Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 10:30:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/05_2023/7v8a_31795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/05_2023/7v8a_31795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/05_2023/7v8a_31795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/05_2023/7v8a_31795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/05_2023/7v8a_31795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/05_2023/7v8a_31795.pdb" } resolution = 2.7 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= -0.001 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 25408 2.51 5 N 6527 2.21 5 O 7792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 39922 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "C" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 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: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "H" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: "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: "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: 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: "C" 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "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: 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: 20.08, per 1000 atoms: 0.50 Number of scatterers: 39922 At special positions: 0 Unit cell: (165, 174.9, 239.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 7792 8.00 N 6527 7.00 C 25408 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.04 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.04 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 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 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.02 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 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 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 341 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 341 " " NAG B2003 " - " ASN B 601 " " NAG B2004 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 341 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F2001 " - " ASN F 53 " " NAG G2001 " - " ASN G 53 " " NAG G2002 " - " ASN G 322 " " NAG H 901 " - " ASN H 322 " " NAG I 1 " - " ASN A 232 " " NAG J 1 " - " ASN A 280 " " NAG K 1 " - " ASN A 329 " " NAG L 1 " - " ASN A 614 " " NAG M 1 " - " ASN A 707 " " NAG N 1 " - " ASN A 715 " " NAG O 1 " - " ASN A 799 " " NAG P 1 " - " ASN A1072 " " NAG Q 1 " - " ASN A1096 " " NAG R 1 " - " ASN A1132 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 163 " " NAG U 1 " - " ASN B 232 " " NAG V 1 " - " ASN B 280 " " NAG W 1 " - " ASN B 329 " " NAG X 1 " - " ASN B 614 " " NAG Y 1 " - " ASN B 707 " " NAG Z 1 " - " ASN B 715 " " NAG a 1 " - " ASN B 799 " " NAG b 1 " - " ASN B1072 " " NAG c 1 " - " ASN B1096 " " NAG d 1 " - " ASN B1132 " " NAG e 1 " - " ASN C 122 " " NAG f 1 " - " ASN C 163 " " NAG g 1 " - " ASN C 232 " " NAG h 1 " - " ASN C 280 " " NAG i 1 " - " ASN C 329 " " NAG j 1 " - " ASN C 614 " " NAG k 1 " - " ASN C 707 " " NAG l 1 " - " ASN C 715 " " NAG m 1 " - " ASN C 799 " " NAG n 1 " - " ASN C1072 " " NAG o 1 " - " ASN C1096 " " NAG p 1 " - " ASN C1132 " " NAG q 1 " - " ASN F 322 " Time building additional restraints: 20.18 Conformation dependent library (CDL) restraints added in 6.2 seconds 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9156 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 52 sheets defined 39.1% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.250A pdb=" N ASN A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.191A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.954A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 781 removed outlier: 3.576A pdb=" N ALA A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.635A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 916 removed outlier: 4.078A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 974 through 981 removed outlier: 3.667A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.262A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 3.793A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.555A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 4.048A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.961A pdb=" N ASN B 386 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.395A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.025A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 781 Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.530A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.656A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 910 through 916 removed outlier: 4.022A pdb=" N LEU B 914 " --> pdb=" O THR B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 removed outlier: 3.756A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.768A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 362 through 368 removed outlier: 4.146A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.456A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 742 Processing helix chain 'C' and resid 744 through 753 removed outlier: 4.180A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 781 Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.588A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.993A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.744A pdb=" N GLN C 933 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 974 through 981 removed outlier: 4.077A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 3.860A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.970A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 