Starting phenix.real_space_refine on Tue Mar 19 05:21:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zwo_6974/03_2024/5zwo_6974_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zwo_6974/03_2024/5zwo_6974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zwo_6974/03_2024/5zwo_6974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zwo_6974/03_2024/5zwo_6974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zwo_6974/03_2024/5zwo_6974_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zwo_6974/03_2024/5zwo_6974_updated.pdb" } resolution = 3.9 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 596 5.49 5 Mg 1 5.21 5 S 157 5.16 5 C 53714 2.51 5 N 17167 2.21 5 O 19626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A TYR 1504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1511": "NH1" <-> "NH2" Residue "A PHE 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 131": "NH1" <-> "NH2" Residue "K ARG 142": "NH1" <-> "NH2" Residue "K TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 393": "NH1" <-> "NH2" Residue "K TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 122": "NH1" <-> "NH2" Residue "L ARG 367": "NH1" <-> "NH2" Residue "L PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "N ARG 134": "NH1" <-> "NH2" Residue "N ARG 143": "NH1" <-> "NH2" Residue "N ARG 211": "NH1" <-> "NH2" Residue "N TYR 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 688": "NH1" <-> "NH2" Residue "J PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J ARG 314": "NH1" <-> "NH2" Residue "J ARG 322": "NH1" <-> "NH2" Residue "J PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 353": "NH1" <-> "NH2" Residue "J ARG 371": "NH1" <-> "NH2" Residue "J PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 89": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 197": "NH1" <-> "NH2" Residue "O ARG 203": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 91261 Number of models: 1 Model: "" Number of chains: 61 Chain: "A" Number of atoms: 17092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2172, 17092 Classifications: {'peptide': 2172} Incomplete info: {'truncation_to_alanine': 223} Link IDs: {'PTRANS': 110, 'TRANS': 2061} Chain breaks: 3 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 824 Unresolved non-hydrogen angles: 1065 Unresolved non-hydrogen dihedrals: 695 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 15, 'TRP:plan': 4, 'ASP:plan': 15, 'PHE:plan': 15, 'GLU:plan': 20, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 462 Chain: "K" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3375 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 3, 'ASN%COO:oxt': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3171 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 17, 'TRANS': 398} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "N" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 4882 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 699} Chain breaks: 23 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1106 Unresolved non-hydrogen angles: 1404 Unresolved non-hydrogen dihedrals: 935 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 16, 'TRP:plan': 7, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 28, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 595 Chain: "J" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2467 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 11, 'TRANS': 296} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "E" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1135 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "M" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 950 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "C" Number of atoms: 6732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6732 Classifications: {'peptide': 843} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 45, 'TRANS': 796} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "z" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 260 Classifications: {'peptide': 65} Incomplete info: {'backbone_only': 61} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 103 Chain: "q" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 368 Classifications: {'peptide': 92} Incomplete info: {'backbone_only': 89} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 397 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 189 Chain: "r" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 308 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 74} Link IDs: {'PTRANS': 2, 'TRANS': 74} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 452 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 138 Chain: "x" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 69} Link IDs: {'TRANS': 73} Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 136 Chain: "t" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 308 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 71} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 453 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 142 Chain: "y" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 264 Classifications: {'peptide': 66} Incomplete info: {'backbone_only': 60} Link IDs: {'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "s" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 308 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 73} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "F" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2043 Classifications: {'RNA': 99} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 45, 'rna3p_pyr': 40} Link IDs: {'rna2p': 13, 'rna3p': 85} Chain breaks: 3 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' C%rna3p_pyr:plan': 1, ' A%rna3p_pur:plan2': 3, ' U%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 1, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 3677 Classifications: {'RNA': 175} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 11, 'rna3p_pur': 78, 'rna3p_pyr': 76} Link IDs: {'rna2p': 21, 'rna3p': 153} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1, ' A%rna3p_pur:plan2': 3, ' A%rna3p_pur:plan': 3} Unresolved non-hydrogen planarities: 44 Chain: "O" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 568 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 74} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 25 Chain: "d" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 316 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 73} Link IDs: {'PTRANS': 4, 'TRANS': 74} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 117 Chain: "a" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 69} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 129 Chain: "b" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 308 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 75} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 107 Chain: "c" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 360 Classifications: {'peptide': 90} Incomplete info: {'backbone_only': 88} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'HIS:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 174 Chain: "e" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 288 Classifications: {'peptide': 72} Incomplete info: {'backbone_only': 68} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 122 Chain: "f" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 280 Classifications: {'peptide': 70} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 424 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 148 Chain: "g" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 280 Classifications: {'peptide': 70} Incomplete info: {'backbone_only': 65} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 108 Chain: "I" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2334 Classifications: {'RNA': 110} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 44, 'rna3p_pyr': 46} Link IDs: {'rna2p': 20, 'rna3p': 89} Chain breaks: 3 Chain: "D" Number of atoms: 8422 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1699, 8420 Classifications: {'peptide': 1699} Incomplete info: {'truncation_to_alanine': 1528} Link IDs: {'PTRANS': 71, 'TRANS': 1627} Chain breaks: 2 Unresolved chain link angles: 71 Unresolved non-hydrogen bonds: 5493 Unresolved non-hydrogen angles: 7052 Unresolved non-hydrogen dihedrals: 4593 Unresolved non-hydrogen chiralities: 511 Planarities with less than four sites: {'GLN:plan1': 62, 'HIS:plan': 36, 'TYR:plan': 62, 'ASN:plan1': 95, 'TRP:plan': 24, 'ASP:plan': 88, 'PHE:plan': 81, 'GLU:plan': 123, 'ARG:plan': 69} Unresolved non-hydrogen planarities: 2950 Conformer: "B" Number of residues, atoms: 1699, 8420 Classifications: {'peptide': 1699} Incomplete info: {'truncation_to_alanine': 1528} Link IDs: {'PTRANS': 71, 'TRANS': 1627} Chain breaks: 2 Unresolved chain link angles: 71 Unresolved non-hydrogen bonds: 5493 Unresolved non-hydrogen angles: 7052 Unresolved non-hydrogen dihedrals: 4593 Unresolved non-hydrogen chiralities: 511 Planarities with less than four sites: {'GLN:plan1': 62, 'HIS:plan': 36, 'TYR:plan': 62, 'ASN:plan1': 95, 'TRP:plan': 24, 'ASP:plan': 88, 'PHE:plan': 81, 'GLU:plan': 123, 'ARG:plan': 69} Unresolved non-hydrogen planarities: 2950 bond proxies already assigned to first conformer: 8414 Chain: "P" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 346 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "Q" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 491 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 389 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 140 Chain: "R" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 457 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'HIS:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 159 Chain: "S" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 404 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 77} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 114 Chain: "T" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 379 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "U" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 359 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 136 Chain: "V" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 369 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1264 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 11, 'rna3p_pur': 18, 'rna3p_pyr': 18} Link IDs: {'rna2p': 24, 'rna3p': 35} Chain: "1" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 4044 Classifications: {'peptide': 816} Incomplete info: {'truncation_to_alanine': 724} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 773} Unresolved chain link angles: 42 Unresolved non-hydrogen bonds: 2557 Unresolved non-hydrogen angles: 3283 Unresolved non-hydrogen dihedrals: 2090 Unresolved non-hydrogen chiralities: 288 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 21, 'TYR:plan': 25, 'ASN:plan1': 42, 'TRP:plan': 6, 'ASP:plan': 37, 'PHE:plan': 29, 'GLU:plan': 50, 'ARG:plan': 43} Unresolved non-hydrogen planarities: 1236 Chain: "2" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1042 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 191} Link IDs: {'PTRANS': 18, 'TRANS': 192} Chain breaks: 2 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 740 Unresolved non-hydrogen angles: 947 Unresolved non-hydrogen dihedrals: 647 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 6, 'ASP:plan': 13, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 387 Chain: "3" Number of atoms: 5852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 5852 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 1088} Link IDs: {'PTRANS': 45, 'TRANS': 1134} Chain breaks: 7 Unresolved chain link angles: 45 Unresolved non-hydrogen bonds: 3720 Unresolved non-hydrogen angles: 4778 Unresolved non-hydrogen dihedrals: 3065 Unresolved non-hydrogen chiralities: 394 Planarities with less than four sites: {'GLN:plan1': 45, 'ARG:plan': 40, 'TYR:plan': 31, 'ASN:plan1': 78, 'TRP:plan': 11, 'HIS:plan': 37, 'PHE:plan': 57, 'GLU:plan': 48, 'ASP:plan': 72} Unresolved non-hydrogen planarities: 1865 Chain: "4" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 862 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 599 Unresolved non-hydrogen angles: 765 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 15, 'ASP:plan': 13, 'PHE:plan': 10, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 339 Chain: "5" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 507 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 171 Chain: "6" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 415 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 167 Chain: "X" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 631 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 441 Unresolved non-hydrogen angles: 567 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 7, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 11, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 275 Chain: "Y" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 439 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 190 Chain: "Z" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 109 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 19} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "H" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3169 Classifications: {'RNA': 150} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 61, 'rna3p_pyr': 76} Link IDs: {'rna2p': 13, 'rna3p': 136} Chain breaks: 8 Chain: "h" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 376 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 117 Chain: "i" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 369 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "j" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 344 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 127 Chain: "k" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 340 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 93 Chain: "l" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 375 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 106 Chain: "m" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 407 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "n" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 323 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 1, 'TRANS': 63} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 Chain: "o" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 673 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 573 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 11, 'HIS:plan': 6, 'PHE:plan': 3, 'GLU:plan': 7, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 237 Chain: "p" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 361 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 308 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 1, 'PHE:plan': 8, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 138 Chain: "u" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 2298 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 432} Link IDs: {'PTRANS': 10, 'TRANS': 451} Chain breaks: 3 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1707 Unresolved non-hydrogen angles: 2149 Unresolved non-hydrogen dihedrals: 1455 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 25, 'TYR:plan': 26, 'ASN:plan1': 24, 'TRP:plan': 4, 'HIS:plan': 11, 'PHE:plan': 26, 'GLU:plan': 55, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1038 Chain: "w" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 633 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 594 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 284 Chain: "v" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 859 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 547 Unresolved non-hydrogen angles: 695 Unresolved non-hydrogen dihedrals: 459 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 289 Chain: "W" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 497 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 469 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 7, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 205 Chain: "0" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 830 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 593 Unresolved non-hydrogen angles: 759 Unresolved non-hydrogen dihedrals: 502 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 5, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 9, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 310 Chain: "9" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 320 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'TRANS': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 164 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 44.06, per 1000 atoms: 0.48 Number of scatterers: 91261 At special positions: 0 Unit cell: (280.98, 333.162, 315.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 157 16.00 P 596 15.00 Mg 1 11.99 O 19626 8.00 N 17167 7.00 C 53714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 31.90 Conformation dependent library (CDL) restraints added in 15.0 seconds 25774 Ramachandran restraints generated. 12887 Oldfield, 0 Emsley, 12887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 501 helices and 134 sheets defined 39.4% alpha, 14.1% beta 161 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 35.93 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 removed outlier: 4.071A pdb=" N ASP A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.772A pdb=" N GLY A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.705A pdb=" N LYS A 174 " --> pdb=" O HIS A 170 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 Processing helix chain 'A' and resid 274 through 280 removed outlier: 4.543A pdb=" N ASP A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TRP A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 473 through 480 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.574A pdb=" N PHE A 506 " --> pdb=" O LYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 564 through 586 Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.772A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 641 Processing helix chain 'A' and resid 647 through 664 removed outlier: 5.381A pdb=" N GLY A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLN A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 672 through 694 removed outlier: 3.520A pdb=" N ARG A 678 " --> pdb=" O HIS A 675 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR A 688 " --> pdb=" O HIS A 685 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN A 692 " --> pdb=" O TYR A 689 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 693 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A 694 " --> pdb=" O PHE A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 removed outlier: 3.592A pdb=" N GLY A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Proline residue: A 720 - end of helix Processing helix chain 'A' and resid 752 through 768 Processing helix chain 'A' and resid 772 through 794 removed outlier: 4.525A pdb=" N GLN A 776 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 836 Processing helix chain 'A' and resid 843 through 869 removed outlier: 3.977A pdb=" N LEU A 849 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 850 " --> pdb=" O LYS A 846 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 855 " --> pdb=" O ARG A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 893 removed outlier: 3.622A pdb=" N THR A 881 " --> pdb=" O GLU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 920 removed outlier: 5.001A pdb=" N LEU A 914 " --> pdb=" O LYS A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 943 Processing helix chain 'A' and resid 947 through 959 Processing helix chain 'A' and resid 986 through 1005 Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1063 through 1073 Processing helix chain 'A' and resid 1076 through 1086 removed outlier: 3.743A pdb=" N TYR A1081 " --> pdb=" O ASN A1077 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1126 removed outlier: 3.719A pdb=" N VAL A1120 " --> pdb=" O TYR A1116 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A1121 " --> pdb=" O TYR A1117 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1135 Processing helix chain 'A' and resid 1150 through 1154 removed outlier: 3.744A pdb=" N LYS A1154 " --> pdb=" O LYS A1150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1150 through 1154' Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1196 through 1200 removed outlier: 4.398A pdb=" N GLY A1200 " --> pdb=" O ASN A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1211 No H-bonds generated for 'chain 'A' and resid 1209 through 1211' Processing helix chain 'A' and resid 1217 through 1233 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1273 through 1276 removed outlier: 4.293A pdb=" N GLU A1276 " --> pdb=" O GLN A1273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1273 through 1276' Processing helix chain 'A' and resid 1308 through 1322 removed outlier: 3.832A pdb=" N PHE A1312 " --> pdb=" O GLU A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1345 Processing helix chain 'A' and resid 1347 through 1350 removed outlier: 4.091A pdb=" N ILE A1350 " --> pdb=" O ARG A1347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1347 through 1350' Processing helix chain 'A' and resid 1354 through 1375 removed outlier: 3.628A pdb=" N THR A1365 " --> pdb=" O VAL A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1388 No H-bonds generated for 'chain 'A' and resid 1385 through 1388' Processing helix chain 'A' and resid 1409 through 1412 Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1447 through 1471 Processing helix chain 'A' and resid 1477 through 1482 removed outlier: 3.735A pdb=" N GLY A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1495 No H-bonds generated for 'chain 'A' and resid 1492 through 1495' Processing helix chain 'A' and resid 1499 through 1502 No H-bonds generated for 'chain 'A' and resid 1499 