Starting phenix.real_space_refine on Sat Nov 18 02:15:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/11_2023/7wo4_32638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/11_2023/7wo4_32638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/11_2023/7wo4_32638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/11_2023/7wo4_32638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/11_2023/7wo4_32638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/11_2023/7wo4_32638.pdb" } resolution = 4.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 300 5.16 5 C 45084 2.51 5 N 11820 2.21 5 O 14004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 98": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F ARG 216": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "I ARG 195": "NH1" <-> "NH2" Residue "J ARG 346": "NH1" <-> "NH2" Residue "J ARG 408": "NH1" <-> "NH2" Residue "J ARG 454": "NH1" <-> "NH2" Residue "J ARG 457": "NH1" <-> "NH2" Residue "J ARG 466": "NH1" <-> "NH2" Residue "K ARG 346": "NH1" <-> "NH2" Residue "K ARG 408": "NH1" <-> "NH2" Residue "K ARG 454": "NH1" <-> "NH2" Residue "K ARG 457": "NH1" <-> "NH2" Residue "K ARG 466": "NH1" <-> "NH2" Residue "L PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 319": "NH1" <-> "NH2" Residue "L ARG 346": "NH1" <-> "NH2" Residue "L ARG 408": "NH1" <-> "NH2" Residue "L ARG 454": "NH1" <-> "NH2" Residue "L ARG 457": "NH1" <-> "NH2" Residue "L ARG 466": "NH1" <-> "NH2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M ARG 106": "NH1" <-> "NH2" Residue "M ARG 216": "NH1" <-> "NH2" Residue "N TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 195": "NH1" <-> "NH2" Residue "O ARG 98": "NH1" <-> "NH2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 216": "NH1" <-> "NH2" Residue "P ARG 195": "NH1" <-> "NH2" Residue "Q ARG 98": "NH1" <-> "NH2" Residue "Q ARG 106": "NH1" <-> "NH2" Residue "Q ARG 216": "NH1" <-> "NH2" Residue "R ARG 195": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 71208 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "F" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "G" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "H" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "I" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "J" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "K" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "L" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "N" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "O" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "P" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "Q" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "R" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "J" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "K" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "L" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 28.27, per 1000 atoms: 0.40 Number of scatterers: 71208 At special positions: 0 Unit cell: (373.43, 209.72, 173.34, 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 300 16.00 O 14004 8.00 N 11820 7.00 C 45084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=104, 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 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 199 " distance=2.03 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 136 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 166 " distance=2.03 Simple disulfide: pdb=" SG CYS J 291 " - pdb=" SG CYS J 301 " distance=2.03 Simple disulfide: pdb=" SG CYS J 336 " - pdb=" SG CYS J 361 " distance=2.03 Simple disulfide: pdb=" SG CYS J 379 " - pdb=" SG CYS J 432 " distance=2.03 Simple disulfide: pdb=" SG CYS J 391 " - pdb=" SG CYS J 525 " distance=2.03 Simple disulfide: pdb=" SG CYS J 480 " - pdb=" SG CYS J 488 " distance=2.03 Simple disulfide: pdb=" SG CYS J 538 " - pdb=" SG CYS J 590 " distance=2.03 Simple disulfide: pdb=" SG CYS J 662 " - pdb=" SG CYS J 671 " distance=2.03 Simple disulfide: pdb=" SG CYS J 743 " - pdb=" SG CYS J 749 " distance=2.03 Simple disulfide: pdb=" SG CYS J1032 " - pdb=" SG CYS J1043 " distance=2.03 Simple disulfide: pdb=" SG CYS J1082 " - pdb=" SG CYS J1126 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.02 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.03 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.03 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.03 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.03 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.03 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.03 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.03 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.03 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 15 " - pdb=" SG CYS L 136 " distance=2.03 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 166 " distance=2.03 Simple disulfide: pdb=" SG CYS L 291 " - pdb=" SG CYS L 301 " distance=2.05 Simple disulfide: pdb=" SG CYS L 336 " - pdb=" SG CYS L 361 " distance=2.03 Simple disulfide: pdb=" SG CYS L 379 " - pdb=" SG CYS L 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 391 " - pdb=" SG CYS L 525 " distance=2.03 Simple disulfide: pdb=" SG CYS L 480 " - pdb=" SG CYS L 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 538 " - pdb=" SG CYS L 590 " distance=2.03 Simple disulfide: pdb=" SG CYS L 617 " - pdb=" SG CYS L 649 " distance=2.04 Simple disulfide: pdb=" SG CYS L 662 " - pdb=" SG CYS L 671 " distance=2.03 Simple disulfide: pdb=" SG CYS L 738 " - pdb=" SG CYS L 760 " distance=2.03 Simple disulfide: pdb=" SG CYS L 743 " - pdb=" SG CYS L 749 " distance=2.03 Simple disulfide: pdb=" SG CYS L1032 " - pdb=" SG CYS L1043 " distance=2.03 Simple disulfide: pdb=" SG CYS L1082 " - pdb=" SG CYS L1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 146 " - pdb=" SG CYS M 202 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 91 " distance=2.03 Simple disulfide: pdb=" SG CYS N 140 " - pdb=" SG CYS N 199 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 146 " - pdb=" SG CYS O 202 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 91 " distance=2.03 Simple disulfide: pdb=" SG CYS P 140 " - pdb=" SG CYS P 199 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 146 " - pdb=" SG CYS Q 202 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 91 " distance=2.03 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 199 " 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 NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 801 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A 17 " " NAG A1314 " - " ASN A 122 " " NAG A1315 " - " ASN A 149 " " NAG B1301 " - " ASN B1134 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 282 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 17 " " NAG B1313 " - " ASN B 149 " " NAG B1314 " - " ASN B 122 " " NAG B1315 " - " ASN B1074 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C 17 " " NAG C1312 " - " ASN C 149 " " NAG C1313 " - " ASN C 61 " " NAG C1314 " - " ASN C 122 " " NAG C1315 " - " ASN C 165 " " NAG J1301 " - " ASN J 165 " " NAG J1302 " - " ASN J 331 " " NAG J1303 " - " ASN J 616 " " NAG J1304 " - " ASN J 709 " " NAG J1305 " - " ASN J 717 " " NAG J1306 " - " ASN J1074 " " NAG J1307 " - " ASN J1134 " " NAG J1308 " - " ASN J 282 " " NAG J1309 " - " ASN J 61 " " NAG J1310 " - " ASN J 801 " " NAG J1311 " - " ASN J1098 " " NAG J1312 " - " ASN J 17 " " NAG J1313 " - " ASN J 122 " " NAG J1314 " - " ASN J 149 " " NAG J1315 " - " ASN J 343 " " NAG K1301 " - " ASN K1134 " " NAG K1302 " - " ASN K1098 " " NAG K1303 " - " ASN K 801 " " NAG K1304 " - " ASN K 717 " " NAG K1305 " - " ASN K 709 " " NAG K1306 " - " ASN K 616 " " NAG K1307 " - " ASN K 343 " " NAG K1308 " - " ASN K 331 " " NAG K1309 " - " ASN K 282 " " NAG K1310 " - " ASN K 165 " " NAG K1311 " - " ASN K 61 " " NAG K1312 " - " ASN K 17 " " NAG K1313 " - " ASN K 149 " " NAG K1314 " - " ASN K 122 " " NAG K1315 " - " ASN K1074 " " NAG L1301 " - " ASN L 282 " " NAG L1302 " - " ASN L 331 " " NAG L1303 " - " ASN L 343 " " NAG L1304 " - " ASN L 616 " " NAG L1305 " - " ASN L 709 " " NAG L1306 " - " ASN L 717 " " NAG L1307 " - " ASN L1074 " " NAG L1308 " - " ASN L1134 " " NAG L1309 " - " ASN L 801 " " NAG L1310 " - " ASN L1098 " " NAG L1311 " - " ASN L 17 " " NAG L1312 " - " ASN L 149 " " NAG L1313 " - " ASN L 61 " " NAG L1314 " - " ASN L 122 " " NAG L1315 " - " ASN L 165 " Time building additional restraints: 20.72 Conformation dependent library (CDL) restraints added in 9.9 seconds 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16920 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 166 sheets defined 16.