85.9622 Evaluate side-chains 218 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 378 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 44 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 338 optimal weight: 20.0000 chunk 406 optimal weight: 40.0000 chunk 245 optimal weight: 50.0000 chunk 469 optimal weight: 30.0000 chunk 346 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 272 optimal weight: 0.4980 chunk 45 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.210356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.153250 restraints weight = 73700.190| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 4.31 r_work: 0.3522 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 40948 Z= 0.186 Angle : 0.638 11.090 55858 Z= 0.311 Chirality : 0.046 0.429 6347 Planarity : 0.004 0.052 7078 Dihedral : 7.389 101.945 6900 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.45 % Allowed : 15.24 % Favored : 83.31 % 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: -0.84 (0.12), residues: 4830 helix: 1.29 (0.13), residues: 1603 sheet: -1.22 (0.19), residues: 661 loop : -1.64 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1036 TYR 0.024 0.001 TYR A1064 PHE 0.033 0.002 PHE C1118 TRP 0.013 0.001 TRP B 883 HIS 0.015 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00452 (40820) covalent geometry : angle 0.61134 (55525) SS BOND : bond 0.00406 ( 48) SS BOND : angle 2.11590 ( 96) hydrogen bonds : bond 0.04221 ( 1497) hydrogen bonds : angle 4.58464 ( 4269) Misc. bond : bond 0.00482 ( 1) link_BETA1-4 : bond 0.00377 ( 31) link_BETA1-4 : angle 1.74990 ( 93) link_NAG-ASN : bond 0.00444 ( 48) link_NAG-ASN : angle 2.97834 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 171 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7861 (p90) cc_final: 0.7299 (p90) REVERT: A 153 MET cc_start: 0.5415 (ppp) cc_final: 0.2600 (mmp) REVERT: A 339 PHE cc_start: 0.8460 (m-80) cc_final: 0.8233 (m-80) REVERT: A 362 TYR cc_start: 0.8743 (m-80) cc_final: 0.8231 (m-80) REVERT: A 422 LEU cc_start: 0.9062 (tt) cc_final: 0.8809 (pp) REVERT: A 505 TYR cc_start: 0.7630 (m-10) cc_final: 0.7371 (m-10) REVERT: A 560 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.5743 (mp10) REVERT: B 52 GLN cc_start: 0.8432 (pp30) cc_final: 0.7985 (pp30) REVERT: D 152 MET cc_start: -0.1351 (ppp) cc_final: -0.2838 (pmm) REVERT: D 190 MET cc_start: 0.6199 (ptm) cc_final: 0.5684 (tmm) REVERT: D 408 MET cc_start: 0.4631 (tpp) cc_final: 0.4038 (tpp) REVERT: D 455 MET cc_start: 0.4585 (ppp) cc_final: 0.3956 (ppp) REVERT: D 462 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.5149 (mmt) REVERT: D 480 MET cc_start: 0.4063 (tmm) cc_final: 0.3755 (tmm) REVERT: E 89 GLN cc_start: 0.4186 (mp10) cc_final: 0.3821 (mm-40) REVERT: E 152 MET cc_start: -0.2873 (OUTLIER) cc_final: -0.3088 (ttp) REVERT: E 557 MET cc_start: 0.2340 (tmm) cc_final: 0.1700 (ttp) REVERT: E 579 MET cc_start: -0.3021 (mmm) cc_final: -0.3518 (ttt) REVERT: F 62 MET cc_start: 0.1549 (mmm) cc_final: 0.1208 (mmm) REVERT: F 132 VAL cc_start: -0.3443 (OUTLIER) cc_final: -0.3714 (t) REVERT: F 249 MET cc_start: 0.1516 (mpp) cc_final: -0.0373 (tpp) REVERT: F 408 MET cc_start: -0.1244 (ptt) cc_final: -0.2872 (ttp) REVERT: F 474 MET cc_start: -0.1721 (mmp) cc_final: -0.2752 (tpp) outliers start: 62 outliers final: 51 residues processed: 225 average time/residue: 0.1978 time to fit residues: 78.7916 Evaluate side-chains 222 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 174 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 377 optimal weight: 20.0000 chunk 343 optimal weight: 7.9990 chunk 448 optimal weight: 10.0000 chunk 445 optimal weight: 50.0000 chunk 467 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 383 optimal weight: 50.0000 chunk 152 optimal weight: 0.9980 chunk 295 optimal weight: 0.6980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.209751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.150202 restraints weight = 73330.349| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 5.47 r_work: 0.3417 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 40948 Z= 0.215 Angle : 0.660 11.092 55858 Z= 0.322 Chirality : 0.047 0.432 6347 Planarity : 0.004 0.052 7078 Dihedral : 7.357 109.220 6900 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.71 % Allowed : 15.12 % Favored : 83.17 % 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: 4830 helix: 1.24 (0.13), residues: 1600 sheet: -1.27 (0.19), residues: 651 loop : -1.70 