through 1502' Processing helix chain 'A' and resid 1508 through 1518 removed outlier: 3.590A pdb=" N GLU A1513 " --> pdb=" O ARG A1509 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A1518 " --> pdb=" O PHE A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1533 No H-bonds generated for 'chain 'A' and resid 1530 through 1533' Processing helix chain 'A' and resid 1540 through 1550 removed outlier: 4.048A pdb=" N THR A1544 " --> pdb=" O ASN A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1559 removed outlier: 4.260A pdb=" N HIS A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1586 Processing helix chain 'A' and resid 1592 through 1609 removed outlier: 3.517A pdb=" N LEU A1598 " --> pdb=" O GLN A1594 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A1599 " --> pdb=" O ARG A1595 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN A1600 " --> pdb=" O THR A1596 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE A1601 " --> pdb=" O GLY A1597 " (cutoff:3.500A) Proline residue: A1602 - end of helix removed outlier: 3.942A pdb=" N PHE A1606 " --> pdb=" O PRO A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1614 No H-bonds generated for 'chain 'A' and resid 1611 through 1614' Processing helix chain 'A' and resid 1617 through 1620 No H-bonds generated for 'chain 'A' and resid 1617 through 1620' Processing helix chain 'A' and resid 1639 through 1648 removed outlier: 3.748A pdb=" N ILE A1643 " --> pdb=" O PRO A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1676 removed outlier: 4.094A pdb=" N GLY A1671 " --> pdb=" O GLN A1667 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ASP A1674 " --> pdb=" O ASP A1670 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL A1675 " --> pdb=" O GLY A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1748 through 1761 Processing helix chain 'A' and resid 1795 through 1806 removed outlier: 4.041A pdb=" N ASN A1800 " --> pdb=" O PRO A1796 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1822 removed outlier: 4.012A pdb=" N ARG A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A1822 " --> pdb=" O ARG A1818 " (cutoff:3.500A) Processing helix chain 'A' and resid 1839 through 1844 Processing helix chain 'A' and resid 1896 through 1899 No H-bonds generated for 'chain 'A' and resid 1896 through 1899' Processing helix chain 'A' and resid 1905 through 1923 Processing helix chain 'A' and resid 1938 through 1948 removed outlier: 3.919A pdb=" N ASP A1942 " --> pdb=" O ALA A1939 " (cutoff:3.500A) Proline residue: A1943 - end of helix removed outlier: 3.817A pdb=" N VAL A1946 " --> pdb=" O PRO A1943 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1970 Processing helix chain 'A' and resid 1972 through 1980 Processing helix chain 'A' and resid 2001 through 2015 Processing helix chain 'A' and resid 2019 through 2027 removed outlier: 4.234A pdb=" N ILE A2025 " --> pdb=" O SER A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2066 removed outlier: 3.540A pdb=" N ILE A2059 " --> pdb=" O MET A2055 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A2060 " --> pdb=" O ARG A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2073 No H-bonds generated for 'chain 'A' and resid 2071 through 2073' Processing helix chain 'A' and resid 2076 through 2084 Processing helix chain 'A' and resid 2153 through 2166 removed outlier: 4.204A pdb=" N THR A2160 " --> pdb=" O ALA A2156 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU A2161 " --> pdb=" O ILE A2157 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A2162 " --> pdb=" O ALA A2158 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR A2163 " --> pdb=" O ASN A2159 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU A2164 " --> pdb=" O THR A2160 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A2165 " --> pdb=" O LEU A2161 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A2166 " --> pdb=" O LEU A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2187 through 2196 Processing helix chain 'A' and resid 2271 through 2281 removed outlier: 3.620A pdb=" N THR A2276 " --> pdb=" O SER A2272 " (cutoff:3.500A) Processing helix chain 'A' and resid 2309 through 2317 removed outlier: 3.692A pdb=" N GLN A2313 " --> pdb=" O ASP A2309 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2329 Processing helix chain 'A' and resid 2389 through 2399 removed outlier: 3.679A pdb=" N LEU A2393 " --> pdb=" O PRO A2389 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A2399 " --> pdb=" O PHE A2395 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 31 Processing helix chain 'K' and resid 33 through 42 removed outlier: 3.765A pdb=" N VAL K 40 " --> pdb=" O ARG K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 58 Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 88 through 91 No H-bonds generated for 'chain 'K' and resid 88 through 91' Processing helix chain 'K' and resid 115 through 145 removed outlier: 3.853A pdb=" N LEU K 129 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU K 130 " --> pdb=" O TYR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 164 removed outlier: 3.679A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN K 160 " --> pdb=" O ARG K 156 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG K 161 " --> pdb=" O THR K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 406 No H-bonds generated for 'chain 'K' and resid 404 through 406' Processing helix chain 'L' and resid 41 through 58 Proline residue: L 48 - end of helix removed outlier: 3.593A pdb=" N ILE L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA L 58 " --> pdb=" O PHE L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 86 removed outlier: 3.708A pdb=" N ILE L 73 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU L 74 " --> pdb=" O THR L 70 " (cutoff:3.500A) Proline residue: L 75 - end of helix Processing helix chain 'L' and resid 95 through 122 Proline residue: L 103 - end of helix removed outlier: 3.669A pdb=" N SER L 118 " --> pdb=" O ASN L 114 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ARG L 122 " --> pdb=" O SER L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 130 No H-bonds generated for 'chain 'L' and resid 127 through 130' Processing helix chain 'L' and resid 134 through 145 Processing helix chain 'L' and resid 156 through 162 Processing helix chain 'L' and resid 169 through 181 Processing helix chain 'L' and resid 191 through 225 removed outlier: 5.739A pdb=" N SER L 223 " --> pdb=" O ALA L 219 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 232 Processing helix chain 'L' and resid 235 through 245 Processing helix chain 'L' and resid 248 through 253 Processing helix chain 'L' and resid 256 through 261 removed outlier: 4.058A pdb=" N ALA L 260 " --> pdb=" O CYS L 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 287 No H-bonds generated for 'chain 'L' and resid 285 through 287' Processing helix chain 'L' and resid 289 through 292 No H-bonds generated for 'chain 'L' and resid 289 through 292' Processing helix chain 'L' and resid 296 through 319 removed outlier: 4.263A pdb=" N LYS L 300 " --> pdb=" O SER L 297 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU L 303 " --> pdb=" O LYS L 300 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS L 307 " --> pdb=" O ARG L 304 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA L 308 " --> pdb=" O MET L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 345 Processing helix chain 'L' and resid 371 through 377 Processing helix chain 'L' and resid 384 through 389 removed outlier: 4.038A pdb=" N ASN L 389 " --> pdb=" O ARG L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 420 removed outlier: 3.632A pdb=" N ALA L 420 " --> pdb=" O SER L 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 416 through 420' Processing helix chain 'L' and resid 439 through 461 Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 17 through 21 Processing helix chain 'N' and resid 73 through 87 Processing helix chain 'N' and resid 99 through 113 removed outlier: 4.594A pdb=" N ASP N 106 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU N 107 " --> pdb=" O GLN N 103 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA N 112 " --> pdb=" O LYS N 108 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA N 113 " --> pdb=" O GLU N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 120 Processing helix chain 'N' and resid 131 through 141 Processing helix chain 'N' and resid 150 through 152 No H-bonds generated for 'chain 'N' and resid 150 through 152' Processing helix chain 'N' and resid 154 through 156 No H-bonds generated for 'chain 'N' and resid 154 through 156' Processing helix chain 'N' and resid 159 through 177 Processing helix chain 'N' and resid 220 through 236 Processing helix chain 'N' and resid 242 through 254 removed outlier: 4.179A pdb=" N GLU N 251 " --> pdb=" O SER N 247 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA N 254 " --> pdb=" O LEU N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 257 through 267 removed outlier: 3.897A pdb=" N LYS N 261 " --> pdb=" O PHE N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 285 Processing helix chain 'N' and resid 289 through 302 removed outlier: 3.738A pdb=" N ALA N 299 " --> pdb=" O LEU N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 320 removed outlier: 3.772A pdb=" N THR N 320 " --> pdb=" O LEU N 316 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 338 removed outlier: 3.971A pdb=" N ILE N 334 " --> pdb=" O ALA N 330 " (cutoff:3.500A) Proline residue: N 335 - end of helix removed outlier: 5.313A pdb=" N GLU N 338 " --> pdb=" O ILE N 334 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 354 Processing helix chain 'N' and resid 358 through 366 Proline residue: N 366 - end of helix Processing helix chain 'N' and resid 375 through 378 No H-bonds generated for 'chain 'N' and resid 375 through 378' Processing helix chain 'N' and resid 380 through 383 No H-bonds generated for 'chain 'N' and resid 380 through 383' Processing helix chain 'N' and resid 391 through 405 removed outlier: 4.411A pdb=" N LEU N 395 " --> pdb=" O PHE N 391 " (cutoff:3.500A) Proline residue: N 396 - end of helix Proline residue: N 399 - end of helix Processing helix chain 'N' and resid 412 through 421 Proline residue: N 417 - end of helix Processing helix chain 'N' and resid 428 through 432 Processing helix chain 'N' and resid 434 through 442 removed outlier: 6.525A pdb=" N THR N 440 " --> pdb=" O GLY N 436 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU N 441 " --> pdb=" O TYR N 437 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER N 442 " --> pdb=" O LYS N 438 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 456 Proline residue: N 455 - end of helix Processing helix chain 'N' and resid 461 through 471 removed outlier: 4.066A pdb=" N TYR N 466 " --> pdb=" O ALA N 463 " (cutoff:3.500A) Processing helix chain 'N' and resid 480 through 485 removed outlier: 3.901A pdb=" N VAL N 485 " --> pdb=" O GLU N 481 " (cutoff:3.500A) Processing helix chain 'N' and resid 487 through 495 Proline residue: N 493 - end of helix Processing helix chain 'N' and resid 504 through 516 Proline residue: N 510 - end of helix removed outlier: 4.119A pdb=" N THR N 513 " --> pdb=" O ASP N 509 " (cutoff:3.500A) Processing helix chain 'N' and resid 524 through 533 Processing helix chain 'N' and resid 544 through 548 Processing helix chain 'N' and resid 550 through 553 No H-bonds generated for 'chain 'N' and resid 550 through 553' Processing helix chain 'N' and resid 557 through 564 Processing helix chain 'N' and resid 576 through 584 Processing helix chain 'N' and resid 594 through 603 removed outlier: 3.782A pdb=" N PHE N 598 " --> pdb=" O LEU N 594 " (cutoff:3.500A) Processing helix chain 'N' and resid 615 through 623 Processing helix chain 'N' and resid 631 through 639 Processing helix chain 'N' and resid 652 through 658 Processing helix chain 'N' and resid 667 through 681 Processing helix chain 'N' and resid 686 through 697 Processing helix chain 'N' and resid 702 through 712 removed outlier: 3.598A pdb=" N VAL N 706 " --> pdb=" O LEU N 703 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER N 709 " --> pdb=" O VAL N 706 " (cutoff:3.500A) Processing helix chain 'N' and resid 722 through 732 removed outlier: 3.704A pdb=" N LYS N 732 " --> pdb=" O ARG N 728 " (cutoff:3.500A) Processing helix chain 'N' and resid 738 through 750 Processing helix chain 'N' and resid 753 through 767 Processing helix chain 'N' and resid 771 through 781 removed outlier: 4.074A pdb=" N PHE N 781 " --> pdb=" O GLN N 777 " (cutoff:3.500A) Processing helix chain 'N' and resid 788 through 801 removed outlier: 3.781A pdb=" N ALA N 797 " --> pdb=" O PHE N 794 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG N 800 " --> pdb=" O ALA N 797 " (cutoff:3.500A) Processing helix chain 'N' and resid 805 through 816 Processing helix chain 'N' and resid 821 through 834 removed outlier: 3.995A pdb=" N LYS N 826 " --> pdb=" O GLU N 822 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP N 827 " --> pdb=" O THR N 823 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS N 834 " --> pdb=" O ARG N 830 " (cutoff:3.500A) Processing helix chain 'N' and resid 839 through 851 removed outlier: 3.584A pdb=" N VAL N 843 " --> pdb=" O GLY N 839 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TRP N 844 " --> pdb=" O ASP N 840 " (cutoff:3.500A) Processing helix chain 'N' and resid 856 through 865 removed outlier: 3.882A pdb=" N TYR N 860 " --> pdb=" O THR N 856 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN N 861 " --> pdb=" O VAL N 857 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET N 862 " --> pdb=" O ASP N 858 " (cutoff:3.500A) Processing helix chain 'N' and resid 888 through 898 removed outlier: 3.570A pdb=" N ASP N 898 " --> pdb=" O ARG N 894 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 134 Processing helix chain 'J' and resid 146 through 149 Processing helix chain 'J' and resid 153 through 163 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing helix chain 'J' and resid 239 through 261 removed outlier: 3.825A pdb=" N LEU J 244 " --> pdb=" O GLU J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 277 No H-bonds generated for 'chain 'J' and resid 274 through 277' Processing helix chain 'J' and resid 290 through 328 Processing helix chain 'J' and resid 350 through 362 removed outlier: 4.039A pdb=" N SER J 360 " --> pdb=" O LEU J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 397 Processing helix chain 'J' and resid 449 through 457 Processing helix chain 'J' and resid 461 through 463 No H-bonds generated for 'chain 'J' and resid 461 through 463' Processing helix chain 'E' and resid 12 through 21 Processing helix chain 'E' and resid 38 through 53 removed outlier: 4.135A pdb=" N ASP E 43 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 74 removed outlier: 4.429A pdb=" N MET E 73 " --> pdb=" O ASP E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 126 removed outlier: 3.634A pdb=" N LYS E 126 " --> pdb=" O ARG E 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 30 removed outlier: 3.589A pdb=" N ASN M 29 " --> pdb=" O GLN M 25 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU M 30 " --> pdb=" O GLN M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 46 Processing helix chain 'M' and resid 61 through 74 removed outlier: 5.176A pdb=" N HIS M 66 " --> pdb=" O ILE M 63 " (cutoff:3.500A) Proline residue: M 68 - end of helix Processing helix chain 'M' and resid 84 through 91 Processing helix chain 'M' and resid 111 through 124 removed outlier: 4.358A pdb=" N LEU M 124 " --> pdb=" O LYS M 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 123 through 128 removed outlier: 4.570A pdb=" N ASN C 128 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 166 through 169 No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 219 through 231 removed outlier: 4.819A pdb=" N ASP C 223 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 281 through 298 removed outlier: 3.932A pdb=" N PHE C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 410 through 413 No H-bonds generated for 'chain 'C' and resid 410 through 413' Processing helix chain 'C' and resid 417 through 428 Processing helix chain 'C' and resid 434 through 442 Processing helix chain 'C' and resid 445 through 455 removed outlier: 4.665A pdb=" N ASP C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 570 Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 612 through 628 Proline residue: C 616 - end of helix Processing helix chain 'C' and resid 649 through 660 Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 737 through 740 Processing helix chain 'C' and resid 744 through 755 Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 779 through 804 Proline residue: C 785 - end of helix removed outlier: 3.595A pdb=" N TYR C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 853 Proline residue: C 840 - end of helix removed outlier: 3.558A pdb=" N ALA C 853 " --> pdb=" O GLY C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 883 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 914 through 921 Processing helix chain 'C' and resid 963 through 973 Processing helix chain 'z' and resid 6 through 8 No H-bonds generated for 'chain 'z' and resid 6 through 8' Processing helix chain 'z' and resid 58 through 60 No H-bonds generated for 'chain 'z' and resid 58 through 60' Processing helix chain 'q' and resid 2 through 10 removed outlier: 3.622A pdb=" N THR q 9 " --> pdb=" O SER q 5 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU q 10 " --> pdb=" O PHE q 6 " (cutoff:3.500A) Processing helix chain 'q' and resid 64 through 66 No H-bonds generated for 'chain 'q' and resid 64 through 66' Processing helix chain 'q' and resid 74 through 76 No H-bonds generated for 'chain 'q' and resid 74 through 76' Processing helix chain 'q' and resid 79 through 88 Processing helix chain 'r' and resid 70 through 72 No H-bonds generated for 'chain 'r' and resid 70 through 72' Processing helix chain 'x' and resid 12 through 18 Processing helix chain 'x' and resid 75 through 77 No H-bonds generated for 'chain 'x' and resid 75 through 77' Processing helix chain 't' and resid 8 through 14 Processing helix chain 't' and resid 75 through 77 No H-bonds generated for 'chain 't' and resid 75 through 77' Processing helix chain 'y' and resid 30 through 33 Processing helix chain 's' and resid 3 through 9 Processing helix chain 's' and resid 73 through 75 No H-bonds generated for 'chain 's' and resid 73 through 75' Processing helix chain 's' and resid 83 through 86 removed outlier: 4.192A pdb=" N ILE s 86 " --> pdb=" O ASP s 83 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 83 through 86' Processing helix chain 'O' and resid 169 through 172 No H-bonds generated for 'chain 'O' and resid 169 through 172' Processing helix chain 'O' and resid 182 through 206 removed outlier: 3.542A pdb=" N GLU O 186 " --> pdb=" O VAL O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 222 Processing helix chain 'd' and resid 6 through 14 removed outlier: 4.196A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' and resid 66 through 68' Processing helix chain 'd' and resid 76 through 79 Processing helix chain 'a' and resid 10 through 14 removed outlier: 3.652A pdb=" N ASN a 14 " --> pdb=" O SER a 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 10 through 14' Processing helix chain 'b' and resid 4 through 7 No H-bonds generated for 'chain 'b' and resid 4 through 7' Processing helix chain 'b' and resid 103 through 106 No H-bonds generated for 'chain 'b' and resid 103 through 106' Processing helix chain 'c' and resid 22 through 28 removed outlier: 3.646A pdb=" N PHE c 26 " --> pdb=" O GLU c 22 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS c 27 " --> pdb=" O GLU c 23 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS c 28 " --> pdb=" O PHE c 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 22 through 28' Processing helix chain 'c' and resid 30 through 39 removed outlier: 3.759A pdb=" N ASP c 36 " --> pdb=" O LEU c 33 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET c 38 " --> pdb=" O ASN c 35 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL c 39 " --> pdb=" O ASP c 36 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 100 No H-bonds generated for 'chain 'c' and resid 98 through 100' Processing helix chain 'e' and resid 13 through 22 removed outlier: 3.644A pdb=" N PHE e 20 " --> pdb=" O CYS e 16 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU e 21 " --> pdb=" O ILE e 17 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN e 22 " --> pdb=" O PHE e 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 22 Processing helix chain 'g' and resid 8 through 10 No H-bonds generated for 'chain 'g' and resid 8 through 10' Processing helix chain 'D' and resid 486 through 489 removed outlier: 3.637A pdb=" N GLU D 489 " --> pdb=" O TRP D 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 486 through 489' Processing helix chain 'D' and resid 503 through 512 Processing helix chain 'D' and resid 526 through 541 Processing helix chain 'D' and resid 564 through 581 removed outlier: 5.635A pdb=" N PHE D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU D 581 " --> pdb=" O ARG D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 596 through 601 removed outlier: 4.212A pdb=" N ASP D 600 " --> pdb=" O ARG D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 617 Processing helix chain 'D' and resid 619 through 627 removed outlier: 3.646A pdb=" N LEU D 622 " --> pdb=" O SER D 619 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA D 623 " --> pdb=" O ASN D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 644 through 656 Processing helix chain 'D' and resid 677 through 683 Processing helix chain 'D' and resid 696 through 698 No H-bonds generated for 'chain 'D' and resid 696 through 698' Processing helix chain 'D' and resid 715 through 736 removed outlier: 3.672A pdb=" N LYS D 720 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 735 " --> pdb=" O LEU D 731 