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'A' and resid 253 through 257 removed outlier: 4.258A pdb=" N GLY A 257 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.935A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.777A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.589A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 782 removed outlier: 3.641A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.462A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 966 removed outlier: 4.099A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.712A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1034 removed outlier: 3.539A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A1034 " --> pdb=" O SER A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.913A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.763A pdb=" N ASN B 74 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.526A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.825A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.504A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.776A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.705A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.475A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.787A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.555A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.513A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.660A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 342 removed outlier: 3.544A pdb=" N VAL C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 342 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 342' Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.210A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.101A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 421' Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.657A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.516A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.534A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.013A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 190 through 194 removed outlier: 3.578A pdb=" N HIS E 194 " --> pdb=" O TRP E 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.557A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.546A pdb=" N ASP G 85 " --> pdb=" O LYS G 82 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 82 through 86' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.896A pdb=" N SER I 31 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 82 through 86 removed outlier: 3.616A pdb=" N GLU I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 257 removed outlier: 4.250A pdb=" N GLY J 257 " --> pdb=" O SER J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 304 Processing helix chain 'J' and resid 337 through 343 removed outlier: 3.928A pdb=" N VAL J 341 " --> pdb=" O PRO J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 368 removed outlier: 3.730A pdb=" N VAL J 367 " --> pdb=" O ASP J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 403 through 407 removed outlier: 3.593A pdb=" N VAL J 407 " --> pdb=" O GLY J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 506 Processing helix chain 'J' and resid 737 through 743 Processing helix chain 'J' and resid 746 through 754 Processing helix chain 'J' and resid 755 through 757 No H-bonds generated for 'chain 'J' and resid 755 through 757' Processing helix chain 'J' and resid 760 through 782 removed outlier: 3.640A pdb=" N ASN J 764 " --> pdb=" O CYS J 760 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR J 778 " --> pdb=" O GLN J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 816 through 826 Processing helix chain 'J' and resid 866 through 884 Processing helix chain 'J' and resid 897 through 907 Processing helix chain 'J' and resid 912 through 941 removed outlier: 4.450A pdb=" N LEU J 916 " --> pdb=" O THR J 912 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS J 921 " --> pdb=" O TYR J 917 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU J 922 " --> pdb=" O GLU J 918 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR J 941 " --> pdb=" O SER J 937 " (cutoff:3.500A) Processing helix chain 'J' and resid 946 through 966 removed outlier: 4.072A pdb=" N VAL J 951 " --> pdb=" O LYS J 947 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL J 952 " --> pdb=" O LEU J 948 " (cutoff:3.500A) Processing helix chain 'J' and resid 976 through 983 removed outlier: 3.720A pdb=" N ILE J 980 " --> pdb=" O VAL J 976 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG J 983 " --> pdb=" O ASP J 979 " (cutoff:3.500A) Processing helix chain 'J' and resid 985 through 1034 removed outlier: 3.530A pdb=" N GLU J1017 " --> pdb=" O ILE J1013 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL J1033 " --> pdb=" O MET J1029 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU J1034 " --> pdb=" O SER J1030 " (cutoff:3.500A) Processing helix chain 'J' and resid 1140 through 1146 removed outlier: 3.908A pdb=" N GLU J1144 " --> pdb=" O PRO J1140 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 74 removed outlier: 3.839A pdb=" N ASN K 74 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 303 Processing helix chain 'K' and resid 338 through 343 removed outlier: 3.544A pdb=" N PHE K 342 " --> pdb=" O PHE K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 368 removed outlier: 3.804A pdb=" N VAL K 367 " --> pdb=" O ASP K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 390 removed outlier: 3.502A pdb=" N LEU K 387 " --> pdb=" O PRO K 384 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN K 388 " --> pdb=" O THR K 385 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU K 390 " --> pdb=" O LEU K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 407 removed outlier: 3.715A pdb=" N GLU K 406 " --> pdb=" O ARG K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 737 through 743 Processing helix chain 'K' and resid 747 through 754 Processing helix chain 'K' and resid 759 through 782 removed outlier: 3.684A pdb=" N THR K 778 " --> pdb=" O GLN K 774 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 826 Processing helix chain 'K' and resid 866 through 884 Processing helix chain 'K' and resid 897 through 910 Processing helix chain 'K' and resid 912 through 941 removed outlier: 4.506A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS K 921 " --> pdb=" O TYR K 917 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU K 922 " --> pdb=" O GLU K 918 " (cutoff:3.500A) Processing helix chain 'K' and resid 942 through 944 No H-bonds generated for 'chain 'K' and resid 942 through 944' Processing helix chain 'K' and resid 945 through 966 removed outlier: 3.765A pdb=" N VAL K 952 " --> pdb=" O LEU K 948 " (cutoff:3.500A) Processing helix chain 'K' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE K 980 " --> pdb=" O VAL K 976 " (cutoff:3.500A) Processing helix chain 'K' and resid 985 through 1033 removed outlier: 3.509A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) Processing helix chain 'K' and resid 1141 through 1146 removed outlier: 3.647A pdb=" N LEU K1145 " --> pdb=" O LEU K1141 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 304 Processing helix chain 'L' and resid 338 through 343 removed outlier: 4.099A pdb=" N PHE L 342 " --> pdb=" O PHE L 338 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN L 343 " --> pdb=" O GLY L 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 338 through 343' Processing helix chain 'L' and resid 383 through 390 removed outlier: 5.084A pdb=" N ASN L 388 " --> pdb=" O THR L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 421 removed outlier: 4.103A pdb=" N ASP L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR L 421 " --> pdb=" O LYS L 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 416 through 421' Processing helix chain 'L' and resid 738 through 743 Processing helix chain 'L' and resid 747 through 754 Processing helix chain 'L' and resid 758 through 782 removed outlier: 3.681A pdb=" N THR L 778 " --> pdb=" O GLN L 774 " (cutoff:3.500A) Processing helix chain 'L' and resid 816 through 826 removed outlier: 3.520A pdb=" N VAL L 826 " --> pdb=" O LEU L 822 " (cutoff:3.500A) Processing helix chain 'L' and resid 866 through 884 Processing helix chain 'L' and resid 897 through 908 Processing helix chain 'L' and resid 915 through 941 removed outlier: 7.300A pdb=" N LYS L 921 " --> pdb=" O TYR L 917 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU L 922 " --> pdb=" O GLU L 918 " (cutoff:3.500A) Processing helix chain 'L' and resid 945 through 965 removed outlier: 3.509A pdb=" N GLN L 949 " --> pdb=" O LEU L 945 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL L 952 " --> pdb=" O LEU L 948 " (cutoff:3.500A) Processing helix chain 'L' and resid 976 through 983 Processing helix chain 'L' and resid 985 through 1033 Processing