Starting phenix.real_space_refine on Mon Mar 25 15:07:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc4_34651/03_2024/8hc4_34651.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc4_34651/03_2024/8hc4_34651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc4_34651/03_2024/8hc4_34651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc4_34651/03_2024/8hc4_34651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc4_34651/03_2024/8hc4_34651.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hc4_34651/03_2024/8hc4_34651.pdb" } resolution = 3.54 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= 0.001 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4452 atoms to isotropic. 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 186 5.16 5 C 28494 2.51 5 N 7476 2.21 5 O 8922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45078 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8340 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 8340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8340 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 8340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8340 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Chain: "J" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203} Chain: "H" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203} Chain: "K" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Chain: "I" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203} Chain: "N" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 22.37, per 1000 atoms: 0.50 Number of scatterers: 45078 At special positions: 0 Unit cell: (203.496, 213.744, 238.632, 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 186 16.00 O 8922 8.00 N 7476 7.00 C 28494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, 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=2.03 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 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " 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=2.03 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=2.04 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=2.03 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=2.04 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 151 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 143 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 219 " - pdb=" SG CYS J 215 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 219 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 151 " - pdb=" SG CYS K 207 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS M 139 " - pdb=" SG CYS M 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 143 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 219 " - pdb=" SG CYS I 215 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 207 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 139 " - pdb=" SG CYS O 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 801 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN A1134 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 15.40 Conformation dependent library (CDL) restraints added in 7.2 seconds 11478 Ramachandran restraints generated. 5739 Oldfield, 0 Emsley, 5739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10734 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 117 sheets defined 14.1% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.619A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.681A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.513A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 removed outlier: 3.823A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.516A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 852 through 857 removed outlier: 4.091A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.724A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.462A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 946 through 966 removed outlier: 3.988A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.755A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.111A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.009A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.586A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 removed outlier: 4.180A pdb=" N GLY B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.171A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.289A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.721A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.612A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.540A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.759A pdb=" N VAL B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR B 917 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU B 918 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.510A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.328A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.254A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.841A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.540A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 removed outlier: 3.950A pdb=" N ASN C 334 " --> pdb=" O ASN C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.640A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.581A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.681A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 411' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 753 removed outlier: 4.162A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.666A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.692A 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 removed outlier: 3.852A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.339A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.818A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.842A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1032 Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.540A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.980A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.823A pdb=" N GLN E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN E 133 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 removed outlier: 4.166A pdb=" N LYS E 191 " --> pdb=" O PRO E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 removed outlier: 4.287A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'J' and resid 122 through 127 removed outlier: 3.628A pdb=" N LYS J 127 " --> pdb=" O GLU J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 188 removed outlier: 3.632A pdb=" N GLU J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 184 through 188' Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.139A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'H' and resid 188 through 192 