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU D 736 " --> pdb=" O GLU D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 764 removed outlier: 3.838A pdb=" N SER D 751 " --> pdb=" O ARG D 747 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 752 " --> pdb=" O LYS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 788 removed outlier: 3.880A pdb=" N ASN D 787 " --> pdb=" O THR D 783 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 788 " --> pdb=" O GLU D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 799 Processing helix chain 'D' and resid 810 through 822 Processing helix chain 'D' and resid 833 through 837 Processing helix chain 'D' and resid 865 through 873 removed outlier: 3.554A pdb=" N GLN D 870 " --> pdb=" O GLN D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 903 removed outlier: 4.317A pdb=" N GLN D 896 " --> pdb=" O GLN D 892 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR D 897 " --> pdb=" O SER D 893 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 900 " --> pdb=" O GLN D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 926 Processing helix chain 'D' and resid 932 through 940 Processing helix chain 'D' and resid 943 through 950 Processing helix chain 'D' and resid 967 through 983 removed outlier: 3.563A pdb=" N ILE D 980 " --> pdb=" O SER D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1008 Processing helix chain 'D' and resid 1012 through 1021 Processing helix chain 'D' and resid 1028 through 1037 removed outlier: 3.664A pdb=" N PHE D1032 " --> pdb=" O GLN D1028 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG D1033 " --> pdb=" O ILE D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1041 No H-bonds generated for 'chain 'D' and resid 1039 through 1041' Processing helix chain 'D' and resid 1051 through 1060 removed outlier: 3.603A pdb=" N GLU D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS D1060 " --> pdb=" O GLN D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1072 through 1084 Processing helix chain 'D' and resid 1092 through 1119 removed outlier: 4.828A pdb=" N GLY D1106 " --> pdb=" O HIS D1102 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG D1107 " --> pdb=" O GLN D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1137 removed outlier: 3.745A pdb=" N ARG D1126 " --> pdb=" O GLY D1122 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET D1127 " --> pdb=" O HIS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1145 through 1148 Processing helix chain 'D' and resid 1154 through 1163 Processing helix chain 'D' and resid 1167 through 1172 Processing helix chain 'D' and resid 1176 through 1182 Processing helix chain 'D' and resid 1189 through 1197 Processing helix chain 'D' and resid 1278 through 1282 Processing helix chain 'D' and resid 1337 through 1341 removed outlier: 3.766A pdb=" N GLU D1341 " --> pdb=" O ASP D1338 " (cutoff:3.500A) Processing helix chain 'D' and resid 1350 through 1360 removed outlier: 3.587A pdb=" N GLN D1354 " --> pdb=" O LYS D1350 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU D1357 " --> pdb=" O SER D1353 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N SER D1358 " --> pdb=" O GLN D1354 " (cutoff:3.500A) Processing helix chain 'D' and resid 1376 through 1390 removed outlier: 3.736A pdb=" N GLN D1390 " --> pdb=" O ASN D1386 " (cutoff:3.500A) Processing helix chain 'D' and resid 1402 through 1413 Processing helix chain 'D' and resid 1416 through 1420 removed outlier: 3.658A pdb=" N ALA D1420 " --> pdb=" O PHE D1416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1416 through 1420' Processing helix chain 'D' and resid 1432 through 1441 Processing helix chain 'D' and resid 1449 through 1457 Processing helix chain 'D' and resid 1463 through 1467 removed outlier: 3.648A pdb=" N SER D1467 " --> pdb=" O LYS D1463 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1463 through 1467' Processing helix chain 'D' and resid 1476 through 1480 Processing helix chain 'D' and resid 1482 through 1502 removed outlier: 3.699A pdb=" N ALA D1486 " --> pdb=" O GLY D1482 " (cutoff:3.500A) Processing helix chain 'D' and resid 1518 through 1525 removed outlier: 3.525A pdb=" N ALA D1525 " --> pdb=" O PHE D1521 " (cutoff:3.500A) Processing helix chain 'D' and resid 1537 through 1539 No H-bonds generated for 'chain 'D' and resid 1537 through 1539' Processing helix chain 'D' and resid 1561 through 1576 Processing helix chain 'D' and resid 1588 through 1604 removed outlier: 3.931A pdb=" N ALA D1604 " --> pdb=" O LYS D1600 " (cutoff:3.500A) Processing helix chain 'D' and resid 1614 through 1620 removed outlier: 4.488A pdb=" N VAL D1618 " --> pdb=" O GLU D1614 " (cutoff:3.500A) Proline residue: D1619 - end of helix No H-bonds generated for 'chain 'D' and resid 1614 through 1620' Processing helix chain 'D' and resid 1629 through 1635 removed outlier: 3.837A pdb=" N HIS D1635 " --> pdb=" O ALA D1631 " (cutoff:3.500A) Processing helix chain 'D' and resid 1646 through 1658 Processing helix chain 'D' and resid 1668 through 1672 removed outlier: 4.103A pdb=" N ALA D1672 " --> pdb=" O ASP D1669 " (cutoff:3.500A) Processing helix chain 'D' and resid 1700 through 1707 Processing helix chain 'D' and resid 1726 through 1737 removed outlier: 4.370A pdb=" N ALA D1730 " --> pdb=" O HIS D1726 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR D1731 " --> pdb=" O ASN D1727 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE D1737 " --> pdb=" O LYS D1733 " (cutoff:3.500A) Processing helix chain 'D' and resid 1746 through 1760 removed outlier: 5.871A pdb=" N HIS D1751 " --> pdb=" O GLN D1747 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP D1752 " --> pdb=" O TYR D1748 " (cutoff:3.500A) Processing helix chain 'D' and resid 1766 through 1774 Processing helix chain 'D' and resid 1777 through 1784 Processing helix chain 'D' and resid 1786 through 1789 No H-bonds generated for 'chain 'D' and resid 1786 through 1789' Processing helix chain 'D' and resid 1796 through 1816 Processing helix chain 'D' and resid 1848 through 1856 Processing helix chain 'D' and resid 1860 through 1869 Processing helix chain 'D' and resid 1876 through 1884 Processing helix chain 'D' and resid 1888 through 1891 removed outlier: 4.098A pdb=" N SER D1891 " --> pdb=" O GLU D1888 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1888 through 1891' Processing helix chain 'D' and resid 1897 through 1908 removed outlier: 4.284A pdb=" N LYS D1907 " --> pdb=" O VAL D1903 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG D1908 " --> pdb=" O LYS D1904 " (cutoff:3.500A) Processing helix chain 'D' and resid 1922 through 1934 Processing helix chain 'D' and resid 1941 through 1967 removed outlier: 3.731A pdb=" N ASN D1945 " --> pdb=" O VAL D1941 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP D1946 " --> pdb=" O ASP D1942 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL D1955 " --> pdb=" O LEU D1951 " (cutoff:3.500A) Proline residue: D1956 - end of helix Processing helix chain 'D' and resid 1971 through 1985 removed outlier: 3.621A pdb=" N GLN D1985 " --> pdb=" O MET D1982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1994 through 1996 No H-bonds generated for 'chain 'D' and resid 1994 through 1996' Processing helix chain 'D' and resid 2002 through 2010 Processing helix chain 'D' and resid 2017 through 2021 removed outlier: 3.721A pdb=" N ALA D2021 " --> pdb=" O TYR D2017 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2017 through 2021' Processing helix chain 'D' and resid 2024 through 2030 Processing helix chain 'D' and resid 2035 through 2047 Processing helix chain 'Q' and resid 3 through 10 removed outlier: 3.815A pdb=" N LEU Q 10 " --> pdb=" O PHE Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'Q' and resid 103 through 107 Processing helix chain 'Q' and resid 110 through 118 Processing helix chain 'R' and resid 18 through 28 Processing helix chain 'R' and resid 30 through 40 removed outlier: 3.661A pdb=" N ASN R 35 " --> pdb=" O SER R 32 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP R 36 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR R 40 " --> pdb=" O ALA R 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 13 Processing helix chain 'S' and resid 76 through 80 removed outlier: 3.642A pdb=" N ASN S 80 " --> pdb=" O LEU S 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 23 Processing helix chain 'U' and resid 15 through 22 Processing helix chain 'U' and resid 75 through 77 No H-bonds generated for 'chain 'U' and resid 75 through 77' Processing helix chain 'V' and resid 8 through 10 No H-bonds generated for 'chain 'V' and resid 8 through 10' Processing helix chain '1' and resid 159 through 174 removed outlier: 3.804A pdb=" N SER 1 167 " --> pdb=" O GLU 1 163 " (cutoff:3.500A) Processing helix chain '1' and resid 178 through 191 removed outlier: 3.857A pdb=" N THR 1 183 " --> pdb=" O ALA 1 179 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG 1 186 " --> pdb=" O ARG 1 182 " (cutoff:3.500A) Processing helix chain '1' and resid 197 through 209 Proline residue: 1 206 - end of helix removed outlier: 3.845A pdb=" N LEU 1 209 " --> pdb=" O LEU 1 205 " (cutoff:3.500A) Processing helix chain '1' and resid 215 through 232 removed outlier: 3.661A pdb=" N LEU 1 220 " --> pdb=" O GLN 1 216 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET 1 221 " --> pdb=" O GLU 1 217 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR 1 224 " --> pdb=" O LEU 1 220 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN 1 231 " --> pdb=" O ARG 1 227 " (cutoff:3.500A) Processing helix chain '1' and resid 237 through 252 Proline residue: 1 249 - end of helix removed outlier: 4.340A pdb=" N ILE 1 252 " --> pdb=" O ALA 1 248 " (cutoff:3.500A) Processing helix chain '1' and resid 256 through 272 removed outlier: 3.727A pdb=" N ILE 1 265 " --> pdb=" O THR 1 261 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE 1 266 " --> pdb=" O GLY 1 262 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR 1 271 " --> pdb=" O THR 1 267 " (cutoff:3.500A) Processing helix chain '1' and resid 274 through 286 removed outlier: 3.896A pdb=" N ILE 1 278 " --> pdb=" O GLY 1 274 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 1 279 " --> pdb=" O LEU 1 275 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR 1 280 " --> pdb=" O LYS 1 276 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG 1 283 " --> pdb=" O LEU 1 279 " (cutoff:3.500A) Proline residue: 1 284 - end of helix Processing helix chain '1' and resid 291 through 308 removed outlier: 3.948A pdb=" N ARG 1 299 " --> pdb=" O ASN 1 295 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 321 Proline residue: 1 315 - end of helix Processing helix chain '1' and resid 327 through 343 removed outlier: 4.065A pdb=" N VAL 1 337 " --> pdb=" O GLY 1 333 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN 1 338 " --> pdb=" O ILE 1 334 " (cutoff:3.500A) Processing helix chain '1' and resid 345 through 347 No H-bonds generated for 'chain '1' and resid 345 through 347' Processing helix chain '1' and resid 349 through 364 removed outlier: 4.495A pdb=" N THR 1 353 " --> pdb=" O ASN 1 350 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU 1 355 " --> pdb=" O LEU 1 352 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE 1 359 " --> pdb=" O MET 1 356 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS 1 360 " --> pdb=" O SER 1 357 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP 1 361 " --> pdb=" O CYS 1 358 " (cutoff:3.500A) Processing helix chain '1' and resid 368 through 385 removed outlier: 3.541A pdb=" N VAL 1 373 " --> pdb=" O PRO 1 369 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA 1 375 " --> pdb=" O ARG 1 371 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER 1 379 " --> pdb=" O ALA 1 375 " (cutoff:3.500A) Processing helix chain '1' and resid 390 through 392 No H-bonds generated for 'chain '1' and resid 390 through 392' Processing helix chain '1' and resid 394 through 404 removed outlier: 4.192A pdb=" N GLU 1 398 " --> pdb=" O ASN 1 394 " (cutoff:3.500A) Proline residue: 1 399 - end of helix removed outlier: 3.741A pdb=" N LYS 1 402 " --> pdb=" O GLU 1 398 " (cutoff:3.500A) Processing helix chain '1' and resid 411 through 425 removed outlier: 3.500A pdb=" N ILE 1 423 " --> pdb=" O VAL 1 419 " (cutoff:3.500A) Proline residue: 1 424 - end of helix Processing helix chain '1' and resid 428 through 445 removed outlier: 3.582A pdb=" N GLY 1 432 " --> pdb=" O PRO 1 428 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR 1 433 " --> pdb=" O GLU 1 429 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR 1 436 " --> pdb=" O GLY 1 432 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG 1 440 " --> pdb=" O THR 1 436 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE 1 441 " --> pdb=" O GLU 1 437 " (cutoff:3.500A) Processing helix chain '1' and resid 451 through 466 removed outlier: 3.526A pdb=" N LEU 1 459 " --> pdb=" O LYS 1 455 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER 1 465 " --> pdb=" O LEU 1 461 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA 1 466 " --> pdb=" O GLN 1 462 " (cutoff:3.500A) Processing helix chain '1' and resid 472 through 477 Processing helix chain '1' and resid 479 through 487 removed outlier: 3.725A pdb=" N GLN 1 485 " --> pdb=" O PRO 1 481 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS 1 486 " --> pdb=" O GLU 1 482 " (cutoff:3.500A) Processing helix chain '1' and resid 490 through 494 removed outlier: 3.748A pdb=" N LEU 1 494 " --> pdb=" O ARG 1 490 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 490 through 494' Processing helix chain '1' and resid 496 through 512 removed outlier: 4.208A pdb=" N VAL 1 501 " --> pdb=" O PRO 1 497 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS 1 511 " --> pdb=" O VAL 1 507 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS 1 512 " --> pdb=" O THR 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 515 through 521 Processing helix chain '1' and resid 523 through 526 No H-bonds generated for 'chain '1' and resid 523 through 526' Processing helix chain '1' and resid 531 through 548 removed outlier: 3.506A pdb=" N MET 1 536 " --> pdb=" O PRO 1 532 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL 1 541 " --> pdb=" O ALA 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 550 through 552 No H-bonds generated for 'chain '1' and resid 550 through 552' Processing helix chain '1' and resid 555 through 570 removed outlier: 3.711A pdb=" N ILE 1 562 " --> pdb=" O GLU 1 558 " (cutoff:3.500A) Processing helix chain '1' and resid 577 through 589 removed outlier: 3.652A pdb=" N LYS 1 581 " --> pdb=" O ILE 1 578 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE 1 583 " --> pdb=" O PHE 1 580 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL 1 586 " --> pdb=" O PHE 1 583 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR 1 587 " --> pdb=" O GLY 1 584 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL 1 588 " --> pdb=" O ALA 1 585 " (cutoff:3.500A) Processing helix chain '1' and resid 591 through 610 removed outlier: 3.639A pdb=" N LYS 1 595 " --> pdb=" O ILE 1 592 " (cutoff:3.500A) Proline residue: 1 596 - end of helix removed outlier: 3.886A pdb=" N ALA 1 599 " --> pdb=" O PRO 1 596 " (cutoff:3.500A) Proline residue: 1 600 - end of helix removed outlier: 3.904A pdb=" N LEU 1 609 " --> pdb=" O LEU 1 606 " (cutoff:3.500A) Processing helix chain '1' and resid 614 through 622 Processing helix chain '1' and resid 624 through 634 Proline residue: 1 629 - end of helix removed outlier: 4.065A pdb=" N ASN 1 633 " --> pdb=" O PRO 1 629 " (cutoff:3.500A) Processing helix chain '1' and resid 637 through 649 Processing helix chain '1' and resid 656 through 672 removed outlier: 3.835A pdb=" N SER 1 661 " --> pdb=" O GLU 1 657 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL 1 672 " --> pdb=" O CYS 1 668 " (cutoff:3.500A) Processing helix chain '1' and resid 682 through 690 Proline residue: 1 687 - end of helix Processing helix chain '1' and resid 699 through 714 Processing helix chain '1' and resid 721 through 732 Processing helix chain '1' and resid 734 through 736 No H-bonds generated for 'chain '1' and resid 734 through 736' Processing helix chain '1' and resid 740 through 756 removed outlier: 3.675A pdb=" N PHE 1 750 " --> pdb=" O ALA 1 746 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY 1 751 " --> pdb=" O ASN 1 747 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE 1 752 " --> pdb=" O ALA 1 748 " (cutoff:3.500A) Processing helix chain '1' and resid 759 through 769 removed outlier: 3.679A pdb=" N VAL 1 764 " --> pdb=" O HIS 1 760 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA 1 765 " --> pdb=" O ASP 1 761 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN 1 769 " --> pdb=" O ALA 1 765 " (cutoff:3.500A) Processing helix chain '1' and resid 775 through 792 removed outlier: 3.541A pdb=" N ALA 1 784 " --> pdb=" O CYS 1 780 " (cutoff:3.500A) Processing helix chain '1' and resid 794 through 806 Proline residue: 1 799 - end of helix removed outlier: 4.207A pdb=" N THR 1 806 " --> pdb=" O MET 1 802 " (cutoff:3.500A) Processing helix chain '1' and resid 810 through 826 removed outlier: 3.540A pdb=" N MET 1 820 " --> pdb=" O VAL 1 816 " (cutoff:3.500A) Processing helix chain '1' and resid 835 through 838 No H-bonds generated for 'chain '1' and resid 835 through 838' Processing helix chain '1' and resid 841 through 846 removed outlier: 3.619A pdb=" N ALA 1 845 " --> pdb=" O LEU 1 841 " (cutoff:3.500A) Processing helix chain '1' and resid 853 through 856 No H-bonds generated for 'chain '1' and resid 853 through 856' Processing helix chain '1' and resid 858 through 868 removed outlier: 4.170A pdb=" N HIS 1 863 " --> pdb=" O ASN 1 859 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN 1 867 " --> pdb=" O HIS 1 863 " (cutoff:3.500A) Processing helix chain '1' and resid 876 through 889 removed outlier: 3.520A pdb=" N LEU 1 884 " --> pdb=" O LEU 1 880 " (cutoff:3.500A) Proline residue: 1 886 - end of helix removed outlier: 4.851A pdb=" N PHE 1 889 " --> pdb=" O ILE 1 885 " (cutoff:3.500A) Processing helix chain '1' and resid 893 through 910 removed outlier: 3.690A pdb=" N ARG 1 898 " --> pdb=" O HIS 1 894 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN 1 908 " --> pdb=" O GLU 1 904 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA 1 909 " --> pdb=" O ALA 1 905 " (cutoff:3.500A) Processing helix chain '1' and resid 912 through 918 removed outlier: 4.870A pdb=" N TYR 1 918 " --> pdb=" O LEU 1 914 " (cutoff:3.500A) Processing helix chain '1' and resid 921 through 923 No H-bonds generated for 'chain '1' and resid 921 through 923' Processing helix chain '1' and resid 930 through 944 removed outlier: 3.719A pdb=" N ARG 1 936 " --> pdb=" O LYS 1 932 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL 1 937 " --> pdb=" O ALA 1 933 " (cutoff:3.500A) Processing helix chain '1' and resid 950 through 952 No H-bonds generated for 'chain '1' and resid 950 through 952' Processing helix chain '1' and resid 965 through 967 No H-bonds generated for 'chain '1' and resid 965 through 967' Processing helix chain '2' and resid 134 through 137 No H-bonds generated for 'chain '2' and resid 134 through 137' Processing helix chain '2' and resid 149 through 153 removed outlier: 3.588A pdb=" N CYS 2 152 " --> pdb=" O TRP 2 149 " (cutoff:3.500A) Processing helix chain '2' and resid 157 through 164 removed outlier: 3.592A pdb=" N SER 2 162 " --> pdb=" O GLY 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 185 through 190 removed outlier: 4.939A pdb=" N GLY 2 190 " --> pdb=" O ARG 2 186 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 203 removed outlier: 4.059A pdb=" N THR 2 203 " --> pdb=" O ILE 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 205 through 208 No H-bonds generated for 'chain '2' and resid 205 through 208' Processing helix chain '2' and resid 244 through 251 removed outlier: 3.756A pdb=" N PHE 2 251 " --> pdb=" O LEU 2 247 " (cutoff:3.500A) Processing helix chain '2' and resid 276 through 288 removed outlier: 3.570A pdb=" N ASN 2 281 " --> pdb=" O PHE 2 277 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS 2 288 " --> pdb=" O ARG 2 284 " (cutoff:3.500A) Processing helix chain '2' and resid 296 through 302 Processing helix chain '2' and resid 313 through 319 Processing helix chain '2' and resid 337 through 339 No H-bonds generated for 'chain '2' and resid 337 through 339' Processing helix chain '2' and resid 362 through 364 No H-bonds generated for 'chain '2' and resid 362 through 364' Processing helix chain '3' and resid 1145 through 1153 removed outlier: 3.599A pdb=" N ILE 31150 " --> pdb=" O GLU 31146 " (cutoff:3.500A) Processing helix chain '3' and resid 1156 through 1160 removed outlier: 3.956A pdb=" N SER 31160 " --> pdb=" O SER 31157 " (cutoff:3.500A) Processing helix chain '3' and resid 1168 through 1176 Processing helix chain '3' and resid 1234 through 1248 removed outlier: 3.640A pdb=" N PHE 31238 " --> pdb=" O LYS 31234 " (cutoff:3.500A) Processing helix chain '3' and resid 1250 through 1263 removed outlier: 3.690A pdb=" N TYR 31255 " --> pdb=" O ASP 31251 " (cutoff:3.500A) Processing helix chain '3' and resid 1304 through 1309 Processing helix chain '3' and resid 1325 through 1327 No H-bonds generated for 'chain '3' and resid 1325 through 1327' Processing helix chain '3' and resid 1331 through 1340 removed outlier: 3.834A pdb=" N LYS 31339 " --> pdb=" O GLU 31335 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASN 31340 " --> pdb=" O PHE 31336 " (cutoff:3.500A) Processing helix chain '3' and resid 1346 through 1358 removed outlier: 4.072A pdb=" N VAL 31356 " --> pdb=" O THR 31352 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG 31357 " --> pdb=" O ILE 31353 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR 31358 " --> pdb=" O ASN 31354 " (cutoff:3.500A) Processing helix chain '4' and resid 22 through 31 removed outlier: 3.738A pdb=" N GLN 4 31 " --> pdb=" O GLU 4 27 " (cutoff:3.500A) Processing helix chain '4' and resid 60 through 70 Processing helix chain '4' and resid 