helix chain 'L' and resid 1140 through 1145 removed outlier: 4.020A pdb=" N GLU L1144 " --> pdb=" O PRO L1140 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 164 No H-bonds generated for 'chain 'M' and resid 162 through 164' Processing helix chain 'N' and resid 82 through 86 Processing helix chain 'N' and resid 190 through 194 removed outlier: 3.585A pdb=" N HIS N 194 " --> pdb=" O TRP N 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.561A pdb=" N THR O 91 " --> pdb=" O ALA O 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 86 removed outlier: 3.540A pdb=" N ASP P 85 " --> pdb=" O LYS P 82 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU P 86 " --> pdb=" O THR P 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 82 through 86' Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.848A pdb=" N SER R 31 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN R 32 " --> pdb=" O ILE R 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 28 through 32' Processing helix chain 'R' and resid 82 through 86 removed outlier: 3.641A pdb=" N GLU R 86 " --> pdb=" O THR R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 194 removed outlier: 3.569A pdb=" N SER R 193 " --> pdb=" O GLN R 190 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS R 194 " --> pdb=" O TRP R 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 190 through 194' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.829A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.597A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.818A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 158 removed outlier: 6.789A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.849A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.527A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.804A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.804A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.217A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.674A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.818A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.818A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.190A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.942A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.513A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.546A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.602A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 153 through 157 removed outlier: 6.332A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.564A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.790A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.536A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 394 through 396 removed outlier: 4.052A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.373A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.489A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.034A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.555A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.732A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.732A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.715A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.715A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 78 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.944A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 103 through 104 removed outlier: 3.677A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.516A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 327 removed outlier: 7.017A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.286A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 394 through 400 removed outlier: 3.604A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.853A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 712 through 713 removed outlier: 4.214A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AF6, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.531A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.174A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.791A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.875A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.304A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.996A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 97 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR D 108 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 126 through 129 removed outlier: 3.585A pdb=" N LYS D 149 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 142 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 126 through 129 removed outlier: 3.585A pdb=" N LYS D 149 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 142 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.279A pdb=" N CYS D 202 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS D 215 " --> pdb=" O CYS D 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.811A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR E 90 " --> pdb=" O TYR E 37 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER E 93 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL E 102 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.811A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR E 90 " --> pdb=" O TYR E 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 63 through 68 removed outlier: 3.539A pdb=" N SER E 66 " --> pdb=" O SER E 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER E 75 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 120 through 121 removed outlier: 5.932A pdb=" N TYR E 178 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER E 181 " --> pdb=" O THR E 168 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.455A pdb=" N LYS E 155 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER E 198 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 3 through 7 removed outlier: 4.088A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU F 18 " --> pdb=" O MET F 83 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET F 83 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP F 73 " --> pdb=" O SER F 78 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.564A pdb=" N TYR F 59 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 97 " --> pdb=" O SER F 35 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.564A pdb=" N TYR F 59 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA F 92 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.772A pdb=" N SER F 186 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER F 185 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE F 172 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL F 187 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 201 through 202 removed outlier: 3.627A pdb=" N CYS F 202 " --> pdb=" O LYS F 215 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS F 215 " --> pdb=" O CYS F 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AH8, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.131A pdb=" N VAL G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR G 107 " --> pdb=" O TYR G 89 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.131A pdb=" N VAL G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR G 107 " --> pdb=" O TYR G 89 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 93 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL G 102 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.800A pdb=" N ILE G 20 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 76 " --> pdb=" O ILE G 20 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 152 through 155 Processing sheet with id=AI3, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.061A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.722A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG H 98 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 126 through 127 removed outlier: 4.271A pdb=" N SER H 126 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS H 149 " --> pdb=" O SER H 126 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 143 through 144 Processing sheet with id=AI7, first strand: chain 'H' and resid 159 through 160 removed outlier: 3.840A pdb=" N SER H 159 " --> pdb=" O ASN H 203 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN H 203 " --> pdb=" O SER H 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.156A pdb=" N VAL I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AJ1, first strand: chain 'I' and resid 45 through 50 removed outlier: 7.158A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP I 88 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL I 102 " --> pdb=" O SER I 93 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP I 95 " --> pdb=" O ASN I 100 