Processing helix chain 'L' and resid 124 through 129 removed outlier: 4.129A pdb=" N SER L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 124 through 129' Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.617A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 190' Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'M' and resid 81 through 85 removed outlier: 4.079A pdb=" N GLU M 85 " --> pdb=" O ALA M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 133 removed outlier: 3.651A pdb=" N GLN M 131 " --> pdb=" O GLU M 128 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN M 133 " --> pdb=" O LEU M 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 4.054A pdb=" N THR G 90 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 161 No H-bonds generated for 'chain 'G' and resid 159 through 161' Processing helix chain 'G' and resid 188 through 192 removed outlier: 3.560A pdb=" N LEU G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 129 removed outlier: 4.249A pdb=" N LYS I 127 " --> pdb=" O ASP I 123 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER I 128 " --> pdb=" O GLU I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.682A pdb=" N GLU I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS I 190 " --> pdb=" O ASP I 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 184 through 190' Processing helix chain 'N' and resid 198 through 202 removed outlier: 3.644A pdb=" N GLY N 201 " --> pdb=" O SER N 198 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 85 removed outlier: 4.086A pdb=" N GLU O 85 " --> pdb=" O ALA O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 133 removed outlier: 3.547A pdb=" N GLU O 129 " --> pdb=" O SER O 126 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN O 131 " --> pdb=" O GLU O 128 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA O 132 " --> pdb=" O GLU O 129 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN O 133 " --> pdb=" O LEU O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 191 removed outlier: 4.150A pdb=" N LYS O 191 " --> pdb=" O PRO O 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.509A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.030A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 158 removed outlier: 5.126A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.759A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.826A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.878A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.878A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.930A pdb=" N ARG A 466 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY D 104 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 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: 6.557A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.549A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.672A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.376A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.758A 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 1125 removed outlier: 4.585A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.645A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.930A 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: 4.223A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.051A 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: 3.518A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.919A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.033A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.808A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.844A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 435 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 466 through 468 removed outlier: 3.980A pdb=" N ARG B 466 " --> pdb=" O GLY K 104 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY K 104 " --> pdb=" O ARG B 466 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 468 " --> pdb=" O TYR K 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR K 102 " --> pdb=" O ILE B 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 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: 7.447A 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 575 through 578 removed outlier: 3.535A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.513A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.703A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 727 removed outlier: 3.545A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.407A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.358A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.787A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.242A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.748A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.007A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.454A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.856A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.658A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.852A pdb=" N ARG C 466 " --> pdb=" O GLY N 104 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY N 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 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 654 through 655 removed outlier: 6.343A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 712 through 719 removed outlier: 6.539A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 722 through 728 Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.581A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.657A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.646A pdb=" N VAL D 20 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 69 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.573A pdb=" N GLU D 10 " --> pdb=" O THR D 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.518A pdb=" N ILE D 57 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS D 96 " --> pdb=" O TRP D 114 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP D 114 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG D 98 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 131 through 135 removed outlier: 3.529A pdb=" N PHE D 133 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 152 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 150 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL D 153 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU D 189 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP D 155 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR D 187 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 131 through 135 removed outlier: 3.529A pdb=" N PHE D 133 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 152 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 150 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 