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1036 TYR 0.027 0.001 TYR A1064 PHE 0.033 0.002 PHE A1118 TRP 0.017 0.001 TRP B 883 HIS 0.006 0.001 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00521 (40820) covalent geometry : angle 0.63230 (55525) SS BOND : bond 0.00434 ( 48) SS BOND : angle 2.21647 ( 96) hydrogen bonds : bond 0.04481 ( 1497) hydrogen bonds : angle 4.67208 ( 4269) Misc. bond : bond 0.00504 ( 1) link_BETA1-4 : bond 0.00378 ( 31) link_BETA1-4 : angle 1.81107 ( 93) link_NAG-ASN : bond 0.00449 ( 48) link_NAG-ASN : angle 3.06462 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 164 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7900 (p90) cc_final: 0.7326 (p90) REVERT: A 153 MET cc_start: 0.5772 (ppp) cc_final: 0.3094 (mmp) REVERT: A 339 PHE cc_start: 0.8460 (m-80) cc_final: 0.8224 (m-80) REVERT: A 362 TYR cc_start: 0.8832 (m-80) cc_final: 0.8245 (m-80) REVERT: A 422 LEU cc_start: 0.9082 (tt) cc_final: 0.8824 (pp) REVERT: A 505 TYR cc_start: 0.7737 (m-10) cc_final: 0.7484 (m-10) REVERT: A 560 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.5590 (mp10) REVERT: A 956 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8892 (mt) REVERT: B 52 GLN cc_start: 0.8499 (pp30) cc_final: 0.8020 (pp30) REVERT: C 1026 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8040 (ttm) REVERT: D 152 MET cc_start: -0.1132 (ppp) cc_final: -0.2784 (pmm) REVERT: D 190 MET cc_start: 0.5892 (ptm) cc_final: 0.5383 (tmm) REVERT: D 366 MET cc_start: 0.6703 (tmm) cc_final: 0.6155 (ppp) REVERT: D 408 MET cc_start: 0.4476 (tpp) cc_final: 0.3969 (tpp) REVERT: D 455 MET cc_start: 0.4544 (ppp) cc_final: 0.4006 (ppp) REVERT: D 462 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.5366 (mmt) REVERT: D 480 MET cc_start: 0.4143 (tmm) cc_final: 0.3857 (tmm) REVERT: D 557 MET cc_start: 0.7920 (tmm) cc_final: 0.6867 (ppp) REVERT: E 89 GLN cc_start: 0.4338 (mp10) cc_final: 0.3988 (mm-40) REVERT: E 152 MET cc_start: -0.3136 (OUTLIER) cc_final: -0.3372 (ttp) REVERT: E 557 MET cc_start: 0.1947 (tmm) cc_final: 0.1356 (ttp) REVERT: E 579 MET cc_start: -0.3473 (mmm) cc_final: -0.3954 (ttt) REVERT: F 62 MET cc_start: 0.1669 (mmm) cc_final: 0.1327 (mmm) REVERT: F 123 MET cc_start: -0.0999 (tmm) cc_final: -0.1807 (mmm) REVERT: F 132 VAL cc_start: -0.2546 (OUTLIER) cc_final: -0.2799 (t) REVERT: F 249 MET cc_start: 0.1605 (mpp) cc_final: -0.0039 (tpp) REVERT: F 408 MET cc_start: -0.1197 (ptt) cc_final: -0.2641 (ttp) REVERT: F 474 MET cc_start: -0.2169 (mmp) cc_final: -0.2678 (tpp) outliers start: 73 outliers final: 62 residues processed: 228 average time/residue: 0.1985 time to fit residues: 81.2184 Evaluate side-chains 231 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 163 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 1094 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 587 CYS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 378 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 306 optimal weight: 1.9990 chunk 420 optimal weight: 50.0000 chunk 416 optimal weight: 40.0000 chunk 280 optimal weight: 0.1980 chunk 122 optimal weight: 10.0000 chunk 272 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.211588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.149326 restraints weight = 73599.676| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 7.09 r_work: 0.3411 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40948 Z= 0.124 Angle : 0.600 11.042 55858 Z= 0.291 Chirality : 0.044 0.431 6347 Planarity : 0.004 0.057 7078 Dihedral : 7.057 114.359 6900 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.52 % Allowed : 15.29 % Favored : 83.19 % 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: -0.76 (0.12), residues: 4830 helix: 1.40 (0.13), residues: 1594 sheet: -1.21 (0.19), residues: 658 loop : -1.60 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 325 TYR 0.021 0.001 TYR B1064 PHE 0.021 0.001 PHE B 238 TRP 0.016 0.001 TRP C 104 HIS 0.005 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00289 (40820) covalent geometry : angle 0.57345 (55525) SS BOND : bond 0.00362 ( 48) SS BOND : angle 1.93288 ( 96) hydrogen bonds : bond 0.03803 ( 1497) hydrogen bonds : angle 4.51309 ( 4269) Misc. bond : bond 0.00431 ( 1) link_BETA1-4 : bond 0.00384 ( 31) link_BETA1-4 : angle 1.83533 ( 93) link_NAG-ASN : bond 0.00452 ( 48) link_NAG-ASN : angle 2.86888 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21340.65 seconds wall clock time: 362 minutes 7.31 seconds (21727.31 seconds total)