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN I 100 " --> pdb=" O ASP I 95 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 152 through 155 removed outlier: 3.928A pdb=" N TYR I 197 " --> pdb=" O VAL I 212 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'I' and resid 167 through 168 removed outlier: 3.618A pdb=" N SER I 181 " --> pdb=" O THR I 168 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 28 through 29 removed outlier: 3.853A pdb=" N VAL J 267 " --> pdb=" O THR J 63 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR J 265 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA J 264 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU J 191 " --> pdb=" O LYS J 206 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS J 202 " --> pdb=" O LYS J 195 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU J 229 " --> pdb=" O PHE J 201 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER J 205 " --> pdb=" O PRO J 225 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'J' and resid 48 through 55 removed outlier: 7.283A pdb=" N THR J 274 " --> pdb=" O ASP J 290 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP J 290 " --> pdb=" O THR J 274 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU J 276 " --> pdb=" O ALA J 288 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA J 288 " --> pdb=" O LEU J 276 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS J 278 " --> pdb=" O THR J 286 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'J' and resid 83 through 85 Processing sheet with id=AJ7, first strand: chain 'J' and resid 117 through 118 removed outlier: 3.560A pdb=" N PHE J 168 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU J 132 " --> pdb=" O CYS J 166 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS J 166 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'J' and resid 154 through 158 removed outlier: 7.022A pdb=" N GLU J 154 " --> pdb=" O TYR J 144 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR J 144 " --> pdb=" O GLU J 154 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU J 156 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY J 142 " --> pdb=" O GLU J 156 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG J 158 " --> pdb=" O PHE J 140 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG J 246 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'J' and resid 311 through 319 removed outlier: 6.832A pdb=" N VAL J 595 " --> pdb=" O THR J 315 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN J 317 " --> pdb=" O GLY J 593 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY J 593 " --> pdb=" O ASN J 317 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY J 594 " --> pdb=" O GLN J 613 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA J 609 " --> pdb=" O ILE J 598 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY J 648 " --> pdb=" O THR J 645 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'J' and resid 325 through 327 removed outlier: 6.482A pdb=" N ILE J 326 " --> pdb=" O ASN J 542 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP J 574 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA J 575 " --> pdb=" O GLY J 566 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'J' and resid 376 through 379 removed outlier: 3.822A pdb=" N THR J 376 " --> pdb=" O ALA J 435 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA J 435 " --> pdb=" O THR J 376 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS J 378 " --> pdb=" O VAL J 433 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL J 433 " --> pdb=" O LYS J 378 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS J 432 " --> pdb=" O LEU J 513 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'J' and resid 376 through 379 removed outlier: 3.822A pdb=" N THR J 376 " --> pdb=" O ALA J 435 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA J 435 " --> pdb=" O THR J 376 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS J 378 " --> pdb=" O VAL J 433 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL J 433 " --> pdb=" O LYS J 378 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS J 432 " --> pdb=" O LEU J 513 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE J 400 " --> pdb=" O VAL J 510 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'J' and resid 452 through 454 Processing sheet with id=AK5, first strand: chain 'J' and resid 473 through 474 removed outlier: 3.508A pdb=" N TYR J 489 " --> pdb=" O TYR J 473 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'J' and resid 654 through 655 removed outlier: 6.171A pdb=" N GLU J 654 " --> pdb=" O ALA J 694 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR J 696 " --> pdb=" O GLU J 654 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN J 675 " --> pdb=" O SER J 691 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER J 673 " --> pdb=" O ILE J 693 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE J 670 " --> pdb=" O ILE J 666 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'J' and resid 712 through 713 removed outlier: 3.668A pdb=" N ILE J 712 " --> pdb=" O PHE J1075 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR J1076 " --> pdb=" O SER J1097 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'J' and resid 718 through 722 removed outlier: 3.856A pdb=" N SER J 721 " --> pdb=" O THR J1066 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'J' and resid 718 through 722 removed outlier: 3.856A pdb=" N SER J 721 " --> pdb=" O THR J1066 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA J1056 " --> pdb=" O GLY J1059 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR J1067 " --> pdb=" O HIS J1048 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N HIS J1048 " --> pdb=" O TYR J1067 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'J' and resid 733 through 736 removed outlier: 4.147A pdb=" N LYS J 733 " --> pdb=" O LEU J 861 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'J' and resid 788 through 790 removed outlier: 5.994A pdb=" N ILE J 788 " --> pdb=" O ASN L 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'J' and resid 1120 through 1122 Processing sheet with id=AL4, first strand: chain 'K' and resid 28 through 30 removed outlier: 7.458A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL K 90 " --> pdb=" O PHE K 194 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU K 96 " --> pdb=" O ASN K 188 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN K 188 " --> pdb=" O GLU K 96 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL K 193 " --> pdb=" O TYR K 204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR K 204 " --> pdb=" O VAL K 193 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER K 205 " --> pdb=" O GLU K 224 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU K 224 " --> pdb=" O SER K 205 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'K' and resid 50 through 55 removed outlier: 4.102A pdb=" N ASP K 53 " --> pdb=" O ARG K 273 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE K 55 " --> pdb=" O GLN K 271 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN K 271 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP K 287 " --> pdb=" O LYS K 278 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'K' and resid 84 through 85 removed outlier: 3.702A pdb=" N ILE K 105 " --> pdb=" O GLN K 239 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'K' and resid 153 through 157 removed outlier: 6.285A pdb=" N GLY K 142 " --> pdb=" O SER K 155 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU K 244 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR K 145 " --> pdb=" O ARG K 246 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'K' and resid 311 through 319 removed outlier: 7.071A pdb=" N VAL K 595 " --> pdb=" O THR K 315 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN K 317 " --> pdb=" O GLY K 593 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY K 593 " --> pdb=" O ASN K 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA K 609 " --> pdb=" O ILE K 598 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL K 610 " --> pdb=" O ILE K 651 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE K 651 " --> pdb=" O VAL K 610 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'K' and resid 325 through 327 removed outlier: 3.769A pdb=" N VAL K 539 " --> pdb=" O GLY K 550 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'K' and resid 376 through 379 removed outlier: 3.515A pdb=" N ALA K 435 " --> pdb=" O THR K 376 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS K 378 " --> pdb=" O VAL K 433 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL K 433 " --> pdb=" O LYS K 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP K 436 " --> pdb=" O ARG K 509 