149 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 163 through 165 removed outlier: 3.720A pdb=" N SER D 164 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN D 208 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS D 220 " --> pdb=" O CYS D 207 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 209 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 218 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AG6, first strand: chain 'E' and resid 9 through 10 removed outlier: 6.701A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 9 through 10 Processing sheet with id=AG8, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.503A pdb=" N PHE E 123 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 179 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP E 143 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N TYR E 177 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.661A pdb=" N LYS E 154 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR E 196 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS E 198 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS E 209 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL E 200 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL E 207 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.614A pdb=" N LEU F 18 " --> pdb=" O MET F 82 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 80 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR F 79 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AH3, first strand: chain 'F' and resid 57 through 59 removed outlier: 4.988A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR F 33 " --> pdb=" O GLY F 98 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA F 96 " --> pdb=" O HIS F 35 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL F 37 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR F 102 " --> pdb=" O LEU F 99 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 123 through 127 removed outlier: 4.039A pdb=" N GLY F 142 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP F 147 " --> pdb=" O TYR F 179 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR F 179 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL F 184 " --> pdb=" O HIS F 167 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 123 through 127 removed outlier: 4.039A pdb=" N GLY F 142 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP F 147 " --> pdb=" O TYR F 179 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR F 179 " --> pdb=" O ASP F 147 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 154 through 157 removed outlier: 3.509A pdb=" N THR F 154 " --> pdb=" O ASN F 202 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN F 202 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TYR F 197 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS F 199 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS F 212 " --> pdb=" O CYS F 199 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL F 201 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 210 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS F 203 " --> pdb=" O THR F 208 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR F 208 " --> pdb=" O HIS F 203 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 4 through 5 removed outlier: 3.637A pdb=" N CYS J 23 " --> pdb=" O PHE J 71 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.713A pdb=" N SER J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR J 87 " --> pdb=" O TYR J 36 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 49 " --> pdb=" O THR J 53 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 112 through 119 removed outlier: 7.229A pdb=" N ALA J 113 " --> pdb=" O PHE J 140 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE J 140 " --> pdb=" O ALA J 113 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER J 115 " --> pdb=" O ASN J 138 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN J 138 " --> pdb=" O SER J 115 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL J 134 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU J 180 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N CYS J 135 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER J 178 " --> pdb=" O CYS J 135 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR J 174 " --> pdb=" O ASN J 139 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 154 through 155 removed outlier: 4.000A pdb=" N TYR J 193 " --> pdb=" O PHE J 210 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE J 210 " --> pdb=" O TYR J 193 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS J 195 " --> pdb=" O LYS J 208 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS J 208 " --> pdb=" O CYS J 195 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL J 197 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL J 206 " --> pdb=" O VAL J 197 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AI3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AI4, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.540A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 57 through 59 removed outlier: 7.080A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR H 93 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR H 110 " --> pdb=" O TYR H 93 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 123 through 127 removed outlier: 4.301A pdb=" N GLY H 142 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP H 147 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR H 179 " --> pdb=" O ASP H 147 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 123 through 127 removed outlier: 4.301A pdb=" N GLY H 142 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP H 147 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR H 179 " --> pdb=" O ASP H 147 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'H' and resid 154 through 157 removed outlier: 3.727A pdb=" N THR H 154 " --> pdb=" O ASN H 202 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN H 202 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS H 199 " --> pdb=" O LYS H 212 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS H 212 " --> pdb=" O CYS H 199 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL H 201 " --> pdb=" O VAL H 210 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL H 210 " --> pdb=" O VAL H 201 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.671A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.572A pdb=" N VAL L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR L 103 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 112 through 119 removed outlier: 7.192A pdb=" N ALA L 113 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE L 140 " --> pdb=" O ALA L 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL L 133 