121 through 129 Processing helix chain '4' and resid 158 through 168 Processing helix chain '4' and resid 192 through 202 Processing helix chain '5' and resid 47 through 49 No H-bonds generated for 'chain '5' and resid 47 through 49' Processing helix chain '5' and resid 53 through 56 No H-bonds generated for 'chain '5' and resid 53 through 56' Processing helix chain '5' and resid 74 through 78 Processing helix chain '5' and resid 81 through 84 removed outlier: 3.728A pdb=" N ASP 5 84 " --> pdb=" O LYS 5 81 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 81 through 84' Processing helix chain '5' and resid 93 through 103 removed outlier: 3.618A pdb=" N LEU 5 97 " --> pdb=" O GLY 5 93 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 18 removed outlier: 3.891A pdb=" N LYS 6 9 " --> pdb=" O GLN 6 5 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN 6 16 " --> pdb=" O LYS 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 28 through 45 removed outlier: 3.728A pdb=" N ASN 6 34 " --> pdb=" O GLN 6 30 " (cutoff:3.500A) Processing helix chain '6' and resid 47 through 57 removed outlier: 3.654A pdb=" N VAL 6 53 " --> pdb=" O SER 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 62 through 73 removed outlier: 3.698A pdb=" N MET 6 73 " --> pdb=" O LEU 6 69 " (cutoff:3.500A) Processing helix chain '6' and resid 75 through 82 removed outlier: 3.873A pdb=" N LYS 6 78 " --> pdb=" O PRO 6 75 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA 6 79 " --> pdb=" O GLY 6 76 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR 6 80 " --> pdb=" O TYR 6 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 13 removed outlier: 3.691A pdb=" N ASP X 9 " --> pdb=" O GLN X 5 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS X 10 " --> pdb=" O GLN X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 21 No H-bonds generated for 'chain 'X' and resid 19 through 21' Processing helix chain 'X' and resid 23 through 26 Processing helix chain 'X' and resid 44 through 52 removed outlier: 3.536A pdb=" N VAL X 50 " --> pdb=" O ASP X 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE X 51 " --> pdb=" O ILE X 47 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N SER X 52 " --> pdb=" O LEU X 48 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 92 removed outlier: 4.201A pdb=" N VAL X 89 " --> pdb=" O ILE X 86 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP X 90 " --> pdb=" O LEU X 87 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN X 91 " --> pdb=" O ALA X 88 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU X 92 " --> pdb=" O VAL X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 127 removed outlier: 5.335A pdb=" N LYS X 117 " --> pdb=" O SER X 114 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA X 121 " --> pdb=" O TYR X 118 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU X 124 " --> pdb=" O ALA X 121 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 163 Processing helix chain 'Y' and resid 166 through 170 Processing helix chain 'Y' and resid 241 through 261 removed outlier: 3.780A pdb=" N PHE Y 246 " --> pdb=" O GLU Y 242 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS Y 256 " --> pdb=" O ILE Y 252 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL Y 257 " --> pdb=" O ASN Y 253 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR Y 260 " --> pdb=" O LYS Y 256 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 42 removed outlier: 4.142A pdb=" N SER Z 42 " --> pdb=" O LEU Z 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 15 No H-bonds generated for 'chain 'h' and resid 13 through 15' Processing helix chain 'i' and resid 13 through 23 Processing helix chain 'i' and resid 84 through 86 No H-bonds generated for 'chain 'i' and resid 84 through 86' Processing helix chain 'j' and resid 15 through 21 Processing helix chain 'j' and resid 75 through 77 No H-bonds generated for 'chain 'j' and resid 75 through 77' Processing helix chain 'l' and resid 6 through 14 Processing helix chain 'm' and resid 3 through 9 Processing helix chain 'm' and resid 103 through 107 Processing helix chain 'o' and resid 5 through 10 removed outlier: 3.512A pdb=" N ASP o 10 " --> pdb=" O SER o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 47 through 50 Processing helix chain 'o' and resid 111 through 119 removed outlier: 4.608A pdb=" N ARG o 116 " --> pdb=" O ASP o 113 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG o 119 " --> pdb=" O ARG o 116 " (cutoff:3.500A) Processing helix chain 'o' and resid 133 through 136 Processing helix chain 'o' and resid 140 through 147 Processing helix chain 'p' and resid 41 through 55 removed outlier: 4.197A pdb=" N THR p 54 " --> pdb=" O LEU p 50 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE p 55 " --> pdb=" O LEU p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 79 through 88 Processing helix chain 'u' and resid 3 through 27 Processing helix chain 'u' and resid 29 through 42 removed outlier: 4.415A pdb=" N HIS u 34 " --> pdb=" O LEU u 31 " (cutoff:3.500A) Processing helix chain 'u' and resid 51 through 56 Processing helix chain 'u' and resid 69 through 96 Processing helix chain 'u' and resid 113 through 124 removed outlier: 3.555A pdb=" N GLU u 122 " --> pdb=" O GLN u 118 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS u 124 " --> pdb=" O GLU u 120 " (cutoff:3.500A) Processing helix chain 'u' and resid 137 through 144 Processing helix chain 'u' and resid 159 through 161 No H-bonds generated for 'chain 'u' and resid 159 through 161' Processing helix chain 'u' and resid 166 through 168 No H-bonds generated for 'chain 'u' and resid 166 through 168' Processing helix chain 'u' and resid 175 through 177 No H-bonds generated for 'chain 'u' and resid 175 through 177' Processing helix chain 'u' and resid 183 through 193 Processing helix chain 'u' and resid 200 through 211 removed outlier: 3.996A pdb=" N LEU u 209 " --> pdb=" O ASP u 205 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE u 210 " --> pdb=" O ILE u 206 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU u 211 " --> pdb=" O LEU u 207 " (cutoff:3.500A) Processing helix chain 'u' and resid 215 through 218 No H-bonds generated for 'chain 'u' and resid 215 through 218' Processing helix chain 'u' and resid 227 through 247 Processing helix chain 'u' and resid 253 through 266 Processing helix chain 'u' and resid 268 through 270 No H-bonds generated for 'chain 'u' and resid 268 through 270' Processing helix chain 'u' and resid 292 through 296 Processing helix chain 'u' and resid 302 through 310 Processing helix chain 'u' and resid 312 through 327 Processing helix chain 'u' and resid 329 through 344 Processing helix chain 'u' and resid 347 through 361 Processing helix chain 'u' and resid 409 through 415 removed outlier: 3.520A pdb=" N LYS u 413 " --> pdb=" O TYR u 409 " (cutoff:3.500A) Processing helix chain 'u' and resid 434 through 440 Processing helix chain 'u' and resid 444 through 453 Processing helix chain 'u' and resid 469 through 477 Processing helix chain 'u' and resid 513 through 515 No H-bonds generated for 'chain 'u' and resid 513 through 515' Processing helix chain 'u' and resid 518 through 527 Processing helix chain 'w' and resid 90 through 103 Processing helix chain 'w' and resid 109 through 116 removed outlier: 4.099A pdb=" N SER w 115 " --> pdb=" O GLU w 111 " (cutoff:3.500A) Processing helix chain 'w' and resid 123 through 125 No H-bonds generated for 'chain 'w' and resid 123 through 125' Processing helix chain 'w' and resid 130 through 145 removed outlier: 4.146A pdb=" N VAL w 139 " --> pdb=" O THR w 136 " (cutoff:3.500A) Processing helix chain 'w' and resid 157 through 194 Processing helix chain 'v' and resid 78 through 85 Processing helix chain 'v' and resid 89 through 102 removed outlier: 3.761A pdb=" N VAL v 94 " --> pdb=" O HIS v 90 " (cutoff:3.500A) Processing helix chain 'v' and resid 235 through 239 Processing helix chain 'W' and resid 34 through 44 Processing helix chain 'W' and resid 46 through 49 No H-bonds generated for 'chain 'W' and resid 46 through 49' Processing helix chain 'W' and resid 92 through 100 Processing helix chain 'W' and resid 102 through 111 Processing helix chain 'W' and resid 129 through 145 Processing helix chain '0' and resid 23 through 25 No H-bonds generated for 'chain '0' and resid 23 through 25' Processing helix chain '0' and resid 28 through 35 Processing helix chain '0' and resid 38 through 43 Processing helix chain '0' and resid 45 through 49 Processing helix chain '0' and resid 54 through 63 Processing helix chain '0' and resid 84 through 95 Processing helix chain '0' and resid 99 through 107 Processing helix chain '0' and resid 119 through 130 Processing helix chain '0' and resid 145 through 159 Processing helix chain '0' and resid 188 through 197 Processing helix chain '9' and resid 125 through 150 Processing helix chain '9' and resid 182 through 215 Processing sheet with id= A, first strand: chain 'A' and resid 557 through 563 Processing sheet with id= B, first strand: chain 'A' and resid 968 through 971 Processing sheet with id= C, first strand: chain 'A' and resid 1246 through 1251 removed outlier: 3.823A pdb=" N MET A1170 " --> pdb=" O LEU A1050 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1160 " --> pdb=" O LEU A1171 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N HIS A1173 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE A1158 " --> pdb=" O HIS A1173 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id= E, first strand: chain 'A' and resid 1258 through 1261 removed outlier: 7.199A pdb=" N LEU A1288 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS A1299 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TRP A1286 " --> pdb=" O LYS A1299 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1414 through 1417 Processing sheet with id= G, first strand: chain 'A' and resid 1573 through 1575 Processing sheet with id= H, first strand: chain 'A' and resid 1681 through 1683 removed outlier: 3.676A pdb=" N MET A1774 " --> pdb=" O TYR A1787 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1889 through 1894 removed outlier: 3.504A pdb=" N VAL A1852 " --> pdb=" O ILE A1934 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA A1955 " --> pdb=" O ILE A1933 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL A1935 " --> pdb=" O ALA A1955 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG A1957 " --> pdb=" O VAL A1935 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1859 through 1863 removed outlier: 4.148A pdb=" N ARG A1859 " --> pdb=" O ILE A1875 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 2218 through 2220 removed outlier: 6.453A pdb=" N VAL A2182 " --> pdb=" O LYS A2219 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2374 through 2376 removed outlier: 6.848A pdb=" N GLY A2209 " --> pdb=" O LEU A2255 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU A2255 " --> pdb=" O GLY A2209 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A2289 " --> pdb=" O TRP A2258 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS A2260 " --> pdb=" O ILE A2289 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A2291 " --> pdb=" O HIS A2260 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLN A2262 " --> pdb=" O ILE A2291 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A2293 " --> pdb=" O GLN A2262 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 2229 through 2232 removed outlier: 3.703A pdb=" N SER A2235 " --> pdb=" O HIS A2232 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 180 through 183 removed outlier: 3.668A pdb=" N ASP K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 223 through 226 removed outlier: 3.745A pdb=" N ALA K 223 " --> pdb=" O CYS K 237 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLN K 247 " --> pdb=" O LEU K 257 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU K 257 " --> pdb=" O GLN K 247 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 270 through 273 removed outlier: 5.675A pdb=" N ASP K 293 " --> pdb=" O GLU K 299 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU K 299 " --> pdb=" O ASP K 293 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 312 through 314 Processing sheet with id= R, first strand: chain 'K' and resid 388 through 390 removed outlier: 4.547A pdb=" N ILE K 372 " --> pdb=" O GLY K 368 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY K 368 " --> pdb=" O ILE K 372 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 398 through 401 removed outlier: 3.672A pdb=" N SER K 412 " --> pdb=" O ASN K 420 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY K 431 " --> pdb=" O VAL K 421 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER K 423 " --> pdb=" O LYS K 429 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS K 429 " --> pdb=" O SER K 423 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 461 through 464 removed outlier: 3.503A pdb=" N SER K 442 " --> pdb=" O GLY K 455 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 399 through 401 Processing sheet with id= V, first strand: chain 'J' and resid 367 through 369 removed outlier: 3.623A pdb=" N TYR J 337 " --> pdb=" O LEU J 432 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN J 343 " --> pdb=" O LYS J 426 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS J 426 " --> pdb=" O GLN J 343 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 406 through 409 Processing sheet with id= X, first strand: chain 'E' and resid 57 through 62 removed outlier: 6.506A pdb=" N LEU E 26 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR E 60 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL E 28 " --> pdb=" O TYR E 60 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N CYS E 62 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ARG E 30 " --> pdb=" O CYS E 62 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 92 through 94 Processing sheet with id= Z, first strand: chain 'M' and resid 33 through 35 Processing sheet with id= AA, first strand: chain 'C' and resid 320 through 322 removed outlier: 9.382A pdb=" N ILE C 312 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE C 265 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ALA C 314 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE C 267 " --> pdb=" O ALA C 314 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL C 136 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN C 211 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL C 138 " --> pdb=" O ASN C 211 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C 213 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N GLY C 140 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 575 through 579 removed outlier: 6.418A pdb=" N LEU C 485 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR C 475 " --> pdb=" O TRP C 483 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP C 483 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 498 through 500 Processing sheet with id= AD, first strand: chain 'C' and resid 542 through 546 removed outlier: 3.763A pdb=" N ILE C 542 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 668 through 670 Processing sheet with id= AF, first strand: chain 'C' and resid 678 through 681 Processing sheet with id= AG, first strand: chain 'C' and resid 707 through 710 removed outlier: 3.772A pdb=" N TYR C 818 " --> pdb=" O VAL C 773 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASN C 776 " --> pdb=" O VAL C 765 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL C 765 " --> pdb=" O ASN C 776 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 928 through 931 removed outlier: 6.844A pdb=" N GLN C 905 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE C 888 " --> pdb=" O GLN C 905 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'z' and resid 61 through 66 removed outlier: 6.663A pdb=" N ILE z 16 " --> pdb=" O ALA z 62 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL z 64 " --> pdb=" O VAL z 14 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL z 14 " --> pdb=" O VAL z 64 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU z 66 " --> pdb=" O ARG z 12 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ARG z 12 " --> pdb=" O LEU z 66 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE z 37 " --> pdb=" O ASN z 28 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'z' and resid 41 through 43 removed outlier: 6.382A pdb=" N ASN z 43 " --> pdb=" O PHE z 49 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE z 49 " --> pdb=" O ASN z 43 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'q' and resid 67 through 71 removed outlier: 6.771A pdb=" N GLU q 18 " --> pdb=" O ARG q 68 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL q 70 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL q 16 " --> pdb=" O VAL q 70 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE q 23 " --> pdb=" O LEU q 19 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS q 39 " --> pdb=" O GLN q 30 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'r' and resid 55 through 63 removed outlier: 3.703A pdb=" N ARG r 24 " --> pdb=" O LEU r 20 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'r' and resid 65 through 68 removed outlier: 6.549A pdb=" N SER r 42 " --> pdb=" O LEU r 30 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU r 30 " --> pdb=" O SER r 42 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'x' and resid 53 through 56 removed outlier: 4.576A pdb=" N LEU x 32 " --> pdb=" O LEU x 28 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'x' and resid 71 through 73 removed outlier: 3.687A pdb=" N SER x 40 " --> pdb=" O ALA x 48 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER x 50 " --> pdb=" O LEU x 38 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU x 38 " --> pdb=" O SER x 50 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 't' and resid 63 through 66 removed outlier: 6.752A pdb=" N GLU t 50 " --> pdb=" O VAL t 64 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 't' and resid 70 through 73 removed outlier: 3.619A pdb=" N GLY t 36 " --> pdb=" O ILE t 44 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU t 46 " --> pdb=" O LEU t 34 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU t 34 " --> pdb=" O GLU t 46 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'y' and resid 67 through 69 removed outlier: 3.548A pdb=" N LYS y 46 " --> pdb=" O LEU y 42 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'y' and resid 92 through 94 removed outlier: 6.550A pdb=" N ASP y 64 " --> pdb=" O LEU y 52 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU y 52 " --> pdb=" O ASP y 64 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 's' and resid 64 through 66 removed outlier: 3.525A pdb=" N PHE s 78 " --> pdb=" O GLU s 18 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 's' and resid 68 through 71 removed outlier: 5.864A pdb=" N SER s 41 " --> pdb=" O LEU s 29 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU s 29 " --> pdb=" O SER s 41 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'd' and resid 69 through 73 removed outlier: 6.806A pdb=" N GLU d 22 " --> pdb=" O LYS d 70 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE d 72 " --> pdb=" O SER d 20 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER d 20 " --> pdb=" O ILE d 72 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS d 32 " --> pdb=" O ARG d 45 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN d 43 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'd' and resid 47 through 50 removed outlier: 3.634A pdb=" N ALA d 49 " --> pdb=" O THR d 57 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR d 57 " --> pdb=" O ALA d 49 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'a' and resid 19 through 23 removed outlier: 3.557A pdb=" N GLN a 33 " --> pdb=" O ASN a 46 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL a 44 " --> pdb=" O MET a 35 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU a 43 " --> pdb=" O LEU a 87 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'b' and resid 92 through 96 removed outlier: 7.006A pdb=" N GLU b 18 " --> pdb=" O ARG b 93 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE b 95 " --> pdb=" O THR b 16 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR b 16 " --> pdb=" O ILE b 95 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR b 28 " --> pdb=" O ASP b 42 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP b 42 " --> pdb=" O THR b 28 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'c' and resid 73 through 75 Processing sheet with id= BA, first strand: chain 'c' and resid 93 through 96 removed outlier: 3.713A pdb=" N ALA c 60 " --> pdb=" O VAL c 68 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU c 70 " --> pdb=" O VAL c 58 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL c 58 " --> pdb=" O GLU c 70 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'e' and resid 27 through 29 removed outlier: 3.508A pdb=" N THR e 28 " --> pdb=" O THR e 91 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR e 91 " --> pdb=" O THR e 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'e' and resid 80 through 82 removed outlier: 3.928A pdb=" N GLY e 45 " --> pdb=" O VAL e 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP e 55 " --> pdb=" O ILE e 43 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE e 43 " --> pdb=" O ASP e 55 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'f' and resid 26 through 30 removed outlier: 3.615A pdb=" N ARG f 39 " --> pdb=" O GLU f 57 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU f 57 " --> pdb=" O ARG f 39 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'g' and resid 14 through 19 removed outlier: 3.769A pdb=" N GLY g 27 " --> pdb=" O ILE g 15 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG g 23 " --> pdb=" O ILE g 19 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS g 24 " --> pdb=" O ILE g 46 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'g' and resid 28 through 32 removed outlier: 6.659A pdb=" N VAL g 39 " --> pdb=" O