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG K 509 " --> pdb=" O TRP K 436 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE K 402 " --> pdb=" O TYR K 508 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'K' and resid 394 through 396 removed outlier: 4.097A pdb=" N ASN K 394 " --> pdb=" O GLU K 516 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU K 516 " --> pdb=" O ASN K 394 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AM4, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AM5, first strand: chain 'K' and resid 565 through 566 removed outlier: 7.423A pdb=" N PHE K 565 " --> pdb=" O PHE L 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM5 Processing sheet with id=AM6, first strand: chain 'K' and resid 664 through 667 removed outlier: 6.498A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER K 673 " --> pdb=" O ILE K 693 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN K 675 " --> pdb=" O SER K 691 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'K' and resid 701 through 702 removed outlier: 6.023A pdb=" N ALA K 701 " --> pdb=" O ILE L 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM7 Processing sheet with id=AM8, first strand: chain 'K' and resid 712 through 715 removed outlier: 3.618A pdb=" N LYS K1073 " --> pdb=" O ILE K 714 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'K' and resid 718 through 722 removed outlier: 3.756A pdb=" N SER K 721 " --> pdb=" O THR K1066 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'K' and resid 718 through 722 removed outlier: 3.756A pdb=" N SER K 721 " --> pdb=" O THR K1066 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.450A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'K' and resid 1120 through 1122 Processing sheet with id=AN4, first strand: chain 'K' and resid 1094 through 1097 Processing sheet with id=AN5, first strand: chain 'L' and resid 27 through 30 removed outlier: 3.820A pdb=" N ALA L 27 " --> pdb=" O TRP L 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR L 63 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL L 267 " --> pdb=" O THR L 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE L 65 " --> pdb=" O TYR L 265 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR L 265 " --> pdb=" O PHE L 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL L 90 " --> pdb=" O PHE L 194 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N PHE L 201 " --> pdb=" O ASP L 228 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP L 228 " --> pdb=" O PHE L 201 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE L 203 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N HIS L 207 " --> pdb=" O ALA L 222 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ALA L 222 " --> pdb=" O HIS L 207 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL L 36 " --> pdb=" O LEU L 223 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'L' and resid 27 through 30 removed outlier: 3.820A pdb=" N ALA L 27 " --> pdb=" O TRP L 64 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG L 78 " --> pdb=" O ILE L 68 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'L' and resid 50 through 55 removed outlier: 3.924A pdb=" N ASP L 53 " --> pdb=" O ARG L 273 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG L 273 " --> pdb=" O ASP L 53 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP L 287 " --> pdb=" O LYS L 278 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'L' and resid 84 through 85 Processing sheet with id=AN9, first strand: chain 'L' and resid 116 through 121 removed outlier: 3.672A pdb=" N CYS L 131 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL L 120 " --> pdb=" O VAL L 127 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'L' and resid 143 through 144 Processing sheet with id=AO2, first strand: chain 'L' and resid 311 through 319 removed outlier: 3.530A pdb=" N GLY L 311 " --> pdb=" O THR L 599 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL L 595 " --> pdb=" O THR L 315 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASN L 317 " --> pdb=" O GLY L 593 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY L 593 " --> pdb=" O ASN L 317 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE L 598 " --> pdb=" O ALA L 609 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR L 612 " --> pdb=" O CYS L 649 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'L' and resid 325 through 326 removed outlier: 3.657A pdb=" N VAL L 539 " --> pdb=" O GLY L 550 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR L 588 " --> pdb=" O VAL L 551 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'L' and resid 394 through 400 removed outlier: 3.567A pdb=" N ILE L 434 " --> pdb=" O VAL L 511 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'L' and resid 473 through 474 Processing sheet with id=AO6, first strand: chain 'L' and resid 664 through 667 removed outlier: 6.871A pdb=" N ILE L 670 " --> pdb=" O ILE L 666 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN L 675 " --> pdb=" O SER L 691 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'L' and resid 712 through 713 removed outlier: 4.262A pdb=" N THR L1076 " --> pdb=" O SER L1097 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'L' and resid 718 through 719 Processing sheet with id=AO9, first strand: chain 'L' and resid 722 through 728 removed outlier: 3.540A pdb=" N ALA L1056 " --> pdb=" O GLY L1059 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET L1050 " --> pdb=" O VAL L1065 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'L' and resid 733 through 736 removed outlier: 4.175A pdb=" N LYS L 733 " --> pdb=" O LEU L 861 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'L' and resid 1120 through 1125 removed outlier: 4.838A pdb=" N ALA L1087 " --> pdb=" O SER L1123 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'M' and resid 6 through 7 removed outlier: 3.850A pdb=" N SER M 7 " --> pdb=" O SER M 21 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU M 18 " --> pdb=" O MET M 83 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.279A pdb=" N GLY M 10 " --> pdb=" O THR M 116 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.981A pdb=" N ALA M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET M 34 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA M 97 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR M 108 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'M' and resid 126 through 129 removed outlier: 3.511A pdb=" N LYS M 149 " --> pdb=" O SER M 126 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA M 142 " --> pdb=" O VAL M 190 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'M' and resid 126 through 129 removed outlier: 3.511A pdb=" N LYS M 149 " --> pdb=" O SER M 126 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA M 142 " --> pdb=" O VAL M 190 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'M' and resid 159 through 160 removed outlier: 4.279A pdb=" N CYS M 202 " --> pdb=" O LYS M 215 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS M 215 " --> pdb=" O CYS M 202 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'N' and resid 46 through 49 removed outlier: 6.787A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR N 90 " --> pdb=" O TYR N 37 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER N 93 " --> pdb=" O VAL N 102 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL N 102 " --> pdb=" O SER N 93 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'N' and resid 46 through 49 removed outlier: 6.787A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR N 90 " --> pdb=" O TYR N 37 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'N' and resid 63 through 68 removed outlier: 3.735A pdb=" N SER N 75 " --> pdb=" O SER N 66 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'N' and resid 120 through 121 removed outlier: 5.941A pdb=" N TYR N 178 " --> pdb=" O ASP N 144 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER N 181 " --> pdb=" O THR N 168 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'N' and resid 152 through 153 removed outlier: 3.605A pdb=" N GLN N 200 " --> pdb=" O ALA N 153 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'O' and resid 3 through 7 removed outlier: 4.131A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER O 25 " --> pdb=" O GLN O 3 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL O 5 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU O 18 " --> pdb=" O MET O 83 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET O 83 " --> pdb=" O LEU O 18 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU O 20 " --> pdb=" O LEU O 81 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER O 78 " --> pdb=" O ASP O 73 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP O 73 " --> pdb=" O SER O 78 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'O' and resid 58 through 60 removed outlier: 3.531A pdb=" N TYR O 59 " --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET O 34 " --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA O 97 " --> pdb=" O SER O 35 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL O 37 " --> pdb=" O PHE O 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA O 92 " --> pdb=" O VAL O 115 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'O' and resid 127 through 129 removed outlier: 3.814A pdb=" N SER O 186 " --> pdb=" O CYS O 146 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER O 185 " --> pdb=" O PHE O 172 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE O 172 " --> pdb=" O SER O 185 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL O 187 " --> pdb=" O HIS O 170 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'O' and resid 201 through 202 removed outlier: 3.582A pdb=" N CYS O 202 " --> pdb=" O LYS O 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS O 215 " --> pdb=" O CYS O 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ8 Processing sheet with id=AQ9, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AR1, first strand: chain 'P' and resid 9 through 12 removed outlier: 6.125A pdb=" N VAL P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR P 107 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'P' and resid 9 through 12 removed outlier: 6.125A pdb=" N VAL P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR P 107 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER P 93 " --> pdb=" O VAL P 102 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL P 102 " --> pdb=" O SER P 93 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'P' and resid 18 through 20 removed outlier: 3.776A pdb=" N ILE P 20 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU P 76 " --> pdb=" O ILE P 20 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'P' and resid 152 through 155 Processing sheet with id=AR5, first strand: chain 'Q' and resid 5 through 7 removed outlier: 4.061A pdb=" N VAL Q 5 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER Q 7 " --> pdb=" O SER Q 21 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER Q 21 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'Q' and resid 45 through 51 removed outlier: 6.711A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N MET Q 34 " --> pdb=" O ASN Q 50 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER Q 35 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA Q 97 " --> pdb=" O SER Q 35 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'Q' and resid 126 through 127 removed outlier: 4.188A pdb=" N SER Q 126 " --> pdb=" O LYS Q 149 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS Q 149 " --> pdb=" O SER Q 126 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'Q' and resid 143 through 144 Processing sheet with id=AR9, first strand: chain 'Q' and resid 159 through 160 removed outlier: 3.897A pdb=" N SER Q 159 " --> pdb=" O ASN Q 203 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN Q 203 " --> pdb=" O SER Q 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR9 Processing sheet with id=AS1, first strand: chain 'R' and resid 10 through 11 removed outlier: 7.177A pdb=" N VAL R 10 " --> pdb=" O THR R 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS1 Processing sheet with id=AS2, first strand: chain 'R' and resid 20 through 21 removed outlier: 3.519A pdb=" N SER R 75 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'R' and resid 45 through 50 removed outlier: 7.182A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR R 37 " --> pdb=" O TYR R 90 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP R 88 " --> pdb=" O GLN R 39 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER R 93 " --> pdb=" O VAL R 102 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL R 102 " --> pdb=" O SER R 93 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP R 95 " --> pdb=" O ASN R 100 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN R 100 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'R' and resid 152 through 155 removed outlier: 3.974A pdb=" N TYR R 197 " --> pdb=" O VAL R 212 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL R 212 " --> pdb=" O TYR R 197 " (cutoff:3.500A) 1997 hydrogen bonds defined for protein. 5385 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: 37.31 Time building geometry restraints manager: 23.13 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: 22716 1.34 - 1.46: 16597 1.46 - 1.58: 33185 1.58 - 1.70: 0 1.70 - 1.83: 378 Bond restraints: 72876 Sorted by residual: bond pdb=" CA ASP B 290 " pdb=" C ASP B 290 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.12e-02 7.97e+03 1.55e+01 bond pdb=" CA ASP J 294 " pdb=" C ASP J 294 " ideal model delta sigma weight residual 1.519 1.553 -0.034 1.01e-02 9.80e+03 1.16e+01 bond pdb=" CA CYS K 291 " pdb=" C CYS K 291 " ideal model delta sigma weight residual 1.527 1.486 0.041 1.20e-02 6.94e+03 1.16e+01 bond pdb=" CA GLN C 613 " pdb=" C GLN C 613 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.35e-02 5.49e+03 7.14e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.17e+00 ... (remaining 72871 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.25: 2597 107.25 - 113.94: 41031 113.94 - 120.62: 26420 120.62 - 127.31: 28557 127.31 - 133.99: 707 Bond angle restraints: 99312 Sorted by residual: angle pdb=" N LEU B 293 " pdb=" CA LEU B 293 " pdb=" C LEU B 293 " ideal model delta sigma weight residual 114.56 105.09 9.47 1.27e+00 6.20e-01 5.55e+01 angle pdb=" N GLN C 613 " pdb=" CA GLN C 613 " pdb=" C GLN C 613 " ideal model delta sigma weight residual 109.59 117.68 -8.09 1.47e+00 4.63e-01 3.03e+01 angle pdb=" N GLN L 613 " pdb=" CA GLN L 613 " pdb=" C GLN L 613 " ideal model delta sigma weight residual 109.59 116.33 -6.74 1.47e+00 4.63e-01 2.10e+01 angle pdb=" C ASP A 290 " pdb=" CA ASP A 290 " pdb=" CB ASP A 290 " ideal model delta sigma weight residual 113.33 103.28 10.05 2.26e+00 1.96e-01 1.98e+01 angle pdb=" N LEU L 293 " pdb=" CA LEU L 293 " pdb=" C LEU L 293 " ideal model delta sigma weight residual 113.23 107.79 5.44 1.24e+00 6.50e-01 1.92e+01 ... (remaining 99307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 41081 17.78 - 35.56: 1301 35.56 - 53.33: 186 53.33 - 71.11: 34 71.11 - 88.89: 22 Dihedral angle restraints: 42624 sinusoidal: 16236 harmonic: 26388 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -123.99 37.99 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" CB CYS J1032 " pdb=" SG CYS J1032 " pdb=" SG CYS J1043 " pdb=" CB CYS J1043 " ideal model delta sinusoidal sigma weight residual -86.00 -122.64 36.64 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 128.24 -35.24 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 42621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 10212 0.069 - 0.137: 1257 0.137 - 0.206: 17 0.206 - 0.274: 4 0.274 - 0.343: 6 Chirality restraints: 11496 Sorted by residual: chirality pdb=" C1 NAG J1315 " pdb=" ND2 ASN J 343 " pdb=" C2 NAG J1315 " pdb=" O5 NAG J1315 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C1 NAG J1306 " pdb=" ND2 ASN J1074 " pdb=" C2 NAG J1306 " pdb=" O5 NAG J1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 11493 not shown) Planarity restraints: 12840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J1315 " -0.071 2.00e-02 2.50e+03 5.88e-02 4.31e+01 pdb=" C7 NAG J1315 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG J1315 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG J1315 " 0.092 2.00e-02 2.50e+03 pdb=" O7 NAG J1315 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU L 560 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO L 561 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 561 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 561 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " 0.034 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 561 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.029 5.00e-02 4.00e+02 ... (remaining 12837 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 10958 2.77 - 3.30: 65264 3.30 - 3.83: 113693 3.83 - 4.37: 125047 4.37 - 4.90: 224704 Nonbonded interactions: 539666 Sorted by model distance: nonbonded pdb=" OE1 GLN O 177 " pdb=" OG SER O 183 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.237 2.440 nonbonded pdb=" OE1 GLN F 177 " pdb=" OG SER F 183 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR J 756 " pdb=" OD1 ASP J 994 " model vdw 2.243 2.440 nonbonded pdb=" O GLY K 880 " pdb=" OG SER K 884 " model vdw 2.250 2.440 ... (remaining 539661 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' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'N' selection = chain 'P' selection = chain 'R' } 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 group one per residue 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: 6.160 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: 0.080 Extract box with map and model: 23.200 Check model and map are aligned: 1.060 Set scattering table: 0.650 Process input model: 155.070 Find NCS groups from input model: 3.880 Set up NCS constraints: 0.630 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: 0.020 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 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 : 0.003 0.050 72876 Z= 0.170 Angle : 0.480 10.052 99312 Z= 0.259 Chirality : 0.042 0.343 11496 Planarity : 0.003 0.059 12750 Dihedral : 8.439 88.889 25392 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.06 % Favored : 93.93 % Rotamer: Outliers : 3.89 % Allowed : 5.85 % Favored : 90.26 % 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: -3.76 (0.08), residues: 9024 helix: 0.76 (0.14), residues: 1250 sheet: -2.67 (0.10), residues: 1940 loop : -3.40 (0.06), residues: 5834 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1655 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1352 time to evaluate : 6.