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU L 180 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'L' and resid 154 through 155 removed outlier: 3.693A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'K' and resid 3 through 5 removed outlier: 3.572A pdb=" N LEU K 83 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL K 20 " --> pdb=" O MET K 81 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET K 81 " --> pdb=" O VAL K 20 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR K 78 " --> pdb=" O ASP K 73 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AJ6, first strand: chain 'K' and resid 58 through 59 removed outlier: 3.773A pdb=" N ASN K 59 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY K 50 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU K 113 " --> pdb=" O ARG K 98 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN K 100 " --> pdb=" O PHE K 111 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE K 111 " --> pdb=" O ASN K 100 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'K' and resid 131 through 135 removed outlier: 3.607A pdb=" N PHE K 133 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU K 152 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY K 150 " --> pdb=" O LEU K 135 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'K' and resid 162 through 165 removed outlier: 4.619A pdb=" N THR K 162 " --> pdb=" O ASN K 210 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN K 210 " --> pdb=" O THR K 162 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER K 164 " --> pdb=" O ASN K 208 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN K 208 " --> pdb=" O SER K 164 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR K 205 " --> pdb=" O VAL K 222 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS K 220 " --> pdb=" O CYS K 207 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'M' and resid 4 through 5 removed outlier: 4.456A pdb=" N VAL M 18 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE M 77 " --> pdb=" O VAL M 18 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'M' and resid 9 through 11 removed outlier: 3.669A pdb=" N THR M 109 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'M' and resid 9 through 11 removed outlier: 3.669A pdb=" N THR M 109 " --> pdb=" O VAL M 10 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'M' and resid 119 through 123 removed outlier: 3.936A pdb=" N PHE M 123 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL M 138 " --> pdb=" O PHE M 123 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA M 179 " --> pdb=" O ILE M 141 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP M 143 " --> pdb=" O TYR M 177 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR M 177 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'M' and resid 119 through 123 removed outlier: 3.936A pdb=" N PHE M 123 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL M 138 " --> pdb=" O PHE M 123 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'M' and resid 159 through 160 removed outlier: 4.736A pdb=" N TRP M 153 " --> pdb=" O VAL M 160 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR M 150 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR M 196 " --> pdb=" O VAL M 211 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N CYS M 198 " --> pdb=" O LYS M 209 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS M 209 " --> pdb=" O CYS M 198 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL M 200 " --> pdb=" O VAL M 207 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL M 207 " --> pdb=" O VAL M 200 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AK7, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.714A pdb=" N THR G 77 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN G 72 " --> pdb=" O THR G 77 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR G 79 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER G 70 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AK9, first strand: chain 'G' and resid 57 through 59 removed outlier: 4.807A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP G 36 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR G 33 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR G 93 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR G 110 " --> pdb=" O TYR G 93 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 123 through 127 removed outlier: 4.421A pdb=" N GLY G 142 " --> pdb=" O LEU G 127 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER G 183 " --> pdb=" O CYS G 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP G 147 " --> pdb=" O TYR G 179 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR G 179 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL G 184 " --> pdb=" O HIS G 167 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 123 through 127 removed outlier: 4.421A pdb=" N GLY G 142 " --> pdb=" O LEU G 127 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER G 183 " --> pdb=" O CYS G 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP G 147 " --> pdb=" O TYR G 179 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR G 179 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'G' and resid 154 through 157 removed outlier: 3.837A pdb=" N CYS G 199 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS G 212 " --> pdb=" O CYS G 199 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G 201 " --> pdb=" O VAL G 210 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL G 210 " --> pdb=" O VAL G 201 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.898A pdb=" N CYS I 23 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.582A pdb=" N VAL I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL5 Processing sheet with id=AL6, first strand: chain 'I' and resid 44 through 46 Processing sheet with id=AL7, first strand: chain 'I' and resid 112 through 119 removed outlier: 7.401A pdb=" N ALA I 113 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE I 140 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER I 115 " --> pdb=" O ASN I 138 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN I 138 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL I 134 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL I 133 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU I 180 " --> pdb=" O VAL I 133 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS I 135 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER I 178 " --> pdb=" O CYS I 135 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'I' and resid 154 through 155 removed outlier: 3.735A pdb=" N TYR I 193 " --> pdb=" O PHE I 210 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE I 210 " --> pdb=" O TYR I 193 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS I 195 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS I 208 " --> pdb=" O CYS I 195 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 197 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL I 206 " --> pdb=" O VAL I 197 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'N' and resid 3 through 5 removed outlier: 3.747A pdb=" N LEU N 83 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL N 20 " --> pdb=" O MET N 81 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET N 81 " --> pdb=" O VAL N 20 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS N 22 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.541A pdb=" N GLY N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY N 50 " --> pdb=" O ASN N 59 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE N 52 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE N 57 " --> pdb=" O ILE N 52 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.634A pdb=" N ARG N 98 " --> pdb=" O ASP N 112 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN N 110 " --> pdb=" O ASN N 100 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'N' and resid 131 through 135 removed outlier: 3.520A pdb=" N PHE N 133 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU N 152 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY N 150 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU N 149 " --> pdb=" O VAL N 193 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'N' and resid 162 through 165 removed outlier: 4.672A pdb=" N THR N 162 " --> pdb=" O ASN N 210 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN N 210 " --> pdb=" O THR N 162 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER N 164 " --> pdb=" O ASN N 208 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR N 205 " --> pdb=" O VAL N 222 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS N 207 " --> pdb=" O LYS N 220 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS N 220 " --> pdb=" O CYS N 207 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL N 209 " --> pdb=" O VAL N 218 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL N 218 " --> pdb=" O VAL N 209 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR N 216 " --> pdb=" O HIS N 211 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'O' and resid 4 through 5 removed outlier: 3.796A pdb=" N THR O 23 " --> pdb=" O THR O 5 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL O 18 " --> pdb=" O ILE O 77 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE O 77 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'O' and resid 9 through 11 removed outlier: 3.941A pdb=" N THR O 109 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'O' and resid 47 through 51 removed outlier: 6.548A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER O 92 " --> pdb=" O VAL O 101 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'O' and resid 119 through 123 removed outlier: 3.630A pdb=" N PHE O 123 " --> pdb=" O VAL O 138 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL O 138 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER O 181 " --> pdb=" O CYS O 139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE O 141 " --> pdb=" O ALA O 179 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA O 179 " --> pdb=" O ILE O 141 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP O 143 " --> pdb=" O TYR O 177 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N TYR O 177 " --> pdb=" O ASP O 143 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'O' and resid 150 through 154 removed outlier: 4.349A pdb=" N THR O 150 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS O 154 " --> pdb=" O SER O 197 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR O 196 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS O 198 " --> pdb=" O LYS O 209 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS O 209 " --> pdb=" O CYS O 198 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL O 200 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL O 207 " --> pdb=" O VAL O 200 " (cutoff:3.500A) 1383 hydrogen bonds defined for protein. 3585 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: 25.88 Time building geometry restraints manager: 16.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 14426 1.35 - 1.47: 11301 1.47 - 1.58: 20134 1.58 - 1.70: 0 1.70 - 1.82: 231 Bond restraints: 46092 Sorted by residual: bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.73e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.49e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 ... (remaining 46087 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.62: 1028 105.62 - 112.73: 24968 112.73 - 119.84: 14002 119.84 - 126.96: 22221 126.96 - 134.07: 535 Bond angle restraints: 62754 Sorted by residual: angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.34 110.40 -7.06 9.30e-01 1.16e+00 5.77e+01 angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.34 110.37 -7.03 9.30e-01 1.16e+00 5.71e+01 angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.34 110.35 -7.01 9.30e-01 1.16e+00 5.68e+01 angle pdb=" N PRO C 899 " pdb=" CA PRO C 899 " pdb=" CB PRO C 899 " ideal model delta sigma weight residual 103.52 110.15 -6.63 1.06e+00 8.90e-01 3.91e+01 angle pdb=" N PRO A 899 " pdb=" CA PRO A 899 " pdb=" CB PRO A 899 " ideal model delta sigma weight residual 103.33 110.20 -6.87 1.10e+00 8.26e-01 3.90e+01 ... (remaining 62749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 24597 17.96 - 35.93: 2735 35.93 - 53.89: 690 53.89 - 71.85: 141 71.85 - 89.81: 58 Dihedral angle restraints: 28221 sinusoidal: 11460 harmonic: 16761 Sorted by residual: dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual -86.00 -3.79 -82.21 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 175.14 -82.14 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -11.45 -74.55 1 1.00e+01 1.00e-02 7.04e+01 ... (remaining 28218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 6828 0.094 - 0.188: 441 0.188 - 0.283: 14 0.283 - 0.377: 2 0.377 - 0.471: 2 Chirality restraints: 7287 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 7284 not shown) Planarity restraints: 8070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 526 " -0.044 2.00e-02 2.50e+03 8.51e-02 7.24e+01 pdb=" C GLY C 526 " 0.147 2.00e-02 2.50e+03 pdb=" O GLY C 526 " -0.055 2.00e-02 2.50e+03 pdb=" N PRO C 527 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 112 " -0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C GLY E 112 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY E 112 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN E 113 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA K 136 " 0.074 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO K 137 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO K 137 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO K 137 " 0.058 5.00e-02 4.00e+02 ... (remaining 8067 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7566 2.77 - 3.30: 37865 3.30 - 3.84: 73078 3.84 - 4.37: 79090 4.37 - 4.90: 142109 Nonbonded interactions: 339708 Sorted by model distance: nonbonded pdb=" OG1 THR H 90 " pdb=" O VAL H 112 " model vdw 2.239 2.440 nonbonded pdb=" OE1 GLU K 6 " pdb=" C GLY K 117 " model vdw 2.245 3.270 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.273 2.440 nonbonded pdb=" OE1 GLU K 6 " pdb=" CA GLY K 117 " model vdw 2.294 3.440 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR F 33 " model vdw 2.296 2.440 ... (remaining 339703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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=0.00 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.030 Extract box with map and model: 8.100 Check model and map are aligned: 0.710 Set scattering table: 0.390 Process input model: 117.260 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4667 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 0.084 46092 Z= 0.180 Angle : 0.532 10.251 62754 Z= 0.278 Chirality : 0.045 0.471 7287 Planarity : 0.004 0.109 8028 Dihedral : 15.956 89.812 17280 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.04 % Allowed : 27.00 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.11), residues: 5739 helix: 0.49 (0.20), residues: 656 sheet: 0.38 (0.14), residues: 1532 loop : -1.15 (0.10), residues: 3551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP N 114 HIS 0.007 0.000 HIS C 245 PHE 0.026 0.001 PHE B 79 TYR 0.032 0.001 TYR C1138 ARG 0.006 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11478 Ramachandran restraints generated. 5739 Oldfield, 0 Emsley, 5739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11478 Ramachandran restraints generated. 5739 Oldfield, 0 Emsley, 5739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 4971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 4.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.2257 (OUTLIER) cc_final: 0.1683 (t-170) REVERT: A 78 ARG cc_start: 0.2184 (ttt-90) cc_final: 0.1635 (ptp90) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.5421 time to fit residues: 216.1594 Evaluate side-chains 207 residues out of total 4971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 4.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 483 optimal weight: 30.0000 chunk 434 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 148 optimal weight: 0.2980 chunk 292 optimal weight: 0.6980 chunk 232 optimal weight: 0.9980 chunk 449 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 273 optimal weight: 8.9990 chunk 334 optimal weight: 0.0370 chunk 520 optimal weight: 0.0270 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 474 GLN A 907 ASN B 751 ASN C 474 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN L 139 ASN O 189 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4716 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 46092 Z= 0.121 Angle : 0.456 7.646 62754 Z= 0.238 Chirality : 0.042 0.401 7287 Planarity : 0.004 0.069 8028 Dihedral : 4.930 59.561 7334 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.78 % Allowed : 25.61 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.11), residues: 5739 helix: 1.21 (0.21), residues: 663 sheet: 0.49 (0.13), residues: 1569 loop : -0.98 (0.10), residues: 3507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 35 HIS 0.003 0.001 HIS A1088 PHE 0.018 0.001 PHE C 140 TYR 0.019 0.001 TYR C 265 ARG 0.003 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11478 Ramachandran restraints generated. 5739 Oldfield, 0 Emsley, 5739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11478 Ramachandran restraints generated. 5739 Oldfield, 0 Emsley, 5739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 232 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.2302 (OUTLIER) cc_final: 0.1754 (t-170) REVERT: A 78 ARG cc_start: 0.2254 (ttt-90) cc_final: 0.1714 (ptp90) REVERT: B 132 GLU cc_start: 0.2042 (OUTLIER) cc_final: 0.0595 (pp20) REVERT: C 754 LEU cc_start: 0.6727 (mt) cc_final: 0.6317 (mp) REVERT: F 32 ASN cc_start: 0.0164 (OUTLIER) cc_final: -0.1238 (t0) REVERT: K 48 MET cc_start: -0.0393 (ptp) cc_final: -0.4158 (mmt) REVERT: K 74 LYS cc_start: 0.3505 (mttm) cc_final: 0.1343 (ptpt) outliers start: 88 outliers final: 45 residues processed: 309 average time/residue: 0.4940 time to fit residues: 271.8723 Evaluate side-chains 252 residues out of total 4971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 204 time to evaluate : 5.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain O residue 54 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 60.595 > 50: distance: 26 - 59: 17.665 distance: 29 - 56: 25.375 distance: 42 - 48: 21.780 distance: 48 - 49: 19.569 distance: 48 - 160: 23.757 distance: 49 - 50: 46.721 distance: 49 - 52: 15.131 distance: 50 - 51: 29.933 distance: 50 - 56: 52.052 distance: 52 - 53: 47.063 distance: 52 - 54: 48.471 distance: 53 - 55: 26.219 distance: 56 - 57: 14.771 distance: 57 - 58: 7.172 distance: 57 - 60: 25.959 distance: 58 - 59: 29.122 distance: 58 - 62: 11.961 distance: 60 - 61: 51.766 distance: 62 - 63: 24.477 distance: 63 - 64: 36.800 distance: 63 - 66: 27.544 distance: 64 - 65: 35.282 distance: 64 - 70: 28.393 distance: 66 - 67: 30.922 distance: 67 - 68: 8.038 distance: 67 - 69: 15.825 distance: 70 - 71: 27.332 distance: 71 - 72: 35.085 distance: 71 - 74: 27.253 distance: 72 - 73: 35.626 distance: 72 - 81: 45.381 distance: 74 - 75: 6.865 distance: 75 - 76: 5.613 distance: 75 - 77: 11.941 distance: 76 - 78: 18.021 distance: 77 - 79: 15.797 distance: 78 - 80: 12.579 distance: 79 - 80: 17.058 distance: 82 - 83: 38.441 distance: 82 - 85: 34.242 distance: 83 - 84: 37.274 distance: 83 - 93: 32.238 distance: 85 - 86: 21.773 distance: 86 - 87: 17.960 distance: 86 - 88: 16.620 distance: 87 - 89: 16.761 distance: 88 - 90: 38.556 distance: 89 - 91: 15.006 distance: 90 - 91: 14.172 distance: 91 - 92: 9.020 distance: 93 - 94: 31.212 distance: 93 - 99: 39.762 distance: 94 - 95: 47.053 distance: 94 - 97: 28.427 distance: 95 - 96: 27.629 distance: 97 - 98: 47.922 distance: 98 - 99: 16.607 distance: 100 - 101: 37.797 distance: 101 - 102: 14.718 distance: 102 - 103: 19.794 distance: 102 - 104: 16.604 distance: 104 - 105: 35.967 distance: 105 - 106: 10.283 distance: 105 - 108: 12.320 distance: 106 - 107: 14.116 distance: 106 - 109: 11.525 distance: 109 - 110: 13.699 distance: 110 - 111: 31.310 distance: 110 - 113: 46.962 distance: 111 - 112: 3.216 distance: 111 - 116: 26.755 distance: 113 - 114: 14.992 distance: 113 - 115: 25.697 distance: 117 - 118: 20.588 distance: 117 - 120: 17.070 distance: 118 - 119: 35.833 distance: 118 - 123: 15.580 distance: 120 - 121: 31.642 distance: 120 - 122: 24.223