ARG g 30 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'D' and resid 801 through 804 removed outlier: 6.361A pdb=" N VAL D 827 " --> pdb=" O GLY D 802 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N HIS D 804 " --> pdb=" O VAL D 827 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL D 829 " --> pdb=" O HIS D 804 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE D 740 " --> pdb=" O LEU D 828 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N CYS D 830 " --> pdb=" O ILE D 740 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL D 742 " --> pdb=" O CYS D 830 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR D 844 " --> pdb=" O ILE D 741 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE D 743 " --> pdb=" O THR D 844 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE D 846 " --> pdb=" O PHE D 743 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU D 885 " --> pdb=" O VAL D 845 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE D 847 " --> pdb=" O GLU D 885 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE D 887 " --> pdb=" O ILE D 847 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 453 " --> pdb=" O HIS D 464 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'D' and resid 691 through 693 removed outlier: 6.453A pdb=" N LEU D 518 " --> pdb=" O PHE D 692 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LYS D 556 " --> pdb=" O ARG D 629 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU D 631 " --> pdb=" O LYS D 556 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 558 " --> pdb=" O LEU D 631 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE D 633 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE D 560 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'D' and resid 852 through 854 removed outlier: 3.684A pdb=" N SER D 859 " --> pdb=" O SER D 854 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'D' and resid 1204 through 1210 Processing sheet with id= BK, first strand: chain 'D' and resid 1302 through 1307 Processing sheet with id= BL, first strand: chain 'D' and resid 1366 through 1369 Processing sheet with id= BM, first strand: chain 'D' and resid 1544 through 1551 removed outlier: 6.820A pdb=" N GLY D1718 " --> pdb=" O GLU D1545 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASN D1547 " --> pdb=" O GLY D1718 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL D1720 " --> pdb=" O ASN D1547 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLN D1549 " --> pdb=" O VAL D1720 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE D1722 " --> pdb=" O GLN D1549 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE D1551 " --> pdb=" O ILE D1722 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR D1724 " --> pdb=" O PHE D1551 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'D' and resid 1686 through 1689 removed outlier: 3.975A pdb=" N ASP D1689 " --> pdb=" O LYS D1694 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS D1694 " --> pdb=" O ASP D1689 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'D' and resid 1820 through 1823 Processing sheet with id= BP, first strand: chain 'D' and resid 2052 through 2057 Processing sheet with id= BQ, first strand: chain 'D' and resid 2154 through 2162 removed outlier: 6.967A pdb=" N GLU D2105 " --> pdb=" O LEU D2111 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU D2111 " --> pdb=" O GLU D2105 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'P' and resid 79 through 83 removed outlier: 6.240A pdb=" N CYS P 48 " --> pdb=" O LEU P 82 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG P 21 " --> pdb=" O VAL P 97 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL P 97 " --> pdb=" O ARG P 21 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU P 23 " --> pdb=" O THR P 95 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR P 95 " --> pdb=" O LEU P 23 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'P' and resid 85 through 87 removed outlier: 3.979A pdb=" N ALA P 36 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN P 46 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU P 34 " --> pdb=" O ASN P 46 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'Q' and resid 80 through 82 removed outlier: 3.974A pdb=" N GLU Q 13 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'Q' and resid 84 through 87 removed outlier: 6.178A pdb=" N THR Q 41 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU Q 29 " --> pdb=" O THR Q 41 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'R' and resid 85 through 91 Processing sheet with id= BW, first strand: chain 'R' and resid 93 through 96 removed outlier: 6.545A pdb=" N GLU R 70 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL R 58 " --> pdb=" O GLU R 70 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'S' and resid 56 through 59 Processing sheet with id= BY, first strand: chain 'S' and resid 61 through 64 removed outlier: 6.487A pdb=" N ARG S 45 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU S 33 " --> pdb=" O ARG S 45 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'T' and resid 89 through 92 removed outlier: 3.632A pdb=" N GLY T 78 " --> pdb=" O ALA T 57 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU T 59 " --> pdb=" O PRO T 76 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'T' and resid 80 through 82 removed outlier: 3.682A pdb=" N GLY T 45 " --> pdb=" O VAL T 53 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP T 55 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE T 43 " --> pdb=" O ASP T 55 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'U' and resid 66 through 69 removed outlier: 3.718A pdb=" N GLY U 66 " --> pdb=" O GLU U 58 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA U 56 " --> pdb=" O LEU U 68 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'U' and resid 71 through 73 removed outlier: 3.613A pdb=" N SER U 44 " --> pdb=" O GLN U 52 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN U 54 " --> pdb=" O LEU U 42 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU U 42 " --> pdb=" O ASN U 54 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'V' and resid 52 through 56 removed outlier: 6.707A pdb=" N ALA V 43 " --> pdb=" O HIS V 55 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS V 24 " --> pdb=" O ILE V 46 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'V' and resid 38 through 40 Processing sheet with id= CF, first strand: chain '2' and resid 328 through 330 Processing sheet with id= CG, first strand: chain '3' and resid 73 through 75 removed outlier: 3.562A pdb=" N ALA 3 115 " --> pdb=" O LEU 3 103 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP 3 105 " --> pdb=" O LEU 3 113 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU 3 113 " --> pdb=" O ASP 3 105 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain '3' and resid 124 through 130 removed outlier: 6.587A pdb=" N THR 3 151 " --> pdb=" O THR 3 125 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET 3 127 " --> pdb=" O ALA 3 149 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA 3 149 " --> pdb=" O MET 3 127 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N SER 3 129 " --> pdb=" O PHE 3 147 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE 3 147 " --> pdb=" O SER 3 129 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER 3 152 " --> pdb=" O ASN 3 156 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN 3 156 " --> pdb=" O SER 3 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL 3 175 " --> pdb=" O ILE 3 159 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLN 3 161 " --> pdb=" O THR 3 173 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR 3 173 " --> pdb=" O GLN 3 161 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE 3 163 " --> pdb=" O LEU 3 171 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU 3 171 " --> pdb=" O ILE 3 163 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N HIS 3 165 " --> pdb=" O LEU 3 169 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU 3 169 " --> pdb=" O HIS 3 165 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain '3' and resid 192 through 195 removed outlier: 4.075A pdb=" N TYR 3 192 " --> pdb=" O SER 3 205 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain '3' and resid 235 through 238 removed outlier: 4.152A pdb=" N VAL 3 266 " --> pdb=" O VAL 3 288 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL 3 288 " --> pdb=" O VAL 3 266 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain '3' and resid 271 through 274 removed outlier: 3.538A pdb=" N HIS 3 279 " --> pdb=" O GLU 3 274 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain '3' and resid 294 through 298 removed outlier: 4.230A pdb=" N PHE 3 326 " --> pdb=" O LEU 3 298 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain '3' and resid 379 through 382 removed outlier: 3.597A pdb=" N THR 3 392 " --> pdb=" O GLN 3 406 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain '3' and resid 437 through 440 removed outlier: 3.576A pdb=" N GLN 3 418 " --> pdb=" O LEU 3 430 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain '3' and resid 490 through 493 Processing sheet with id= CP, first strand: chain '3' and resid 519 through 522 removed outlier: 3.732A pdb=" N SER 3 848 " --> pdb=" O ILE 3 865 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain '3' and resid 534 through 538 Processing sheet with id= CR, first strand: chain '3' and resid 588 through 593 removed outlier: 7.058A pdb=" N VAL 3 602 " --> pdb=" O ILE 3 589 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR 3 591 " --> pdb=" O ILE 3 600 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE 3 600 " --> pdb=" O THR 3 591 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU 3 593 " --> pdb=" O SER 3 598 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER 3 598 " --> pdb=" O LEU 3 593 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU 3 622 " --> pdb=" O HIS 3 609 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL 3 611 " --> pdb=" O ASN 3 620 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASN 3 620 " --> pdb=" O VAL 3 611 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR 3 613 " --> pdb=" O TYR 3 618 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR 3 618 " --> pdb=" O THR 3 613 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain '3' and resid 634 through 637 Processing sheet with id= CT, first strand: chain '3' and resid 692 through 694 Processing sheet with id= CU, first strand: chain '3' and resid 728 through 732 removed outlier: 4.135A pdb=" N LEU 3 739 " --> pdb=" O ILE 3 755 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain '3' and resid 928 through 931 Processing sheet with id= CW, first strand: chain '3' and resid 982 through 985 removed outlier: 4.918A pdb=" N ASP 3 992 " --> pdb=" O ILE 31008 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG 31002 " --> pdb=" O ALA 3 998 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain '3' and resid 1033 through 1037 removed outlier: 4.572A pdb=" N ALA 31033 " --> pdb=" O ALA 31044 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY 31053 " --> pdb=" O ARG 31061 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG 31061 " --> pdb=" O GLY 31053 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain '3' and resid 1077 through 1080 removed outlier: 3.654A pdb=" N LEU 31085 " --> pdb=" O PHE 31097 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain '3' and resid 1128 through 1130 removed outlier: 5.838A pdb=" N ARG 31142 " --> pdb=" O LEU 31189 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU 31189 " --> pdb=" O ARG 31142 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain '3' and resid 60 through 66 removed outlier: 6.322A pdb=" N VAL 31225 " --> pdb=" O LEU 3 65 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain '4' and resid 82 through 85 Processing sheet with id= DC, first strand: chain '4' and resid 179 through 182 Processing sheet with id= DD, first strand: chain '4' and resid 171 through 173 Processing sheet with id= DE, first strand: chain '5' and resid 39 through 42 removed outlier: 6.296A pdb=" N TYR 5 72 " --> pdb=" O LYS 5 40 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'X' and resid 103 through 106 removed outlier: 3.519A pdb=" N LEU X 77 " --> pdb=" O ILE X 33 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE X 74 " --> pdb=" O SER X 63 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'h' and resid 78 through 83 removed outlier: 6.282A pdb=" N CYS h 48 " --> pdb=" O LEU h 82 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'h' and resid 43 through 45 Processing sheet with id= DI, first strand: chain 'i' and resid 58 through 61 removed outlier: 3.545A pdb=" N GLN i 34 " --> pdb=" O LEU i 31 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU i 31 " --> pdb=" O GLN i 34 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N GLY i 36 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 11.470A pdb=" N ILE i 29 " --> pdb=" O GLY i 36 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ARG i 38 " --> pdb=" O VAL i 27 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N VAL i 27 " --> pdb=" O ARG i 38 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'i' and resid 52 through 54 removed outlier: 3.845A pdb=" N VAL i 52 " --> pdb=" O LEU i 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU i 82 " --> pdb=" O VAL i 52 " (cutoff:3.500A) Processing sheet with id= DK, first strand: chain 'j' and resid 37 through 39 removed outlier: 7.118A pdb=" N GLU j 58 " --> pdb=" O THR j 67 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR j 67 " --> pdb=" O GLU j 58 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'j' and resid 71 through 73 removed outlier: 3.636A pdb=" N GLN j 52 " --> pdb=" O SER j 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER j 44 " --> pdb=" O GLN j 52 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASN j 54 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU j 42 " --> pdb=" O ASN j 54 " (cutoff:3.500A) Processing sheet with id= DM, first strand: chain 'j' and resid 28 through 31 removed outlier: 4.003A pdb=" N TYR j 80 " --> pdb=" O LYS j 30 " (cutoff:3.500A) Processing sheet with id= DN, first strand: chain 'k' and resid 23 through 25 Processing sheet with id= DO, first strand: chain 'k' and resid 60 through 63 removed outlier: 6.049A pdb=" N ASP k 41 " --> pdb=" O LEU k 29 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU k 29 " --> pdb=" O ASP k 41 " (cutoff:3.500A) Processing sheet with id= DP, first strand: chain 'l' and resid 69 through 73 removed outlier: 6.950A pdb=" N GLU l 22 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE l 72 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER l 20 " --> pdb=" O ILE l 72 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN l 43 " --> pdb=" O VAL l 34 " (cutoff:3.500A) Processing sheet with id= DQ, first strand: chain 'l' and resid 47 through 49 Processing sheet with id= DR, first strand: chain 'm' and resid 80 through 82 removed outlier: 3.706A pdb=" N GLU m 13 " --> pdb=" O LEU m 29 " (cutoff:3.500A) Processing sheet with id= DS, first strand: chain 'm' and resid 84 through 87 removed outlier: 6.500A pdb=" N THR m 41 " --> pdb=" O LEU m 29 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU m 29 " --> pdb=" O THR m 41 " (cutoff:3.500A) Processing sheet with id= DT, first strand: chain 'n' and resid 53 through 55 removed outlier: 3.578A pdb=" N ARG n 89 " --> pdb=" O GLU n 74 " (cutoff:3.500A) Processing sheet with id= DU, first strand: chain 'n' and resid 67 through 70 Processing sheet with id= DV, first strand: chain 'n' and resid 45 through 48 removed outlier: 3.635A pdb=" N VAL n 103 " --> pdb=" O SER n 47 " (cutoff:3.500A) Processing sheet with id= DW, first strand: chain 'o' and resid 13 through 15 removed outlier: 7.107A pdb=" N ILE o 56 " --> pdb=" O LEU o 36 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR o 78 " --> pdb=" O LEU o 57 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN o 100 " --> pdb=" O LEU o 79 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN o 126 " --> pdb=" O LEU o 101 " (cutoff:3.500A) Processing sheet with id= DX, first strand: chain 'p' and resid 72 through 74 Processing sheet with id= ), first strand: chain 'u' and resid 421 through 423 Processing sheet with id= *, first strand: chain 'v' and resid 58 through 60 removed outlier: 3.559A pdb=" N THR v 73 " --> pdb=" O CYS v 68 " (cutoff:3.500A) Processing sheet with id= +, first strand: chain 'v' and resid 155 through 158 Processing sheet with id= ,, first strand: chain 'v' and resid 179 through 184 Processing sheet with id= -, first strand: chain 'W' and resid 80 through 82 Processing sheet with id= ., first strand: chain '0' and resid 164 through 167 4029 hydrogen bonds defined for protein. 10878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 397 hydrogen bonds 742 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 78.97 Time building geometry restraints manager: 34.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.51: 68489 1.51 - 1.88: 24883 1.88 - 2.25: 0 2.25 - 2.62: 0 2.62 - 2.99: 1 Bond restraints: 93373 Sorted by residual: bond pdb=" C PRO N 304 " pdb=" N LEU N 308 " ideal model delta sigma weight residual 1.332 2.991 -1.659 1.40e-02 5.10e+03 1.40e+04 bond pdb=" O3' U H1161 " pdb=" P U H1162 " ideal model delta sigma weight residual 1.607 1.419 0.188 1.50e-02 4.44e+03 1.57e+02 bond pdb=" O3' A H1092 " pdb=" P C H1093 " ideal model delta sigma weight residual 1.607 1.429 0.178 1.50e-02 4.44e+03 1.41e+02 bond pdb=" O5' C H1163 " pdb=" C5' C H1163 " ideal model delta sigma weight residual 1.420 1.586 -0.166 1.50e-02 4.44e+03 1.22e+02 bond pdb=" CA ASP o 69 " pdb=" CB ASP o 69 " ideal model delta sigma weight residual 1.532 1.380 0.152 1.42e-02 4.96e+03 1.14e+02 ... (remaining 93368 not shown) Histogram of bond angle deviations from ideal: 83.01 - 95.31: 10 95.31 - 107.61: 7688 107.61 - 119.91: 77976 119.91 - 132.21: 44120 132.21 - 144.50: 198 Bond angle restraints: 129992 Sorted by residual: angle pdb=" C4' U H1151 " pdb=" C3' U H1151 " pdb=" O3' U H1151 " ideal model delta sigma weight residual 113.00 83.01 29.99 1.50e+00 4.44e-01 4.00e+02 angle pdb=" CA LEU 1 548 " pdb=" C LEU 1 548 " pdb=" N GLY 1 549 " ideal model delta sigma weight residual 118.13 141.61 -23.48 1.28e+00 6.10e-01 3.37e+02 angle pdb=" O3' A H1092 " pdb=" C3' A H1092 " pdb=" C2' A H1092 " ideal model delta sigma weight residual 113.70 140.51 -26.81 1.50e+00 4.44e-01 3.20e+02 angle pdb=" C3' G H1097 " pdb=" C2' G H1097 " pdb=" O2' G H1097 " ideal model delta sigma weight residual 110.70 135.39 -24.69 1.50e+00 4.44e-01 2.71e+02 angle pdb=" N PRO o 44 " pdb=" CA PRO o 44 " pdb=" CB PRO o 44 " ideal model delta sigma weight residual 103.23 113.87 -10.64 6.70e-01 2.23e+00 2.52e+02 ... (remaining 129987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 53137 35.51 - 71.03: 1688 71.03 - 106.54: 182 106.54 - 142.06: 36 142.06 - 177.57: 21 Dihedral angle restraints: 55064 sinusoidal: 18718 harmonic: 36346 Sorted by residual: dihedral pdb=" CA THR 3 667 " pdb=" C THR 3 667 " pdb=" N THR 3 668 " pdb=" CA THR 3 668 " ideal model delta harmonic sigma weight residual 180.00 46.96 133.04 0 5.00e+00 4.00e-02 7.08e+02 dihedral pdb=" CA LEU 3 666 " pdb=" C LEU 3 666 " pdb=" N THR 3 667 " pdb=" CA THR 3 667 " ideal model delta harmonic sigma weight residual -180.00 -50.51 -129.49 0 5.00e+00 4.00e-02 6.71e+02 dihedral pdb=" CA LYS 31012 " pdb=" C LYS 31012 " pdb=" N ASP 31013 " pdb=" CA ASP 31013 " ideal model delta harmonic sigma weight residual 180.00 50.54 129.46 0 5.00e+00 4.00e-02 6.70e+02 ... (remaining 55061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.263: 15680 0.263 - 0.526: 151 0.526 - 0.789: 9 0.789 - 1.052: 0 1.052 - 1.315: 2 Chirality restraints: 15842 Sorted by residual: chirality pdb=" C3' A H1147 " pdb=" C4' A H1147 " pdb=" O3' A H1147 " pdb=" C2' A H1147 " both_signs ideal model delta sigma weight residual False -2.48 -1.16 -1.31 2.00e-01 2.50e+01 4.32e+01 chirality pdb=" C2' G H1097 " pdb=" C3' G H1097 " pdb=" O2' G H1097 " pdb=" C1' G H1097 " both_signs ideal model delta sigma weight residual False -2.75 -1.59 -1.16 2.00e-01 2.50e+01 3.39e+01 chirality pdb=" CA TYR 1 386 " pdb=" N TYR 1 386 " pdb=" C TYR 1 386 " pdb=" CB TYR 1 386 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 15839 not shown) Planarity restraints: 15601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO N 304 " 0.078 2.00e-02 2.50e+03 1.16e-01 1.35e+02 pdb=" C PRO N 304 " -0.199 2.00e-02 2.50e+03 pdb=" O PRO N 304 " 0.085 2.00e-02 2.50e+03 pdb=" N LEU N 308 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C H1141 " 0.015 2.00e-02 2.50e+03 5.63e-02 7.13e+01 pdb=" N1 C H1141 " -0.019 2.00e-02 2.50e+03 pdb=" C2 C H1141 " -0.116 2.00e-02 2.50e+03 pdb=" O2 C H1141 " 0.098 2.00e-02 2.50e+03 pdb=" N3 C H1141 " -0.047 2.00e-02 2.50e+03 pdb=" C4 C H1141 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C H1141 " 0.045 2.00e-02 2.50e+03 pdb=" C5 C H1141 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C H1141 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS 31183 " -0.039 2.00e-02 2.50e+03 8.19e-02 6.71e+01 pdb=" C CYS 31183 " 0.142 2.00e-02 2.50e+03 pdb=" O CYS 31183 " -0.053 2.00e-02 2.50e+03 pdb=" N LYS 31184 " -0.049 2.00e-02 2.50e+03 ... (remaining 15598 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 103 2.15 - 2.84: 34378 2.84 - 3.52: 128889 3.52 - 4.21: 200204 4.21 - 4.90: 314442 Nonbonded interactions: 678016 Sorted by model distance: nonbonded pdb=" OG1 THR C 147 " pdb="MG MG C1501 " model vdw 1.462 2.170 nonbonded pdb=" NH2 ARG A 716 " pdb=" O2 C B 111 " model vdw 1.819 2.520 nonbonded pdb=" N6 A F 34 " pdb=" N7 A F 47 " model vdw 1.834 2.600 nonbonded pdb=" N ALA A1651 " pdb=" OP2 A F 49 " model vdw 1.838 2.520 nonbonded pdb=" O2' A G 487 " pdb=" OP1 A G 488 " model vdw 1.849 2.440 ... (remaining 678011 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 'P' and ((resid 12 through 53 and (name N or name CA or name C or name O \ )) or (resid 77 through 102 and (name N or name CA or name C or name O )))) selection = (chain 'a' and resid 12 through 102) selection = (chain 'h' and ((resid 12 through 53 and (name N or name CA or name C or name O \ )) or (resid 77 through 102 and (name N or name CA or name C or name O )))) } ncs_group { reference = (chain 'R' and ((resid 20 through 80 and (name N or name CA or name C or name O \ )) or (resid 82 through 108 and (name N or name CA or name C or name O )))) selection = (chain 'c' and resid 20 through 108) } ncs_group { reference = (chain 'S' and ((resid 5 through 50 and (name N or name CA or name C or name O ) \ ) or (resid 56 through 83 and (name N or name CA or name C or name O )))) selection = (chain 'd' and (resid 5 through 50 or resid 56 through 83)) selection = (chain 'l' and (resid 5 through 83 and (name N or name CA or name C or name O )) \ ) } ncs_group { reference = (chain 'T' and ((resid 10 through 60 and (name N or name CA or name C or name O \ )) or (resid 73 and (name N or name CA or name C or name O )) or (resid 79 throu \ gh 92 and (name N or name CA or name C or name O )))) selection = (chain 'e' and (resid 10 through 60 or resid 73 through 92)) selection = (chain 'i' and ((resid 10 through 60 and (name N or name CA or name C or name O \ )) or (resid 73 and (name N or name CA or name C or name O )) or (resid 79 throu \ gh 92 and (name N or name CA or name C or name O )))) } ncs_group { reference = (chain 'U' and ((resid 12 through 32 and (name N or name CA or name C or name O \ )) or (resid 36 through 83 and (name N or name CA or name C or name O )))) selection = (chain 'f' and resid 12 through 83) selection = (chain 'j' and ((resid 12 through 32 and (name N or name CA or name C or name O \ )) or (resid 36 through 83 and (name N or name CA or name C or name O )))) } ncs_group { reference = (chain 'V' and ((resid 2 through 47 and (name N or name CA or name C or name O ) \ ) or (resid 54 through 58 and (name N or name CA or name C or name O )) or (resi \ d 61 through 76 and (name N or name CA or name C or name O )))) selection = (chain 'g' and (resid 2 through 47 or resid 54 through 76)) selection = (chain 'k' and ((resid 2 through 58 and (name N or name CA or name C or name O ) \ ) or (resid 61 through 76 and (name N or name CA or name C or name O )))) } ncs_group { reference = (chain 'b' and (resid 1 through 47 or resid 75 through 76 or resid 78 through 79 \ or resid 90 through 109)) selection = (chain 'm' and ((resid 1 through 47 and (name N or name CA or name C or name O ) \ ) or (resid 80 through 81 and (name N or name CA or name C or name O )) or (resi \ d 86 through 87 and (name N or name CA or name C or name O )) or (resid 90 throu \ gh 109 and (name N or name CA or name C or name O )))) } 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=0.50 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 16.800 Check model and map are aligned: 1.000 Set scattering table: 0.640 Process input model: 263.810 Find NCS groups from input model: 3.640 Set up NCS constraints: 0.500 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: 0.030 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 293.