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 303 outliers final: 51 residues processed: 1570 average time/residue: 0.7235 time to fit residues: 1932.5672 Evaluate side-chains 644 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 593 time to evaluate : 6.016 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 3 residues processed: 51 average time/residue: 0.5641 time to fit residues: 61.4666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 0.9980 chunk 682 optimal weight: 2.9990 chunk 378 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 460 optimal weight: 2.9990 chunk 364 optimal weight: 0.9980 chunk 705 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 428 optimal weight: 6.9990 chunk 525 optimal weight: 0.4980 chunk 817 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 23 GLN A 69 HIS A 146 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 185 ASN A 360 ASN A 409 GLN A 439 ASN A 450 ASN A 474 GLN A 493 GLN A 607 GLN A 655 HIS A 675 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 872 GLN A 935 GLN A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1011 GLN A1048 HIS A1101 HIS B 23 GLN B 49 HIS B 69 HIS B 164 ASN B 183 GLN B 218 GLN B 271 GLN B 280 ASN B 409 GLN B 414 GLN B 439 ASN B 460 ASN B 493 GLN B 498 GLN B 536 ASN B 607 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1011 GLN B1048 HIS C 23 GLN C 188 ASN C 218 GLN C 409 GLN C 437 ASN C 474 GLN C 493 GLN C 580 GLN C 613 GLN C 774 GLN C 872 GLN C 901 GLN C 920 GLN C 954 GLN C 965 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN F 74 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 HIS G 200 GLN H 6 GLN H 39 GLN H 84 ASN ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 72 ASN I 134 ASN J 14 GLN J 23 GLN J 99 ASN J 134 GLN J 183 GLN J 185 ASN J 360 ASN J 409 GLN J 414 GLN J 439 ASN J 450 ASN J 474 GLN J 493 GLN J 655 HIS J 675 GLN ** J 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 GLN J 804 GLN J 872 GLN J 913 GLN ** J 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN J1011 GLN J1048 HIS J1101 HIS K 23 GLN K 30 ASN K 146 HIS ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 GLN K 354 ASN K 409 GLN K 414 GLN K 439 ASN K 460 ASN ** K 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 493 GLN K 498 GLN K 536 ASN K 901 GLN K 907 ASN K1011 GLN K1048 HIS L 23 GLN L 125 ASN L 218 GLN L 409 GLN L 437 ASN L 474 GLN L 481 ASN L 493 GLN L 580 GLN L 613 GLN L 784 GLN L 872 GLN ** L 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 914 ASN L 920 GLN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 954 GLN L 965 GLN ** L 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1002 GLN L1011 GLN L1048 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 GLN M 161 ASN ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 190 GLN O 74 ASN ** O 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 99 HIS P 100 ASN P 200 GLN Q 6 GLN Q 77 ASN ** Q 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 210 ASN R 38 GLN R 100 ASN R 114 GLN R 200 GLN Total number of N/Q/H flips: 142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 72876 Z= 0.239 Angle : 0.587 12.139 99312 Z= 0.296 Chirality : 0.047 0.713 11496 Planarity : 0.004 0.059 12750 Dihedral : 3.451 31.600 9762 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.10 % Allowed : 3.26 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -3.03 (0.08), residues: 9024 helix: 1.59 (0.15), residues: 1255 sheet: -2.06 (0.11), residues: 2088 loop : -3.03 (0.07), residues: 5681 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 809 time to evaluate : 6.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 816 average time/residue: 0.6760 time to fit residues: 947.5078 Evaluate side-chains 513 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 511 time to evaluate : 5.917 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5086 time to fit residues: 9.9852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 454 optimal weight: 0.9990 chunk 253 optimal weight: 10.0000 chunk 680 optimal weight: 8.9990 chunk 556 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 818 optimal weight: 10.0000 chunk 884 optimal weight: 9.9990 chunk 729 optimal weight: 5.9990 chunk 811 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 656 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 992 GLN A1010 GLN B 125 ASN B 134 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN C 49 HIS C 115 GLN C 146 HIS C 409 GLN C 474 GLN C 774 GLN C 856 ASN C 992 GLN C1002 GLN C1048 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN D 161 ASN D 170 HIS F 74 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 658 ASN ** J 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 HIS ** K 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 GLN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN K1088 HIS L 49 HIS L 207 HIS L 245 HIS L 474 GLN L 774 GLN L 784 GLN ** L 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 992 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 ASN M 111 GLN M 170 HIS ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN O 82 GLN P 6 GLN P 38 GLN P 100 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN Q 111 GLN Q 170 HIS ** Q 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 ASN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 72876 Z= 0.476 Angle : 0.742 16.003 99312 Z= 0.384 Chirality : 0.051 0.660 11496 Planarity : 0.005 0.057 12750 Dihedral : 4.628 37.888 9762 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.45 % Favored : 89.52 % Rotamer: Outliers : 0.15 % Allowed : 4.17 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.06 (0.08), residues: 9024 helix: 1.11 (0.15), residues: 1270 sheet: -1.96 (0.11), residues: 2110 loop : -3.00 (0.07), residues: 5644 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 707 time to evaluate : 6.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 719 average time/residue: 0.6723 time to fit residues: 836.7814 Evaluate side-chains 477 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 468 time to evaluate : 5.955 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5109 time to fit residues: 16.8851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 0.9980 chunk 615 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 390 optimal weight: 2.9990 chunk 549 optimal weight: 0.9980 chunk 821 optimal weight: 5.9990 chunk 869 optimal weight: 3.9990 chunk 429 optimal weight: 10.0000 chunk 778 optimal weight: 3.9990 chunk 234 optimal weight: 0.0170 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 173 GLN A 690 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 69 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 607 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 675 GLN C 774 GLN C 804 GLN C 949 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 ASN J 66 HIS J 690 GLN ** J 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN K 69 HIS K 125 ASN K 218 GLN K 271 GLN K 354 ASN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 564 GLN L 774 GLN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 170 HIS M 203 ASN M 205 ASN ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN ** O 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN ** Q 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 210 ASN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 72876 Z= 0.258 Angle : 0.597 12.468 99312 Z= 0.302 Chirality : 0.047 0.554 11496 Planarity : 0.004 0.060 12750 Dihedral : 4.268 37.432 9762 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.71 (0.08), residues: 9024 helix: 1.70 (0.15), residues: 1252 sheet: -1.83 (0.11), residues: 2122 loop : -2.78 (0.07), residues: 5650 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 666 time to evaluate : 6.