79 removed outlier: 3.514A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.710A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.649A pdb=" N SER F 106 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 158 through 174 Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.534A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 265 through 268 removed outlier: 4.092A 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 293 through 301 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.792A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.400A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.989A 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 473 through 485 removed outlier: 3.726A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG F 482 " --> pdb=" O TRP F 478 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.638A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 512 through 532 removed outlier: 4.069A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.598A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 597 removed outlier: 3.875A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 3.526A pdb=" N GLN G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 79 removed outlier: 4.152A pdb=" N ASN G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN G 76 " --> pdb=" O PHE G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.565A pdb=" N VAL G 107 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 129 removed outlier: 3.817A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.798A pdb=" N LEU G 162 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 194 Processing helix chain 'G' and resid 198 through 205 Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 218 through 229 removed outlier: 3.818A pdb=" N LEU G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR G 229 " --> pdb=" O ASP G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 250 Processing helix chain 'G' and resid 293 through 300 Processing helix chain 'G' and resid 303 through 319 Processing helix chain 'G' and resid 326 through 331 Processing helix chain 'G' and resid 365 through 385 Processing helix chain 'G' and resid 389 through 393 removed outlier: 3.909A pdb=" N ARG G 393 " --> pdb=" O PHE G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 412 removed outlier: 4.154A pdb=" N HIS G 401 " --> pdb=" O ASN G 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU G 402 " --> pdb=" O GLU G 398 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER G 409 " --> pdb=" O GLY G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 431 through 446 removed outlier: 3.830A pdb=" N THR G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 466 Processing helix chain 'G' and resid 473 through 485 removed outlier: 3.548A pdb=" N ARG G 482 " --> pdb=" O TRP G 478 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU G 483 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 508 removed outlier: 4.219A pdb=" N SER G 507 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN G 508 " --> pdb=" O PHE G 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 503 through 508' Processing helix chain 'G' and resid 512 through 532 removed outlier: 4.078A pdb=" N TYR G 516 " --> pdb=" O PHE G 512 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR G 519 " --> pdb=" O TYR G 515 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU G 520 " --> pdb=" O TYR G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 559 removed outlier: 4.038A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 564 removed outlier: 4.207A pdb=" N GLU G 564 " --> pdb=" O GLY G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 570 Processing helix chain 'G' and resid 581 through 588 removed outlier: 3.599A pdb=" N PHE G 588 " --> pdb=" O LEU G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 599 removed outlier: 3.595A pdb=" N ASP G 597 " --> pdb=" O THR G 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 53 removed outlier: 3.519A pdb=" N GLN H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 80 removed outlier: 3.742A pdb=" N MET H 62 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN H 76 " --> pdb=" O PHE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 103 through 108 removed outlier: 4.085A pdb=" N SER H 106 " --> pdb=" O ASN H 103 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL H 107 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU H 108 " --> pdb=" O SER H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 103 through 108' Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'H' and resid 159 through 172 removed outlier: 3.560A pdb=" N VAL H 172 " --> pdb=" O TRP H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 194 removed outlier: 4.353A pdb=" N LEU H 179 " --> pdb=" O GLN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 removed outlier: 3.607A pdb=" N TYR H 202 " --> pdb=" O ASP H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 218 through 229 removed outlier: 3.638A pdb=" N ILE H 223 " --> pdb=" O ARG H 219 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing helix chain 'H' and resid 233 through 252 removed outlier: 3.547A pdb=" N MET H 249 " --> pdb=" O ARG H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 280 removed outlier: 4.193A pdb=" N SER H 280 " --> pdb=" O THR H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 301 Processing helix chain 'H' and resid 303 through 319 Processing helix chain 'H' and resid 326 through 331 Processing helix chain 'H' and resid 365 through 385 Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.773A pdb=" N ARG H 393 " --> pdb=" O PHE H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 