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 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 : 0.014 1.659 93373 Z= 0.911 Angle : 1.416 29.989 129992 Z= 0.902 Chirality : 0.084 1.315 15842 Planarity : 0.007 0.119 15601 Dihedral : 17.267 177.569 31916 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.08 % Favored : 90.02 % Rotamer: Outliers : 0.63 % Allowed : 1.63 % Favored : 97.73 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.01 % Twisted Proline : 2.53 % Twisted General : 0.36 % 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: -4.00 (0.06), residues: 12887 helix: -3.19 (0.05), residues: 4974 sheet: -1.84 (0.09), residues: 2162 loop : -2.33 (0.07), residues: 5751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.005 TRP A1790 HIS 0.017 0.003 HIS M 66 PHE 0.063 0.004 PHE E 105 TYR 0.059 0.004 TYR A1081 ARG 0.019 0.002 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25774 Ramachandran restraints generated. 12887 Oldfield, 0 Emsley, 12887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25774 Ramachandran restraints generated. 12887 Oldfield, 0 Emsley, 12887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 792 time to evaluate : 7.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.5501 (OUTLIER) cc_final: 0.5243 (tttm) REVERT: A 258 ILE cc_start: 0.8645 (tp) cc_final: 0.8299 (pt) REVERT: A 397 SER cc_start: 0.8260 (m) cc_final: 0.8044 (p) REVERT: A 753 TYR cc_start: 0.8400 (m-10) cc_final: 0.8126 (m-80) REVERT: A 769 MET cc_start: 0.8004 (mmm) cc_final: 0.7622 (mmt) REVERT: A 918 ASP cc_start: 0.9315 (m-30) cc_final: 0.8860 (t0) REVERT: A 944 TYR cc_start: 0.9286 (t80) cc_final: 0.8978 (t80) REVERT: A 1275 MET cc_start: 0.8634 (tpp) cc_final: 0.8265 (tpp) REVERT: A 1306 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8901 (tp30) REVERT: A 1472 ASN cc_start: 0.8224 (m-40) cc_final: 0.7591 (t0) REVERT: A 1834 PHE cc_start: 0.8158 (m-10) cc_final: 0.7723 (m-80) REVERT: A 1910 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8142 (mttp) REVERT: A 1911 TRP cc_start: 0.6513 (m100) cc_final: 0.6243 (m100) REVERT: A 1949 LEU cc_start: 0.9039 (mt) cc_final: 0.8834 (mt) REVERT: A 2079 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8267 (mp) REVERT: L 354 LYS cc_start: 0.9009 (tttp) cc_final: 0.8773 (mtmm) REVERT: L 364 LYS cc_start: 0.8262 (mtmm) cc_final: 0.8035 (tmtt) REVERT: N 102 ARG cc_start: 0.8355 (mtt90) cc_final: 0.7933 (ttp80) REVERT: N 139 GLU cc_start: 0.9458 (pt0) cc_final: 0.9055 (tm-30) REVERT: J 419 MET cc_start: 0.5532 (mmp) cc_final: 0.4931 (mmm) REVERT: E 34 LYS cc_start: 0.8919 (pttm) cc_final: 0.8629 (tppt) REVERT: E 73 MET cc_start: 0.8332 (ptm) cc_final: 0.8095 (ptp) REVERT: C 164 MET cc_start: 0.8628 (mtt) cc_final: 0.8396 (mtp) REVERT: C 362 LYS cc_start: 0.8821 (tttt) cc_final: 0.8602 (ttmm) REVERT: C 834 MET cc_start: 0.7384 (mmm) cc_final: 0.6896 (mmm) REVERT: O 188 ASN cc_start: 0.8387 (m-40) cc_final: 0.7913 (p0) REVERT: O 192 GLU cc_start: 0.8604 (tp30) cc_final: 0.8302 (mp0) REVERT: O 197 ARG cc_start: 0.6701 (mtm-85) cc_final: 0.6361 (mmt180) REVERT: O 199 MET cc_start: 0.7775 (ttp) cc_final: 0.7501 (tmm) outliers start: 26 outliers final: 10 residues processed: 814 average time/residue: 0.8045 time to fit residues: 1139.9569 Evaluate side-chains 517 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 504 time to evaluate : 9.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 675 HIS Chi-restraints excluded: chain A residue 701 CYS Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 900 PHE Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1910 LYS Chi-restraints excluded: chain A residue 2079 ILE Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain C residue 190 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1351 random chunks: chunk 1140 optimal weight: 50.0000 chunk 1023 optimal weight: 10.0000 chunk 568 optimal weight: 40.0000 chunk 349 optimal weight: 7.9990 chunk 690 optimal weight: 50.0000 chunk 547 optimal weight: 0.0020 chunk 1058 optimal weight: 1.9990 chunk 409 optimal weight: 3.9990 chunk 643 optimal weight: 4.9990 chunk 788 optimal weight: 40.0000 chunk 1226 optimal weight: 20.0000 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 368 ASN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN A 576 HIS A 592 HIS A 648 GLN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN A 974 ASN ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 HIS ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 GLN A1424 HIS ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN A1603 ASN A1635 HIS A1809 ASN A1845 ASN ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2018 ASN A2068 ASN A2076 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 66 ASN K 205 GLN ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 250 ASN ** K 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 360 ASN ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 420 ASN L 185 ASN L 273 HIS L 331 HIS ** L 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 140 GLN N 803 ASN J 163 ASN J 247 ASN J 433 GLN J 448 GLN ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS M 45 ASN M 113 GLN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN C 260 ASN C 721 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 GLN C 837 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 93373 Z= 0.353 Angle : 0.757 13.814 129992 Z= 0.402 Chirality : 0.046 0.267 15842 Planarity : 0.005 0.122 15601 Dihedral : 17.754 179.054 22536 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.77 % Favored : 94.76 % Rotamer: Outliers : 2.97 % Allowed : 7.26 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.01 % Twisted Proline : 1.95 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.07), residues: 12889 helix: -0.96 (0.07), residues: 5040 sheet: -1.40 (0.10), residues: 2246 loop : -1.70 (0.08), residues: 5603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1790 HIS 0.011 0.002 HIS L 160 PHE 0.029 0.002 PHE A1574 TYR 0.035 0.003 TYR A1345 ARG 0.015 0.001 ARG K 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 598 time to evaluate : 7.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 SER cc_start: 0.8151 (m) cc_final: 0.7900 (p) REVERT: A 569 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9009 (mm) REVERT: A 1090 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8549 (mt) REVERT: A 1170 MET cc_start: 0.8296 (mtp) cc_final: 0.7936 (mtp) REVERT: A 1213 MET cc_start: 0.8498 (tpp) cc_final: 0.7962 (ttm) REVERT: A 1306 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8983 (tp30) REVERT: A 1472 ASN cc_start: 0.8206 (m-40) cc_final: 0.7653 (t0) REVERT: A 1518 SER cc_start: 0.9009 (p) cc_final: 0.8742 (t) REVERT: A 1766 MET cc_start: 0.9024 (tmm) cc_final: 0.8757 (mmt) REVERT: A 1834 PHE cc_start: 0.8148 (m-10) cc_final: 0.7820 (m-80) REVERT: K 188 MET cc_start: 0.8063 (mmm) cc_final: 0.7740 (mmm) REVERT: K 287 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8225 (mpp) REVERT: K 443 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8523 (tt) REVERT: L 159 PHE cc_start: 0.8797 (t80) cc_final: 0.8438 (t80) REVERT: L 354 LYS cc_start: 0.8967 (tttp) cc_final: 0.8746 (mtmm) REVERT: L 365 LYS cc_start: 0.8414 (ttpt) cc_final: 0.8193 (ttpp) REVERT: N 102 ARG cc_start: 0.8256 (mtt90) cc_final: 0.7811 (ttp80) REVERT: N 139 GLU cc_start: 0.9445 (pt0) cc_final: 0.9015 (tm-30) REVERT: N 840 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6660 (m-30) REVERT: N 896 MET cc_start: 0.8440 (mmm) cc_final: 0.7455 (mtt) REVERT: J 442 MET cc_start: 0.7229 (ttp) cc_final: 0.6807 (tmm) REVERT: E 34 LYS cc_start: 0.8947 (pttm) cc_final: 0.8363 (tppp) REVERT: E 72 GLU cc_start: 0.9008 (tp30) cc_final: 0.8319 (mm-30) REVERT: C 126 MET cc_start: 0.8573 (tpp) cc_final: 0.8246 (tpp) REVERT: C 164 MET cc_start: 0.8536 (mtt) cc_final: 0.8245 (mtp) REVERT: C 763 ARG cc_start: 0.8333 (tpt90) cc_final: 0.8051 (tpt170) REVERT: C 834 MET cc_start: 0.7379 (mmm) cc_final: 0.7120 (mmm) REVERT: C 877 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8948 (mm-30) REVERT: O 192 GLU cc_start: 0.8749 (tp30) cc_final: 0.8366 (mm-30) REVERT: O 197 ARG cc_start: 0.6455 (mtm-85) cc_final: 0.5901 (mmt180) REVERT: O 199 MET cc_start: 0.8004 (ttp) cc_final: 0.7678 (tmm) REVERT: O 218 GLU cc_start: 0.8077 (tp30) cc_final: 0.7842 (tp30) outliers start: 122 outliers final: 61 residues processed: 685 average time/residue: 0.7489 time to fit residues: 928.2269 Evaluate side-chains 567 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 501 time to evaluate : 7.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 972 MET Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1477 PHE Chi-restraints excluded: chain A residue 1485 ASP Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1703 MET Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1942 ASP Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 287 MET Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 443 LEU Chi-restraints excluded: chain K residue 458 ASP Chi-restraints excluded: chain L residue 443 HIS Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 752 ASN Chi-restraints excluded: chain N residue 840 ASP Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 796 ILE Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 889 TYR Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 200 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1351 random chunks: chunk 681 optimal weight: 30.0000 chunk 380 optimal weight: 2.9990 chunk 1021 optimal weight: 40.0000 chunk 835 optimal weight: 40.0000 chunk 338 optimal weight: 0.7980 chunk 1229 optimal weight: 7.9990 chunk 1327 optimal weight: 7.9990 chunk 1094 optimal weight: 7.9990 chunk 1218 optimal weight: 50.0000 chunk 419 optimal weight: 0.9990 chunk 986 optimal weight: 50.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 ASN ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1907 GLN A2054 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 HIS ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 ASN ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 420 ASN L 108 ASN L 114 ASN L 273 HIS ** L 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 461 HIS ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 93373 Z= 0.366 Angle : 0.696 13.966 129992 Z= 0.366 Chirality : 0.045 0.286 15842 Planarity : 0.005 0.103 15601 Dihedral : 17.277 179.534 22516 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.11 % Favored : 93.52 % Rotamer: Outliers : 4.29 % Allowed : 9.75 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.01 % Twisted Proline : 1.56 % Twisted General : 0.13 % 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: -1.17 (0.07), residues: 12889 helix: 0.18 (0.07), residues: 5094 sheet: -1.06 (0.10), residues: 2257 loop : -1.48 (0.08), residues: 5538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1335 HIS 0.014 0.002 HIS K 34 PHE 0.040 0.002 PHE E 105 TYR 0.040 0.002 TYR A1101 ARG 0.009 0.001 ARG C 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 530 time to evaluate : 7.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.8247 (mmm) cc_final: 0.7871 (tmm) REVERT: A 493 MET cc_start: 0.8161 (mmt) cc_final: 0.7713 (mmt) REVERT: A 569 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8979 (mm) REVERT: A 644 VAL cc_start: 0.7035 (OUTLIER) cc_final: 0.6820 (p) REVERT: A 946 ASN cc_start: 0.9535 (OUTLIER) cc_final: 0.9256 (m-40) REVERT: A 950 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8756 (t) REVERT: A 996 ASP cc_start: 0.9333 (OUTLIER) cc_final: 0.8978 (t0) REVERT: A 1170 MET cc_start: 0.8200 (mtp) cc_final: 0.7951 (mtm) REVERT: A 1306 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9062 (tp30) REVERT: A 1405 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6245 (tp) REVERT: A 1472 ASN cc_start: 0.8292 (m-40) cc_final: 0.7695 (t0) REVERT: A 1663 PHE cc_start: 0.9257 (t80) cc_final: 0.9039 (t80) REVERT: A 1830 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7664 (p) REVERT: A 1834 PHE cc_start: 0.8183 (m-10) cc_final: 0.7841 (m-80) REVERT: A 2008 LEU cc_start: 0.8605 (tp) cc_final: 0.8381 (tt) REVERT: K 87 LEU cc_start: 0.8750 (mt) cc_final: 0.8528 (pp) REVERT: K 188 MET cc_start: 0.7986 (mmm) cc_final: 0.7777 (mmm) REVERT: K 287 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8407 (mpp) REVERT: L 100 GLU cc_start: 0.9126 (tt0) cc_final: 0.8872 (tp30) REVERT: L 159 PHE cc_start: 0.8849 (t80) cc_final: 0.8608 (t80) REVERT: L 177 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8404 (mtm) REVERT: N 102 ARG cc_start: 0.8244 (mtt90) cc_final: 0.7710 (tmm-80) REVERT: N 139 GLU cc_start: 0.9452 (pt0) cc_final: 0.9026 (tm-30) REVERT: N 840 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6942 (m-30) REVERT: N 896 MET cc_start: 0.8263 (mmm) cc_final: 0.7456 (mtt) REVERT: J 442 MET cc_start: 0.7524 (ttp) cc_final: 0.7024 (tmm) REVERT: E 80 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7809 (ptm) REVERT: E 135 TYR cc_start: 0.8279 (m-10) cc_final: 0.7934 (m-10) REVERT: E 137 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.6671 (p90) REVERT: C 126 MET cc_start: 0.8588 (tpp) cc_final: 0.8290 (tpp) REVERT: C 164 MET cc_start: 0.8257 (mtt) cc_final: 0.7887 (mtp) REVERT: C 189 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8575 (pp) REVERT: C 877 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8908 (mm-30) REVERT: O 192 GLU cc_start: 0.8876 (tp30) cc_final: 0.8469 (mm-30) REVERT: O 197 ARG cc_start: 0.6648 (mtm-85) cc_final: 0.5833 (mmt180) REVERT: O 199 MET cc_start: 0.8044 (ttp) cc_final: 0.7613 (tmm) REVERT: O 222 GLU cc_start: 0.5078 (mt-10) cc_final: 0.4704 (mt-10) outliers start: 176 outliers final: 97 residues processed: 677 average time/residue: 0.7480 time to fit residues: 923.6992 Evaluate side-chains 593 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 483 time to evaluate : 7.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 950 THR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1254 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1405 ILE Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1477 PHE Chi-restraints excluded: chain A residue 1485 ASP Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1744 ASP Chi-restraints excluded: chain A residue 1758 ASP Chi-restraints excluded: chain A residue 1819 ILE Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1942 ASP Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 287 MET Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 443 LEU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 152 ASN Chi-restraints excluded: chain L residue 177 MET Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 443 HIS Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 150 ASP Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 733 ASN Chi-restraints excluded: chain N residue 752 ASN Chi-restraints excluded: chain N residue 760 VAL Chi-restraints excluded: chain N residue 840 ASP Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 TYR Chi-restraints excluded: chain M residue 39 GLU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 769 TYR Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 889 TYR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 200 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1351 random chunks: chunk 1214 optimal weight: 50.0000 chunk 924 optimal weight: 10.0000 chunk 637 optimal weight: 50.0000 chunk 136 optimal weight: 0.7980 chunk 586 optimal weight: 1.9990 chunk 825 optimal weight: 50.0000 chunk 1233 optimal weight: 10.0000 chunk 1305 optimal weight: 50.0000 chunk 644 optimal weight: 7.9990 chunk 1169 optimal weight: 50.0000 chunk 351 optimal weight: 20.0000 overall best weight: 6.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN A 580 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN A 868 GLN ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 GLN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1594 GLN ** A1809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1907 GLN K 31 GLN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 GLN ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 HIS ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 152 ASN ** L 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 ASN N 668 HIS ** N 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 HIS ** J 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN C 158 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 93373 Z= 0.498 Angle : 0.786 15.724 129992 Z= 0.411 Chirality : 0.047 0.258 15842 Planarity : 0.005 0.105 15601 Dihedral : 17.286 179.774 22512 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.72 % Favored : 92.88 % Rotamer: Outliers : 5.70 % Allowed : 12.26 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.01 % Twisted Proline : 1.56 % Twisted General : 0.11 % 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: -1.26 (0.07), residues: 12889 helix: 0.12 (0.07), residues: 5078 sheet: -0.92 (0.10), residues: 2276 loop : -1.65 (0.08), residues: 5535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP K 195 HIS 0.012 0.002 HIS C 869 PHE 0.035 0.003 PHE A 352 TYR 0.043 0.003 TYR A1345 ARG 0.012 0.001 ARG A 934 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 486 time to evaluate : 7.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.8341 (mmm) cc_final: 0.7888 (tmm) REVERT: A 569 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9055 (mm) REVERT: A 844 MET cc_start: 0.9147 (tpp) cc_final: 0.8856 (tpp) REVERT: A 935 GLU cc_start: 0.9540 (tm-30) cc_final: 0.8864 (tm-30) REVERT: A 996 ASP cc_start: 0.9377 (OUTLIER) cc_final: 0.9110 (t0) REVERT: A 1170 MET cc_start: 0.8171 (mtp) cc_final: 0.7821 (mtm) REVERT: A 1306 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9214 (tp30) REVERT: A 1379 MET cc_start: 0.9129 (tpp) cc_final: 0.8919 (tpp) REVERT: A 1472 ASN cc_start: 0.8294 (m-40) cc_final: 0.7576 (t0) REVERT: A 1485 ASP cc_start: 0.9284 (OUTLIER) cc_final: 0.8661 (t0) REVERT: A 1550 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.8902 (tt) REVERT: A 1830 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7722 (p) REVERT: A 1834 PHE cc_start: 0.8255 (m-10) cc_final: 0.7825 (m-80) REVERT: A 1953 ASN cc_start: 0.7096 (OUTLIER) cc_final: 0.6840 (m-40) REVERT: A 2008 LEU cc_start: 0.8620 (tp) cc_final: 0.8289 (tt) REVERT: K 287 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8447 (mpp) REVERT: L 100 GLU cc_start: 0.9132 (tt0) cc_final: 0.8863 (tp30) REVERT: L 175 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9180 (tt) REVERT: L 177 MET cc_start: 0.8786 (mtm) cc_final: 0.8415 (mtm) REVERT: L 419 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8249 (mp10) REVERT: L 441 MET cc_start: 0.8611 (tpp) cc_final: 0.8284 (ttm) REVERT: N 102 ARG cc_start: 0.8228 (mtt90) cc_final: 0.7674 (tmm-80) REVERT: N 840 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7004 (m-30) REVERT: N 896 MET cc_start: 0.8200 (mmm) cc_final: 0.7469 (mtt) REVERT: J 379 ILE cc_start: 0.8150 (tp) cc_final: 0.7819 (tt) REVERT: J 419 MET cc_start: 0.3108 (mmm) cc_final: 0.2775 (mmt) REVERT: E 72 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8742 (mm-30) REVERT: E 92 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6916 (mtt) REVERT: E 137 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.6738 (p90) REVERT: C 108 GLN cc_start: 0.4452 (OUTLIER) cc_final: 0.3369 (mm-40) REVERT: C 126 MET cc_start: 0.8430 (tpp) cc_final: 0.8185 (tpp) REVERT: C 164 MET cc_start: 0.8262 (mtt) cc_final: 0.7762 (mtp) REVERT: C 189 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8605 (pp) REVERT: C 877 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8929 (mm-30) REVERT: O 192 GLU cc_start: 0.8802 (tp30) cc_final: 0.8591 (mm-30) REVERT: O 197 ARG cc_start: 0.6733 (mtm-85) cc_final: 0.5704 (mmt180) REVERT: O 199 MET cc_start: 0.7990 (ttp) cc_final: 0.7577 (tmm) REVERT: O 218 GLU cc_start: 0.7987 (tp30) cc_final: 0.7673 (mm-30) outliers start: 234 outliers final: 138 residues processed: 688 average time/residue: 0.7331 time to fit residues: 926.8816 Evaluate side-chains 608 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 456 time to evaluate : 7.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1254 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1369 ASN Chi-restraints excluded: chain A residue 1389 TYR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1467 GLU Chi-restraints excluded: chain A residue 1477 PHE Chi-restraints excluded: chain A residue 1485 ASP Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1661 ILE Chi-restraints excluded: chain A residue 1668 ILE Chi-restraints excluded: chain A residue 1674 ASP Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1744 ASP Chi-restraints excluded: chain A residue 1758 ASP Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1847 ASP Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1942 ASP Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 1953 ASN Chi-restraints excluded: chain A residue 2003 THR Chi-restraints excluded: chain A residue 2074 LEU Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 287 MET Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 443 LEU Chi-restraints excluded: chain K residue 458 ASP Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 197 ILE Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 419 GLN Chi-restraints excluded: chain L residue 443 HIS Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 733 ASN Chi-restraints excluded: chain N residue 752 ASN Chi-restraints excluded: chain N residue 840 ASP Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 137 TYR Chi-restraints excluded: chain M residue 39 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 769 TYR Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 889 TYR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 200 ASN Chi-restraints excluded: chain O residue 216 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1351 random chunks: chunk 1087 optimal weight: 50.0000 chunk 741 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 972 optimal weight: 5.9990 chunk 538 optimal weight: 6.9990 chunk 1114 optimal weight: 50.0000 chunk 902 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 666 optimal weight: 9.9990 chunk 1172 optimal weight: 50.0000 chunk 329 optimal weight: 2.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN A 868 GLN ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1839 ASN ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 770 ASN ** J 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 93373 Z= 0.367 Angle : 0.661 13.486 129992 Z= 0.348 Chirality : 0.044 0.252 15842 Planarity : 0.004 0.098 15601 Dihedral : 17.090 179.779 22510 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.18 % Favored : 93.44 % Rotamer: Outliers : 5.51 % Allowed : 14.16 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.01 % Twisted Proline : 1.56 % Twisted General : 0.10 % 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: -0.97 (0.07), residues: 12889 helix: 0.41 (0.07), residues: 5137 sheet: -0.81 (0.11), residues: 2262 loop : -1.54 (0.08), residues: 5490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 505 HIS 0.008 0.002 HIS L 160 PHE 0.026 0.002 PHE A1574 TYR 0.030 0.002 TYR A1101 ARG 0.015 0.001 ARG A 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 485 time to evaluate : 7.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.8152 (tmm) cc_final: 0.7810 (tmm) REVERT: A 493 MET cc_start: 0.8244 (mmt) cc_final: 0.7809 (mmt) REVERT: A 569 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9009 (mm) REVERT: A 868 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.9206 (tp40) REVERT: A 946 ASN cc_start: 0.9474 (OUTLIER) cc_final: 0.9195 (m-40) REVERT: A 996 ASP cc_start: 0.9311 (OUTLIER) cc_final: 0.8993 (t0) REVERT: A 1170 MET cc_start: 0.8133 (mtp) cc_final: 0.7681 (mtm) REVERT: A 1306 GLU cc_start: 0.9392 (mt-10) cc_final: 0.9169 (tp30) REVERT: A 1472 ASN cc_start: 0.8364 (m-40) cc_final: 0.7677 (t0) REVERT: A 1485 ASP cc_start: 0.9244 (OUTLIER) cc_final: 0.8696 (t0) REVERT: A 1766 MET cc_start: 0.9149 (tmm) cc_final: 0.8784 (mmt) REVERT: A 1830 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7837 (p) REVERT: A 1834 PHE cc_start: 0.8238 (m-10) cc_final: 0.7890 (m-80) REVERT: A 1879 ILE cc_start: 0.7666 (mt) cc_final: 0.7410 (mp) REVERT: A 2008 LEU cc_start: 0.8587 (tp) cc_final: 0.8319 (tt) REVERT: K 172 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7837 (mt) REVERT: K 287 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8425 (mpp) REVERT: L 115 PHE cc_start: 0.9044 (t80) cc_final: 0.8740 (t80) REVERT: L 367 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7062 (ptp-170) REVERT: N 102 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7558 (tmm-80) REVERT: N 896 MET cc_start: 0.8266 (mmm) cc_final: 0.7751 (mtt) REVERT: J 379 ILE cc_start: 0.8287 (tp) cc_final: 0.7907 (tt) REVERT: J 419 MET cc_start: 0.2899 (mmm) cc_final: 0.2357 (mmm) REVERT: E 92 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6759 (mtt) REVERT: E 137 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.6516 (p90) REVERT: C 164 MET cc_start: 0.8254 (mtt) cc_final: 0.7765 (mtp) REVERT: C 189 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8577 (pp) REVERT: C 715 MET cc_start: 0.8736 (mmm) cc_final: 0.8262 (mmm) REVERT: C 877 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8878 (mm-30) REVERT: O 192 GLU cc_start: 0.8754 (tp30) cc_final: 0.8530 (mm-30) REVERT: O 197 ARG cc_start: 0.6581 (mtm-85) cc_final: 0.5647 (mmt180) REVERT: O 199 MET cc_start: 0.7952 (ttp) cc_final: 0.7548 (tmm) outliers start: 226 outliers final: 151 residues processed: 683 average time/residue: 0.7206 time to fit residues: 902.4007 Evaluate side-chains 630 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 467 time to evaluate : 7.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 868 GLN Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1254 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1335 TRP Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1477 PHE Chi-restraints excluded: chain A residue 1485 ASP Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1674 ASP Chi-restraints excluded: chain A residue 1711 VAL Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1744 ASP Chi-restraints excluded: chain A residue 1758 ASP Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1847 ASP Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1942 ASP Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 2033 THR Chi-restraints excluded: chain A residue 2074 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 287 MET Chi-restraints excluded: chain K residue 292 TRP Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 443 LEU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 197 ILE Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 358 ILE Chi-restraints excluded: chain L residue 367 ARG Chi-restraints excluded: chain L residue 370 ARG Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 443 HIS Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 150 ASP Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 733 ASN Chi-restraints excluded: chain N residue 752 ASN Chi-restraints excluded: chain N residue 807 VAL Chi-restraints excluded: chain N residue 848 THR Chi-restraints excluded: chain N residue 891 ILE Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 352 ILE Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 137 TYR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 763 ARG Chi-restraints excluded: chain C residue 769 TYR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 889 TYR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 200 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1351 random chunks: chunk 439 optimal weight: 0.9990 chunk 1176 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 chunk 766 optimal weight: 30.0000 chunk 322 optimal weight: 6.9990 chunk 1307 optimal weight: 50.0000 chunk 1085 optimal weight: 4.9990 chunk 605 optimal weight: 50.0000 chunk 108 optimal weight: 1.9990 chunk 432 optimal weight: 7.9990 chunk 686 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1197 ASN A1221 ASN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1470 GLN ** A1809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1888 HIS ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 GLN ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 ASN ** L 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 240 ASN ** J 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN C 108 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 93373 Z= 0.294 Angle : 0.614 12.449 129992 Z= 0.323 Chirality : 0.043 0.242 15842 Planarity : 0.004 0.095 15601 Dihedral : 16.962 179.776 22510 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.81 % Favored : 93.82 % Rotamer: Outliers : 5.31 % Allowed : 15.48 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.01 % Twisted Proline : 1.56 % Twisted General : 0.08 % 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: -0.68 (0.07), residues: 12889 helix: 0.72 (0.07), residues: 5138 sheet: -0.70 (0.11), residues: 2252 loop : -1.45 (0.08), residues: 5499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 505 HIS 0.010 0.001 HIS A 576 PHE 0.032 0.002 PHE A1144 TYR 0.038 0.002 TYR C 931 ARG 0.017 0.001 ARG A1272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 502 time to evaluate : 7.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 MET cc_start: 0.8193 (mmt) cc_final: 0.7727 (mmt) REVERT: A 721 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8112 (tt) REVERT: A 935 GLU cc_start: 0.9489 (tm-30) cc_final: 0.8931 (tm-30) REVERT: A 946 ASN cc_start: 0.9391 (OUTLIER) cc_final: 0.9104 (m-40) REVERT: A 996 ASP cc_start: 0.9286 (OUTLIER) cc_final: 0.9024 (t0) REVERT: A 1170 MET cc_start: 0.7963 (mtp) cc_final: 0.7442 (mtm) REVERT: A 1231 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8824 (tp40) REVERT: A 1306 GLU cc_start: 0.9376 (mt-10) cc_final: 0.9160 (tp30) REVERT: A 1314 SER cc_start: 0.9312 (OUTLIER) cc_final: 0.8913 (t) REVERT: A 1379 MET cc_start: 0.9115 (tpp) cc_final: 0.8788 (tpp) REVERT: A 1472 ASN cc_start: 0.8416 (m-40) cc_final: 0.7758 (t0) REVERT: A 1485 ASP cc_start: 0.9301 (OUTLIER) cc_final: 0.8727 (t0) REVERT: A 1550 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8690 (tt) REVERT: A 1830 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7640 (p) REVERT: A 1834 PHE cc_start: 0.8360 (m-10) cc_final: 0.8007 (m-80) REVERT: A 1879 ILE cc_start: 0.7662 (mt) cc_final: 0.7371 (mp) REVERT: A 1953 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6806 (m-40) REVERT: A 2008 LEU cc_start: 0.8540 (tp) cc_final: 0.8321 (tt) REVERT: K 172 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7842 (tp) REVERT: L 115 PHE cc_start: 0.9033 (t80) cc_final: 0.8735 (t80) REVERT: L 120 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: L 367 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6845 (ptp-170) REVERT: N 102 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7545 (tmm-80) REVERT: N 139 GLU cc_start: 0.9354 (pt0) cc_final: 0.8953 (tm-30) REVERT: N 896 MET cc_start: 0.8384 (mmm) cc_final: 0.7909 (mtt) REVERT: J 379 ILE cc_start: 0.8260 (tp) cc_final: 0.7830 (tt) REVERT: J 419 MET cc_start: 0.2574 (mmm) cc_final: 0.2159 (mmm) REVERT: E 92 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6735 (mtt) REVERT: E 137 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.6307 (p90) REVERT: C 108 GLN cc_start: 0.4095 (OUTLIER) cc_final: 0.2856 (mm-40) REVERT: C 164 MET cc_start: 0.8184 (mtt) cc_final: 0.7882 (mtp) REVERT: C 189 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8530 (pp) REVERT: C 375 GLU cc_start: 0.9253 (tp30) cc_final: 0.9014 (mm-30) REVERT: C 715 MET cc_start: 0.8740 (mmm) cc_final: 0.8279 (mmm) REVERT: C 877 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8872 (mm-30) REVERT: O 192 GLU cc_start: 0.8751 (tp30) cc_final: 0.8543 (mm-30) REVERT: O 197 ARG cc_start: 0.6595 (mtm-85) cc_final: 0.5640 (mmt180) REVERT: O 199 MET cc_start: 0.7808 (ttp) cc_final: 0.7498 (tmm) outliers start: 218 outliers final: 150 residues processed: 686 average time/residue: 0.7299 time to fit residues: 916.5717 Evaluate side-chains 644 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 478 time to evaluate : 7.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1059 GLU Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1203 ASN Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1231 GLN Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1254 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1335 TRP Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1477 PHE Chi-restraints excluded: chain A residue 1485 ASP Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1668 ILE Chi-restraints excluded: chain A residue 1674 ASP Chi-restraints excluded: chain A residue 1711 VAL Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1744 ASP Chi-restraints excluded: chain A residue 1758 ASP Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1819 ILE Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1847 ASP Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1942 ASP Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 1953 ASN Chi-restraints excluded: chain A residue 2074 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 292 TRP Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 458 ASP Chi-restraints excluded: chain L residue 120 TYR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 197 ILE Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 358 ILE Chi-restraints excluded: chain L residue 367 ARG Chi-restraints excluded: chain L residue 443 HIS Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 240 ASN Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 752 ASN Chi-restraints excluded: chain N residue 807 VAL Chi-restraints excluded: chain N residue 891 ILE Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 137 TYR Chi-restraints excluded: chain M residue 39 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 ILE Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 769 TYR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 889 TYR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 200 ASN Chi-restraints excluded: chain O residue 209 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1351 random chunks: chunk 1260 optimal weight: 50.0000 chunk 147 optimal weight: 0.9990 chunk 744 optimal weight: 9.9990 chunk 954 optimal weight: 7.9990 chunk 739 optimal weight: 6.9990 chunk 1100 optimal weight: 50.0000 chunk 729 optimal weight: 9.9990 chunk 1302 optimal weight: 0.9990 chunk 814 optimal weight: 50.0000 chunk 793 optimal weight: 7.9990 chunk 601 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN A 785 HIS ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1809 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 273 HIS ** L 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 93373 Z= 0.412 Angle : 0.703 15.384 129992 Z= 0.368 Chirality : 0.045 0.293 15842 Planarity : 0.005 0.098 15601 Dihedral : 17.031 179.865 22510 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.18 % Favored : 92.43 % Rotamer: Outliers : 5.95 % Allowed : 16.36 % Favored : 77.69 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.01 % Twisted Proline : 1.56 % Twisted General : 0.09 % 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: -0.80 (0.07), residues: 12889 helix: 0.61 (0.07), residues: 5070 sheet: -0.72 (0.11), residues: 2228 loop : -1.49 (0.08), residues: 5591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP A 505 HIS 0.010 0.002 HIS L 160 PHE 0.031 0.002 PHE A1574 TYR 0.028 0.002 TYR A1164 ARG 0.009 0.001 ARG L 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 478 time to evaluate : 7.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8037 (t) REVERT: A 237 MET cc_start: 0.8194 (tmm) cc_final: 0.7606 (tmm) REVERT: A 493 MET cc_start: 0.8263 (mmt) cc_final: 0.7866 (mmt) REVERT: A 569 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9066 (mm) REVERT: A 886 MET cc_start: 0.8545 (tpt) cc_final: 0.8252 (tpt) REVERT: A 946 ASN cc_start: 0.9497 (OUTLIER) cc_final: 0.9191 (m-40) REVERT: A 996 ASP cc_start: 0.9370 (OUTLIER) cc_final: 0.9068 (t0) REVERT: A 1170 MET cc_start: 0.8254 (mtp) cc_final: 0.7805 (mtm) REVERT: A 1231 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8882 (tp40) REVERT: A 1306 GLU cc_start: 0.9418 (mt-10) cc_final: 0.9178 (tp30) REVERT: A 1379 MET cc_start: 0.9150 (tpp) cc_final: 0.8752 (tpp) REVERT: A 1472 ASN cc_start: 0.8558 (m-40) cc_final: 0.7859 (t0) REVERT: A 1485 ASP cc_start: 0.9338 (m-30) cc_final: 0.8777 (t0) REVERT: A 1550 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8760 (tt) REVERT: A 1684 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6960 (tm-30) REVERT: A 1766 MET cc_start: 0.9137 (tmm) cc_final: 0.8729 (mmt) REVERT: A 1830 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7585 (p) REVERT: A 1834 PHE cc_start: 0.8477 (m-10) cc_final: 0.8148 (m-80) REVERT: A 1879 ILE cc_start: 0.7541 (mt) cc_final: 0.7270 (mp) REVERT: A 1953 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6826 (m-40) REVERT: L 115 PHE cc_start: 0.9061 (t80) cc_final: 0.8771 (t80) REVERT: L 177 MET cc_start: 0.8847 (mtm) cc_final: 0.8466 (mtm) REVERT: L 367 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7200 (ptp-170) REVERT: L 441 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8161 (ttm) REVERT: L 453 ASP cc_start: 0.8888 (t0) cc_final: 0.8678 (t0) REVERT: N 102 ARG cc_start: 0.8156 (mtt90) cc_final: 0.7588 (tmm-80) REVERT: N 139 GLU cc_start: 0.9369 (pt0) cc_final: 0.9016 (tm-30) REVERT: N 896 MET cc_start: 0.8302 (mmm) cc_final: 0.8008 (mtt) REVERT: J 419 MET cc_start: 0.2695 (mmm) cc_final: 0.2246 (mmm) REVERT: E 72 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8942 (tm-30) REVERT: E 92 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6795 (mtt) REVERT: E 137 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.6361 (p90) REVERT: C 164 MET cc_start: 0.8258 (mtt) cc_final: 0.7929 (mtp) REVERT: C 189 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8624 (pp) REVERT: C 715 MET cc_start: 0.8805 (mmm) cc_final: 0.8310 (mmm) REVERT: C 877 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8893 (mm-30) REVERT: O 192 GLU cc_start: 0.8762 (tp30) cc_final: 0.8528 (mm-30) REVERT: O 197 ARG cc_start: 0.6605 (mtm-85) cc_final: 0.5676 (mmt-90) REVERT: O 199 MET cc_start: 0.7789 (ttp) cc_final: 0.7468 (tmm) outliers start: 244 outliers final: 188 residues processed: 690 average time/residue: 0.7444 time to fit residues: 944.4719 Evaluate side-chains 662 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 461 time to evaluate : 7.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1028 TRP Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1203 ASN Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1231 GLN Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1254 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1335 TRP Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1369 ASN Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1477 PHE Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1674 ASP Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1711 VAL Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1744 ASP Chi-restraints excluded: chain A residue 1758 ASP Chi-restraints excluded: chain A residue 1785 ASP Chi-restraints excluded: chain A residue 1791 PHE Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1819 ILE Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1847 ASP Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1942 ASP Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 1953 ASN Chi-restraints excluded: chain A residue 2003 THR Chi-restraints excluded: chain A residue 2033 THR Chi-restraints excluded: chain A residue 2074 LEU Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 292 TRP Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 458 ASP Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 197 ILE Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 358 ILE Chi-restraints excluded: chain L residue 367 ARG Chi-restraints excluded: chain L residue 382 SER Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 441 MET Chi-restraints excluded: chain L residue 443 HIS Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 150 ASP Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 240 ASN Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 733 ASN Chi-restraints excluded: chain N residue 752 ASN Chi-restraints excluded: chain N residue 757 GLU Chi-restraints excluded: chain N residue 807 VAL Chi-restraints excluded: chain N residue 841 THR Chi-restraints excluded: chain N residue 891 ILE Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 352 ILE Chi-restraints excluded: chain J residue 462 HIS Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 137 TYR Chi-restraints excluded: chain M residue 39 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 769 TYR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 889 TYR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 200 ASN Chi-restraints excluded: chain O residue 209 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1351 random chunks: chunk 805 optimal weight: 50.0000 chunk 520 optimal weight: 50.0000 chunk 777 optimal weight: 40.0000 chunk 392 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 827 optimal weight: 50.0000 chunk 887 optimal weight: 8.9990 chunk 643 optimal weight: 40.0000 chunk 121 optimal weight: 0.9990 chunk 1023 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 240 ASN ** J 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 93373 Z= 0.261 Angle : 0.598 13.571 129992 Z= 0.313 Chirality : 0.042 0.251 15842 Planarity : 0.004 0.093 15601 Dihedral : 16.865 178.906 22510 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.40 % Favored : 94.23 % Rotamer: Outliers : 4.63 % Allowed : 17.92 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.01 % Twisted Proline : 1.36 % Twisted General : 0.09 % 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: -0.53 (0.08), residues: 12889 helix: 0.91 (0.08), residues: 5099 sheet: -0.71 (0.11), residues: 2258 loop : -1.37 (0.08), residues: 5532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 505 HIS 0.016 0.001 HIS A 785 PHE 0.030 0.002 PHE C 364 TYR 0.026 0.002 TYR A1101 ARG 0.006 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 505 time to evaluate : 7.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.7857 (t) REVERT: A 411 ILE cc_start: 0.8370 (mp) cc_final: 0.8111 (tp) REVERT: A 493 MET cc_start: 0.8184 (mmt) cc_final: 0.7704 (mmt) REVERT: A 569 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9030 (mm) REVERT: A 721 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8138 (tt) REVERT: A 946 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.9090 (m-40) REVERT: A 1170 MET cc_start: 0.8029 (mtp) cc_final: 0.7339 (mtp) REVERT: A 1231 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8790 (tp40) REVERT: A 1306 GLU cc_start: 0.9341 (mt-10) cc_final: 0.9103 (tp30) REVERT: A 1314 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8861 (t) REVERT: A 1472 ASN cc_start: 0.8559 (m-40) cc_final: 0.7881 (t0) REVERT: A 1485 ASP cc_start: 0.9305 (m-30) cc_final: 0.8756 (t0) REVERT: A 1550 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8657 (tt) REVERT: A 1830 VAL cc_start: 0.7829 (OUTLIER) cc_final: 0.7563 (p) REVERT: A 1834 PHE cc_start: 0.8566 (m-10) cc_final: 0.8198 (m-80) REVERT: A 1953 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6681 (m-40) REVERT: L 100 GLU cc_start: 0.8788 (tp30) cc_final: 0.8505 (pt0) REVERT: L 115 PHE cc_start: 0.9009 (t80) cc_final: 0.8655 (t80) REVERT: L 120 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: L 177 MET cc_start: 0.8719 (mtm) cc_final: 0.8195 (mtm) REVERT: L 453 ASP cc_start: 0.9069 (t0) cc_final: 0.8776 (t0) REVERT: N 102 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7530 (tmm-80) REVERT: N 139 GLU cc_start: 0.9341 (pt0) cc_final: 0.8943 (tm-30) REVERT: N 896 MET cc_start: 0.8280 (mmm) cc_final: 0.7910 (mtt) REVERT: J 379 ILE cc_start: 0.8201 (tp) cc_final: 0.7796 (tp) REVERT: J 419 MET cc_start: 0.2497 (mmm) cc_final: 0.2110 (mmm) REVERT: E 72 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8817 (tm-30) REVERT: E 92 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6634 (mtt) REVERT: E 108 ASP cc_start: 0.8808 (m-30) cc_final: 0.8461 (p0) REVERT: E 137 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6270 (p90) REVERT: C 164 MET cc_start: 0.8172 (mtt) cc_final: 0.7834 (mtp) REVERT: C 715 MET cc_start: 0.8718 (mmm) cc_final: 0.8249 (mmm) REVERT: C 877 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8881 (mm-30) REVERT: O 197 ARG cc_start: 0.6566 (mtm-85) cc_final: 0.5687 (mmt-90) REVERT: O 199 MET cc_start: 0.7499 (ttp) cc_final: 0.7267 (tmm) outliers start: 190 outliers final: 145 residues processed: 673 average time/residue: 0.7304 time to fit residues: 904.2020 Evaluate side-chains 634 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 477 time to evaluate : 7.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1231 GLN Chi-restraints excluded: chain A residue 1254 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1477 PHE Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1599 SER Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1711 VAL Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1758 ASP Chi-restraints excluded: chain A residue 1791 PHE Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1819 ILE Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1847 ASP Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1942 ASP Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 1953 ASN Chi-restraints excluded: chain A residue 2003 THR Chi-restraints excluded: chain A residue 2033 THR Chi-restraints excluded: chain A residue 2074 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 292 TRP Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 458 ASP Chi-restraints excluded: chain L residue 120 TYR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 358 ILE Chi-restraints excluded: chain L residue 382 SER Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 443 HIS Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 752 ASN Chi-restraints excluded: chain N residue 757 GLU Chi-restraints excluded: chain N residue 807 VAL Chi-restraints excluded: chain N residue 841 THR Chi-restraints excluded: chain N residue 891 ILE Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 462 HIS Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 137 TYR Chi-restraints excluded: chain M residue 39 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 98 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 769 TYR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 889 TYR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain O residue 200 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1351 random chunks: chunk 1184 optimal weight: 50.0000 chunk 1247 optimal weight: 7.9990 chunk 1138 optimal weight: 50.0000 chunk 1213 optimal weight: 30.0000 chunk 730 optimal weight: 30.0000 chunk 528 optimal weight: 50.0000 chunk 952 optimal weight: 7.9990 chunk 372 optimal weight: 40.0000 chunk 1096 optimal weight: 8.9990 chunk 1147 optimal weight: 20.0000 chunk 1209 optimal weight: 40.0000 overall best weight: 14.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS A 705 GLN A 733 GLN ** A 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN ** A1532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1932 GLN K 38 GLN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 GLN ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 298 GLN ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 ASN ** N 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 777 GLN ** N 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 HIS ** C 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 830 ASN ** C 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.191 93373 Z= 1.102 Angle : 1.273 24.369 129992 Z= 0.657 Chirality : 0.061 0.484 15842 Planarity : 0.009 0.153 15601 Dihedral : 17.800 178.998 22510 Min Nonbonded Distance : 1.571 Molprobity Statistics. All-atom Clashscore : 32.16 Ramachandran Plot: Outliers : 0.77 % Allowed : 11.10 % Favored : 88.13 % Rotamer: Outliers : 6.22 % Allowed : 17.48 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.01 % Twisted Proline : 1.75 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.07), residues: 12889 helix: -0.94 (0.07), residues: 4976 sheet: -1.07 (0.11), residues: 2033 loop : -2.21 (0.07), residues: 5880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.006 TRP K 195 HIS 0.022 0.004 HIS C 290 PHE 0.065 0.005 PHE A1574 TYR 0.061 0.005 TYR A1081 ARG 0.023 0.002 ARG A 928 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 443 time to evaluate : 7.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8216 (t) REVERT: A 237 MET cc_start: 0.8160 (tmm) cc_final: 0.7827 (tmm) REVERT: A 397 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8111 (p) REVERT: A 493 MET cc_start: 0.8457 (mmt) cc_final: 0.8081 (mmt) REVERT: A 569 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9118 (mm) REVERT: A 1028 TRP cc_start: 0.9577 (OUTLIER) cc_final: 0.9015 (t-100) REVERT: A 1145 MET cc_start: 0.8469 (mmt) cc_final: 0.7876 (mmt) REVERT: A 1170 MET cc_start: 0.8446 (mtp) cc_final: 0.8016 (mtm) REVERT: A 1231 GLN cc_start: 0.9564 (OUTLIER) cc_final: 0.9268 (tm-30) REVERT: A 1306 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9263 (tm-30) REVERT: A 1472 ASN cc_start: 0.8371 (m-40) cc_final: 0.7861 (t0) REVERT: A 1830 VAL cc_start: 0.7633 (OUTLIER) cc_final: 0.7382 (p) REVERT: A 1834 PHE cc_start: 0.8430 (m-10) cc_final: 0.8037 (m-80) REVERT: A 1879 ILE cc_start: 0.7761 (mt) cc_final: 0.7484 (mp) REVERT: A 1953 ASN cc_start: 0.7034 (OUTLIER) cc_final: 0.6759 (m-40) REVERT: K 188 MET cc_start: 0.8226 (mmm) cc_final: 0.7895 (mmm) REVERT: L 367 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7809 (ptp-170) REVERT: N 102 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7864 (tmm-80) REVERT: N 896 MET cc_start: 0.8051 (mmm) cc_final: 0.7782 (mtt) REVERT: J 379 ILE cc_start: 0.8599 (tp) cc_final: 0.7962 (tp) REVERT: J 419 MET cc_start: 0.3907 (mmm) cc_final: 0.3266 (mmm) REVERT: E 92 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7075 (mtt) REVERT: C 164 MET cc_start: 0.8386 (mtt) cc_final: 0.7927 (mtp) REVERT: C 189 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8713 (pp) REVERT: C 213 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9217 (mm) REVERT: O 197 ARG cc_start: 0.6812 (mtm-85) cc_final: 0.5877 (mmt180) REVERT: O 199 MET cc_start: 0.7854 (ttp) cc_final: 0.7618 (tmm) REVERT: O 211 ASN cc_start: 0.6664 (t0) cc_final: 0.6461 (t0) REVERT: O 216 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6413 (m-30) outliers start: 255 outliers final: 192 residues processed: 670 average time/residue: 0.7375 time to fit residues: 910.3432 Evaluate side-chains 635 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 431 time to evaluate : 7.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 643 ASN Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 671 TYR Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1028 TRP Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1095 MET Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1203 ASN Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1231 GLN Chi-restraints excluded: chain A residue 1254 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1358 ASP Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1369 ASN Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1477 PHE Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1523 SER Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1599 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1663 PHE Chi-restraints excluded: chain A residue 1674 ASP Chi-restraints excluded: chain A residue 1675 VAL Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1744 ASP Chi-restraints excluded: chain A residue 1758 ASP Chi-restraints excluded: chain A residue 1791 PHE Chi-restraints excluded: chain A residue 1809 ASN Chi-restraints excluded: chain A residue 1819 ILE Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1847 ASP Chi-restraints excluded: chain A residue 1863 HIS Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1942 ASP Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 1953 ASN Chi-restraints excluded: chain A residue 2003 THR Chi-restraints excluded: chain A residue 2033 THR Chi-restraints excluded: chain A residue 2074 LEU Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 430 MET Chi-restraints excluded: chain K residue 452 LEU Chi-restraints excluded: chain K residue 458 ASP Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 197 ILE Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 288 SER Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 367 ARG Chi-restraints excluded: chain L residue 382 SER Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 443 HIS Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 150 ASP Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 752 ASN Chi-restraints excluded: chain N residue 841 THR Chi-restraints excluded: chain N residue 848 THR Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 283 ASN Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 449 ASP Chi-restraints excluded: chain J residue 462 HIS Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 TYR Chi-restraints excluded: chain M residue 39 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 769 TYR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 889 TYR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain O residue 200 ASN Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 216 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1351 random chunks: chunk 796 optimal weight: 7.9990 chunk 1283 optimal weight: 6.9990 chunk 783 optimal weight: 8.9990 chunk 608 optimal weight: 40.0000 chunk 891 optimal weight: 50.0000 chunk 1345 optimal weight: 50.0000 chunk 1238 optimal weight: 30.0000 chunk 1071 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 827 optimal weight: 50.0000 chunk 657 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1600 GLN A1845 ASN A2018 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 ASN ** N 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 HIS C 557 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.135 93373 Z= 0.576 Angle : 0.829 15.861 129992 Z= 0.432 Chirality : 0.048 0.285 15842 Planarity : 0.005 0.104 15601 Dihedral : 17.458 179.968 22510 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.63 % Favored : 90.93 % Rotamer: Outliers : 4.71 % Allowed : 19.16 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.39 % Cis-general : 0.01 % Twisted Proline : 1.56 % Twisted General : 0.13 % 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: -1.93 (0.07), residues: 12889 helix: -0.44 (0.07), residues: 5021 sheet: -1.13 (0.11), residues: 2024 loop : -2.06 (0.08), residues: 5844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 505 HIS 0.011 0.002 HIS C 423 PHE 0.037 0.003 PHE A1574 TYR 0.046 0.003 TYR A1740 ARG 0.013 0.001 ARG C 763 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25778 Ramachandran restraints generated. 12889 Oldfield, 0 Emsley, 12889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 461 time to evaluate : 7.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8018 (t) REVERT: A 237 MET cc_start: 0.8117 (tmm) cc_final: 0.7686 (tmm) REVERT: A 493 MET cc_start: 0.8350 (mmt) cc_final: 0.7955 (mmt) REVERT: A 569 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9137 (mm) REVERT: A 946 ASN cc_start: 0.9426 (OUTLIER) cc_final: 0.9108 (m-40) REVERT: A 1028 TRP cc_start: 0.9476 (OUTLIER) cc_final: 0.8605 (t-100) REVERT: A 1145 MET cc_start: 0.8362 (mmt) cc_final: 0.7620 (mmt) REVERT: A 1170 MET cc_start: 0.8332 (mtp) cc_final: 0.7853 (mtm) REVERT: A 1231 GLN cc_start: 0.9433 (OUTLIER) cc_final: 0.8971 (tp40) REVERT: A 1306 GLU cc_start: 0.9460 (mt-10) cc_final: 0.9243 (tp30) REVERT: A 1379 MET cc_start: 0.9254 (tpp) cc_final: 0.8940 (tpp) REVERT: A 1472 ASN cc_start: 0.8443 (m-40) cc_final: 0.7973 (t0) REVERT: A 1485 ASP cc_start: 0.9418 (m-30) cc_final: 0.8822 (t0) REVERT: A 1830 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7564 (p) REVERT: A 1834 PHE cc_start: 0.8617 (m-10) cc_final: 0.8276 (m-80) REVERT: A 1879 ILE cc_start: 0.7554 (mt) cc_final: 0.7299 (mp) REVERT: A 1953 ASN cc_start: 0.7165 (OUTLIER) cc_final: 0.6844 (m-40) REVERT: K 188 MET cc_start: 0.8361 (mmm) cc_final: 0.8000 (mmm) REVERT: K 332 MET cc_start: 0.8319 (tmm) cc_final: 0.7707 (tmm) REVERT: L 115 PHE cc_start: 0.9189 (t80) cc_final: 0.8935 (t80) REVERT: L 177 MET cc_start: 0.8944 (mtm) cc_final: 0.8723 (mtm) REVERT: L 367 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7053 (ptp-170) REVERT: N 102 ARG cc_start: 0.8270 (mtt90) cc_final: 0.7766 (tmm-80) REVERT: J 281 PHE cc_start: 0.8354 (t80) cc_final: 0.8141 (t80) REVERT: J 379 ILE cc_start: 0.8375 (tp) cc_final: 0.7770 (tp) REVERT: J 419 MET cc_start: 0.3160 (mmm) cc_final: 0.2639 (mmm) REVERT: E 92 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6792 (mtt) REVERT: C 164 MET cc_start: 0.8333 (mtt) cc_final: 0.7881 (mtp) REVERT: C 189 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8620 (pp) REVERT: C 213 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8910 (mm) REVERT: C 715 MET cc_start: 0.8783 (mmm) cc_final: 0.8422 (mmm) REVERT: O 197 ARG cc_start: 0.6601 (mtm-85) cc_final: 0.5696 (mmt180) REVERT: O 199 MET cc_start: 0.7760 (ttp) cc_final: 0.7526 (tmm) REVERT: O 211 ASN cc_start: 0.6725 (t0) cc_final: 0.6462 (t0) outliers start: 193 outliers final: 155 residues processed: 632 average time/residue: 0.7329 time to fit residues: 854.1448 Evaluate side-chains 618 residues out of total 11933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 452 time to evaluate : 7.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1028 TRP Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1061 ILE Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1094 ASP Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1177 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1231 GLN Chi-restraints excluded: chain A residue 1254 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1319 ILE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1381 THR Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1477 PHE Chi-restraints excluded: chain A residue 1488 ILE Chi-restraints excluded: chain A residue 1498 ASP Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1599 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1646 ILE Chi-restraints excluded: chain A residue 1674 ASP Chi-restraints excluded: chain A residue 1725 LYS Chi-restraints excluded: chain A residue 1744 ASP Chi-restraints excluded: chain A residue 1758 ASP Chi-restraints excluded: chain A residue 1791 PHE Chi-restraints excluded: chain A residue 1819 ILE Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1847 ASP Chi-restraints excluded: chain A residue 1935 VAL Chi-restraints excluded: chain A residue 1942 ASP Chi-restraints excluded: chain A residue 1944 LEU Chi-restraints excluded: chain A residue 1953 ASN Chi-restraints excluded: chain A residue 2003 THR Chi-restraints excluded: chain A residue 2033 THR Chi-restraints excluded: chain A residue 2074 LEU Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 215 ASP Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 458 ASP Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 367 ARG Chi-restraints excluded: chain L residue 382 SER Chi-restraints excluded: chain L residue 384 VAL Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 443 HIS Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 132 ASN Chi-restraints excluded: chain N residue 150 ASP Chi-restraints excluded: chain N residue 212 VAL Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 220 LEU Chi-restraints excluded: chain N residue 277 ILE Chi-restraints excluded: chain N residue 672 LEU Chi-restraints excluded: chain N residue 752 ASN Chi-restraints excluded: chain N residue 841 THR Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 237 THR Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 284 ASP Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 462 HIS Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 137 TYR Chi-restraints excluded: chain M residue 39 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 769 TYR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain C residue 878 GLU Chi-restraints excluded: chain C residue 889 TYR Chi-restraints excluded: chain C residue 928 CYS Chi-restraints excluded: chain C residue 936 ILE Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 200 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1351 random chunks: chunk 851 optimal weight: 50.0000 chunk 1141 optimal weight: 40.0000 chunk 328 optimal weight: 4.9990 chunk 988 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 297 optimal weight: 0.9980 chunk 1073 optimal weight: 50.0000 chunk 449 optimal weight: 0.8980 chunk 1102 optimal weight: 20.0000 chunk 135 optimal weight: 0.5980 chunk 197 optimal weight: 50.0000 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 ASN ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 GLN A1600 GLN A1932 GLN A2018 ASN ** K 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 GLN ** K 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 HIS ** L 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 448 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.147959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.128973 restraints weight = 436709.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.125520 restraints weight = 551627.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.123224 restraints weight = 452734.183| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4149 r_free = 0.4149 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4149 r_free = 0.4149 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 93373 Z= 0.199 Angle : 0.628 14.072 129992 Z= 0.326 Chirality : 0.043 0.276 15842 Planarity : 0.004 0.097 15601 Dihedral : 17.042 179.192 22510 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.07 % Favored : 93.54 % Rotamer: Outliers : 2.66 % Allowed : 21.09 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.01 % Twisted Proline : 1.17 % Twisted General : 0.10 % 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: -1.07 (0.07), residues: 12889 helix: 0.49 (0.07), residues: 5045 sheet: -0.96 (0.11), residues: 2071 loop : -1.68 (0.08), residues: 5773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 505 HIS 0.012 0.001 HIS A 785 PHE 0.035 0.002 PHE C 799 TYR 0.030 0.002 TYR A1101 ARG 0.019 0.001 ARG N 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17443.78 seconds wall clock time: 307 minutes 32.82 seconds (18452.82 seconds total)