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 671 average time/residue: 0.6892 time to fit residues: 801.5900 Evaluate side-chains 471 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 468 time to evaluate : 5.970 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.5369 time to fit residues: 11.1492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 724 optimal weight: 3.9990 chunk 493 optimal weight: 10.0000 chunk 12 optimal weight: 0.0370 chunk 647 optimal weight: 8.9990 chunk 358 optimal weight: 3.9990 chunk 742 optimal weight: 3.9990 chunk 601 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 444 optimal weight: 6.9990 chunk 780 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 overall best weight: 1.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 146 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 14 GLN B 49 HIS B 271 GLN B 607 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 675 GLN C 774 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN F 74 ASN F 206 HIS ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 658 ASN ** J 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN K 271 GLN K 360 ASN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 HIS L 774 GLN L 856 ASN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 170 HIS ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 ASN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN ** O 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN ** Q 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 72876 Z= 0.317 Angle : 0.625 12.480 99312 Z= 0.318 Chirality : 0.047 0.504 11496 Planarity : 0.004 0.066 12750 Dihedral : 4.407 33.669 9762 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.31 % Favored : 89.66 % Rotamer: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.67 (0.08), residues: 9024 helix: 1.58 (0.15), residues: 1270 sheet: -1.80 (0.11), residues: 2194 loop : -2.74 (0.07), residues: 5560 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 646 time to evaluate : 6.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 648 average time/residue: 0.7331 time to fit residues: 824.7472 Evaluate side-chains 473 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 5.990 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 4.9990 chunk 783 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 510 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 870 optimal weight: 0.5980 chunk 722 optimal weight: 2.9990 chunk 403 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 288 optimal weight: 0.0870 chunk 457 optimal weight: 3.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 30 ASN B 271 GLN B 607 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 194 HIS ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 GLN ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 658 ASN ** J 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN K 271 GLN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 774 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 74 ASN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 77 ASN Q 177 GLN ** Q 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 72876 Z= 0.257 Angle : 0.595 12.010 99312 Z= 0.301 Chirality : 0.046 0.469 11496 Planarity : 0.004 0.066 12750 Dihedral : 4.323 36.701 9762 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.12 % Favored : 90.87 % Rotamer: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.53 (0.08), residues: 9024 helix: 1.72 (0.15), residues: 1270 sheet: -1.72 (0.11), residues: 2260 loop : -2.65 (0.08), residues: 5494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 635 time to evaluate : 6.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 636 average time/residue: 0.6782 time to fit residues: 748.5189 Evaluate side-chains 464 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 464 time to evaluate : 6.083 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 496 optimal weight: 0.0980 chunk 635 optimal weight: 5.9990 chunk 492 optimal weight: 3.9990 chunk 733 optimal weight: 1.9990 chunk 486 optimal weight: 0.5980 chunk 867 optimal weight: 6.9990 chunk 542 optimal weight: 4.9990 chunk 528 optimal weight: 6.9990 chunk 400 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 146 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 271 GLN B 607 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN F 74 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 GLN J 52 GLN ** J 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN K 271 GLN ** K 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 314 GLN L 774 GLN L 784 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 ASN N 38 GLN N 100 ASN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 74 ASN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 77 ASN ** Q 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 72876 Z= 0.247 Angle : 0.590 11.210 99312 Z= 0.299 Chirality : 0.046 0.471 11496 Planarity : 0.004 0.065 12750 Dihedral : 4.282 33.327 9762 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.67 % Favored : 90.31 % Rotamer: Outliers : 0.03 % Allowed : 1.27 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -2.42 (0.09), residues: 9024 helix: 1.85 (0.15), residues: 1256 sheet: -1.61 (0.11), residues: 2222 loop : -2.58 (0.08), residues: 5546 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 632 time to evaluate : 6.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 633 average time/residue: 0.7109 time to fit residues: 779.5316 Evaluate side-chains 460 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 459 time to evaluate : 5.963 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6103 time to fit residues: 9.0031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.7614 > 50: distance: 100 - 103: 5.333 distance: 103 - 104: 7.881 distance: 104 - 105: 14.127 distance: 104 - 107: 11.439 distance: 105 - 106: 3.125 distance: 105 - 109: 25.276 distance: 107 - 108: 8.261 distance: 109 - 110: 8.869 distance: 110 - 111: 8.449 distance: 110 - 113: 8.497 distance: 111 - 112: 12.004 distance: 111 - 117: 4.246 distance: 113 - 114: 7.644 distance: 114 - 115: 19.137 distance: 114 - 116: 23.008 distance: 117 - 118: 5.120 distance: 118 - 119: 8.437 distance: 118 - 121: 4.533 distance: 119 - 120: 5.825 distance: 119 - 129: 4.959 distance: 121 - 122: 5.755 distance: 122 - 124: 7.129 distance: 124 - 126: 3.735 distance: 125 - 127: 6.455 distance: 126 - 127: 3.751 distance: 127 - 128: 6.738 distance: 129 - 130: 9.903 distance: 130 - 131: 23.508 distance: 130 - 133: 21.701 distance: 131 - 132: 24.292 distance: 131 - 136: 8.507 distance: 133 - 134: 9.711 distance: 133 - 135: 7.867 distance: 136 - 137: 13.246 distance: 136 - 332: 8.148 distance: 137 - 138: 11.319 distance: 137 - 140: 7.481 distance: 138 - 139: 13.295 distance: 139 - 329: 5.310 distance: 140 - 141: 3.953 distance: 141 - 142: 15.805 distance: 142 - 143: 13.178 distance: 145 - 146: 13.347 distance: 146 - 147: 4.287 distance: 146 - 149: 8.763 distance: 147 - 148: 19.253 distance: 147 - 159: 5.129 distance: 148 - 239: 23.285 distance: 149 - 150: 7.757 distance: 150 - 151: 4.066 distance: 150 - 152: 5.944 distance: 151 - 153: 3.008 distance: 152 - 154: 4.083 distance: 152 - 155: 3.544 distance: 153 - 154: 3.053 distance: 156 - 158: 3.555 distance: 157 - 158: 3.487 distance: 159 - 160: 4.219 distance: 159 - 317: 10.465 distance: 160 - 161: 5.587 distance: 160 - 163: 4.009 distance: 161 - 162: 7.616 distance: 161 - 171: 6.110 distance: 163 - 164: 5.479 distance: 164 - 166: 12.891 distance: 165 - 167: 7.862 distance: 166 - 168: 4.710 distance: 167 - 169: 7.187 distance: 168 - 169: 9.700 distance: 169 - 170: 4.046 distance: 171 - 172: 9.554 distance: 171 - 229: 11.268 distance: 172 - 173: 4.537 distance: 173 - 174: 12.056 distance: 173 - 180: 15.237 distance: 174 - 226: 15.384 distance: 175 - 176: 12.743 distance: 176 - 177: 11.049 distance: 177 - 178: 8.915 distance: 177 - 179: 9.114 distance: 180 - 181: 11.222 distance: 180 - 299: 14.874 distance: 181 - 182: 5.279 distance: 181 - 184: 10.856 distance: 182 - 183: 5.831 distance: 182 - 189: 15.951 distance: 183 - 296: 14.921 distance: 184 - 185: 15.763 distance: 185 - 186: 13.273 distance: 186 - 187: 16.528 distance: 186 - 188: 14.050 distance: 190 - 191: 7.469 distance: 190 - 193: 6.460 distance: 191 - 192: 11.460 distance: 191 - 200: 9.800 distance: 193 - 194: 8.100 distance: 194 - 195: 4.775 distance: 197 - 198: 9.611 distance: 197 - 199: 25.609