412 removed outlier: 4.109A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 421 Processing helix chain 'H' and resid 431 through 447 removed outlier: 3.789A pdb=" N THR H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 466 Processing helix chain 'H' and resid 473 through 484 removed outlier: 3.509A pdb=" N TRP H 477 " --> pdb=" O TRP H 473 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG H 482 " --> pdb=" O TRP H 478 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU H 483 " --> pdb=" O GLU H 479 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 508 removed outlier: 3.911A pdb=" N SER H 507 " --> pdb=" O LEU H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 512 through 532 removed outlier: 4.304A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 559 removed outlier: 3.586A pdb=" N GLY H 551 " --> pdb=" O SER H 547 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 560 through 564 removed outlier: 3.978A pdb=" N SER H 563 " --> pdb=" O LEU H 560 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU H 564 " --> pdb=" O GLY H 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 560 through 564' Processing helix chain 'H' and resid 565 through 570 Processing helix chain 'H' and resid 581 through 588 Processing helix chain 'H' and resid 588 through 599 removed outlier: 3.980A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN H 599 " --> pdb=" O LEU H 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.958A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.951A pdb=" N PHE A 43 " --> pdb=" O ARG C 565 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.056A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.196A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.554A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.865A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.808A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.359A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 701 removed outlier: 6.716A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.722A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 726 removed outlier: 6.038A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.531A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 removed outlier: 3.503A pdb=" N ASN C 701 " --> pdb=" O ILE A 786 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.045A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.167A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.566A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 323 through 324 removed outlier: 5.740A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY B 564 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.711A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 652 through 658 removed outlier: 6.007A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N VAL B 654 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 699 through 700 removed outlier: 6.927A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 709 through 711 removed outlier: 3.684A pdb=" N THR B1074 " --> pdb=" O SER B1095 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B1076 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE B1093 " --> pdb=" O ALA B1076 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 715 through 726 removed outlier: 3.541A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.496A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.879A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.063A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.191A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.381A pdb=" N VAL C 126 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 10.081A pdb=" N GLU C 167 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N ILE C 128 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR C 165 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL C 130 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLU C 132 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA C 161 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN C 134 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.047A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE2, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.632A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.032A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 711 removed outlier: 3.602A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA C1076 " --> pdb=" O PHE C1093 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1093 " --> pdb=" O ALA C1076 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.531A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.413A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AF1, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.745A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF4, first strand: chain 'G' and resid 132 through 134 removed outlier: 4.097A pdb=" N ASN G 134 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU G 140 " --> pdb=" O ASN G 134 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 347 through 350 Processing sheet with id=AF6, first strand: chain 'H' and resid 132 through 134 removed outlier: 4.303A pdb=" N ASN H 134 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU H 140 " --> pdb=" O ASN H 134 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 347 through 350 1709 hydrogen bonds defined for protein. 4830 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: 18.52 Time building geometry restraints manager: 21.73 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: 12682 1.34 - 1.46: 9956 1.46 - 1.58: 17956 1.58 - 1.70: 0 1.70 - 1.82: 282 Bond restraints: 40876 Sorted by residual: bond pdb=" C1 NAG n 1 " pdb=" O5 NAG n 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C1 NAG q 1 " pdb=" O5 NAG q 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.04e+00 ... (remaining 40871 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.03: 745 105.03 - 112.30: 20793 112.30 - 119.56: 13143 119.56 - 126.83: 20334 126.83 - 134.09: 574 Bond angle restraints: 55589 Sorted by residual: angle pdb=" N VAL H 506 " pdb=" CA VAL H 506 " pdb=" C VAL H 506 " ideal model delta sigma weight residual 113.71 107.87 5.84 9.50e-01 1.11e+00 3.78e+01 angle pdb=" N VAL H 172 " pdb=" CA VAL H 172 " pdb=" C VAL H 172 " ideal model delta sigma weight residual 113.53 108.42 5.11 9.80e-01 1.04e+00 2.71e+01 angle pdb=" N VAL B 157 " pdb=" CA VAL B 157 " pdb=" C VAL B 157 " ideal model delta sigma weight residual 113.42 108.42 5.00 1.17e+00 7.31e-01 1.82e+01 angle pdb=" N ILE A 803 " pdb=" CA ILE A 803 " pdb=" C ILE A 803 " ideal model delta sigma weight residual 113.53 110.00 3.53 9.80e-01 1.04e+00 1.30e+01 angle pdb=" CB ARG G 192 " pdb=" CG ARG G 192 " pdb=" CD ARG G 192 " ideal model delta sigma weight residual 111.30 118.15 -6.85 2.30e+00 1.89e-01 8.87e+00 ... (remaining 55584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 21145 17.90 - 35.79: 1940 35.79 - 53.69: 358 53.69 - 71.59: 66 71.59 - 89.48: 50 Dihedral angle restraints: 23559 sinusoidal: 9342 harmonic: 14217 Sorted by residual: dihedral pdb=" CB CYS C 289 " pdb=" SG CYS C 289 " pdb=" SG CYS C 299 " pdb=" CB CYS C 299 " ideal model delta sinusoidal sigma weight residual -86.00 -175.48 89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual 93.00 178.89 -85.89 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS B1080 " pdb=" SG CYS B1080 " pdb=" SG CYS B1124 " pdb=" CB CYS B1124 " ideal model delta sinusoidal sigma weight residual -86.00 -0.23 -85.77 1 1.00e+01 1.00e-02 8.89e+01 ... (remaining 23556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5594 0.069 - 0.138: 767 0.138 - 0.207: 31 0.207 - 0.277: 3 0.277 - 0.346: 1 Chirality restraints: 6396 Sorted by residual: chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN C 232 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C4 NAG n 1 " pdb=" C3 NAG n 1 " pdb=" C5 NAG n 1 " pdb=" O4 NAG n 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 707 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 6393 not shown) Planarity restraints: 7132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 232 " 0.024 2.00e-02 2.50e+03 2.18e-02 5.91e+00 pdb=" CG ASN C 232 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 232 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 232 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 232 " -0.019 2.00e-02 2.50e+03 1.81e-02 4.10e+00 pdb=" CG ASN A 232 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 232 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 232 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 884 " 0.013 2.00e-02 2.50e+03 1.15e-02 3.30e+00 pdb=" CG TRP C 884 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 884 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 884 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 884 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 884 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 884 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 884 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 884 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 884 " 0.002 2.00e-02 2.50e+03 ... (remaining 7129 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 856 2.68 - 3.23: 39140 3.23 - 3.79: 63104 3.79 - 4.34: 81585 4.34 - 4.90: 135190 Nonbonded interactions: 319875 Sorted by model distance: nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.123 2.440 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.142 2.440 nonbonded pdb=" OG1 THR C 124 " pdb=" OD1 ASN C 125 " model vdw 2.157 2.440 nonbonded pdb=" OD1 ASP H 382 " pdb=" OH TYR H 385 " model vdw 2.163 2.440 nonbonded pdb=" OD1 ASP B 566 " pdb=" OG1 THR B 570 " model vdw 2.180 2.440 ... (remaining 319870 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 19 through 614 or resid 2001)) selection = chain 'H' } 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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.490 Check model and map are aligned: 0.530 Set scattering table: 0.300 Process input model: 106.890 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.820 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:31.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 0.057 40876 Z= 0.280 Angle : 0.579 9.410 55589 Z= 0.287 Chirality : 0.045 0.346 6396 Planarity : 0.004 0.065 7079 Dihedral : 14.333 89.477 14259 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.92 % Favored : 95.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 4815 helix: 1.64 (0.13), residues: 1657 sheet: 0.30 (0.19), residues: 725 loop : -1.36 (0.12), residues: 2433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 397 average time/residue: 1.3265 time to fit residues: 646.1629 Evaluate side-chains 187 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 3.386 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.2806 time to fit residues: 6.2966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 40.0000 chunk 366 optimal weight: 30.0000 chunk 203 optimal weight: 0.1980 chunk 125 optimal weight: 0.9990 chunk 246 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 378 optimal weight: 10.0000 chunk 146 optimal weight: 40.0000 chunk 230 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 50.0000 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: