Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 10:33:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/05_2023/7v7z_31784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/05_2023/7v7z_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/05_2023/7v7z_31784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/05_2023/7v7z_31784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/05_2023/7v7z_31784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7z_31784/05_2023/7v7z_31784.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "D ASP 427": "OD1" <-> "OD2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/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 chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 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 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 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 chiralities: 1 Time building chain proxies: 17.01, per 1000 atoms: 0.43 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 - 3.50 Amino acid : False - 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: 15.28 Conformation dependent library (CDL) restraints added in 5.3 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: 1.89 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: 13.27 Time building geometry restraints manager: 16.68 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: 94.19 - 102.16: 97 102.16 - 110.13: 7280 110.13 - 118.10: 23538 118.10 - 126.07: 23967 126.07 - 134.04: 643 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 - 17.96: 21161 17.96 - 35.92: 1955 35.92 - 53.88: 347 53.88 - 71.84: 59 71.84 - 89.80: 43 Dihedral angle restraints: 23565 sinusoidal: 9312 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 23562 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 2.440 nonbonded pdb=" OG1 THR A 713 " pdb=" O GLN A1068 " model vdw 2.153 2.440 nonbonded pdb=" OD2 ASP C 575 " pdb=" OG1 THR C 578 " model vdw 2.166 2.440 nonbonded pdb=" OD2 ASP A 575 " pdb=" OG1 THR A 578 " model vdw 2.172 2.440 nonbonded pdb=" OG1 THR A 497 " pdb=" OH TYR D 41 " model vdw 2.173 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 1143 or resid 2001 through 2004)) selection = (chain 'C' and (resid 14 through 1143 or resid 2001 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.070 Extract box with map and model: 40.230 Check model and map are aligned: 0.000 Set scattering table: 0.540 Process input model: 85.670 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.670 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: