Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 18:57:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/04_2023/5m32_4146_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/04_2023/5m32_4146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/04_2023/5m32_4146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/04_2023/5m32_4146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/04_2023/5m32_4146_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m32_4146/04_2023/5m32_4146_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 400 5.16 5 C 47773 2.51 5 N 13346 2.21 5 O 14554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "G TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 198": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 153": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "K ARG 186": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O ARG 90": "NH1" <-> "NH2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "Q ARG 57": "NH1" <-> "NH2" Residue "Q PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 101": "NH1" <-> "NH2" Residue "S ARG 125": "NH1" <-> "NH2" Residue "S ARG 164": "NH1" <-> "NH2" Residue "U TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 198": "NH1" <-> "NH2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "X ARG 95": "NH1" <-> "NH2" Residue "X ARG 153": "NH1" <-> "NH2" Residue "X GLU 192": "OE1" <-> "OE2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ARG 186": "NH1" <-> "NH2" Residue "Z ARG 28": "NH1" <-> "NH2" Residue "Z PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 173": "NH1" <-> "NH2" Residue "c PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 144": "NH1" <-> "NH2" Residue "c GLU 168": "OE1" <-> "OE2" Residue "c ARG 284": "NH1" <-> "NH2" Residue "c ARG 312": "NH1" <-> "NH2" Residue "d GLU 145": "OE1" <-> "OE2" Residue "d GLU 254": "OE1" <-> "OE2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "d ARG 343": "NH1" <-> "NH2" Residue "d ARG 346": "NH1" <-> "NH2" Residue "d PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 410": "NH1" <-> "NH2" Residue "d ARG 411": "NH1" <-> "NH2" Residue "d TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 121": "NH1" <-> "NH2" Residue "e ARG 252": "NH1" <-> "NH2" Residue "e ARG 287": "NH1" <-> "NH2" Residue "e ARG 338": "NH1" <-> "NH2" Residue "e ARG 339": "NH1" <-> "NH2" Residue "f TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 85": "NH1" <-> "NH2" Residue "f TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 125": "OE1" <-> "OE2" Residue "f ASP 126": "OD1" <-> "OD2" Residue "f ARG 255": "NH1" <-> "NH2" Residue "g ARG 304": "NH1" <-> "NH2" Residue "g ARG 347": "NH1" <-> "NH2" Residue "g GLU 422": "OE1" <-> "OE2" Residue "h ARG 113": "NH1" <-> "NH2" Residue "h ARG 117": "NH1" <-> "NH2" Residue "h GLU 358": "OE1" <-> "OE2" Residue "m ARG 125": "NH1" <-> "NH2" Residue "m GLU 169": "OE1" <-> "OE2" Residue "m ARG 176": "NH1" <-> "NH2" Residue "m ARG 177": "NH1" <-> "NH2" Residue "m ARG 179": "NH1" <-> "NH2" Residue "m PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 76085 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1763 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1836 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1771 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1757 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1805 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 224} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1818 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Chain breaks: 1 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1806 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1663 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1590 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "J" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1560 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1545 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1637 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1634 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 213, 1634 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 1660 Chain: "M" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Chain: "N" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1513 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 194} Chain: "O" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1764 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "P" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1875 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 238} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "Q" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1785 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 228} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1768 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "S" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1834 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 228} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "T" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1877 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1841 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "V" Number of atoms: 1627 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1622 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 220, 1622 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1643 Chain: "W" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1586 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1563 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 188} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "Z" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1642 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "a" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1679 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1519 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2728 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 21, 'TRANS': 325} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "d" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2560 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "e" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2776 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 343} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "f" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2692 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 330} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "g" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2777 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "h" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2518 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 314} Chain breaks: 3 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "i" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1145 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 625 Unresolved non-hydrogen angles: 805 Unresolved non-hydrogen dihedrals: 508 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 12, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 348 Chain: "j" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 779 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 3 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 641 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 5, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 283 Chain: "k" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 1819 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 331} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 357} Chain breaks: 4 Unresolved non-hydrogen bonds: 1186 Unresolved non-hydrogen angles: 1496 Unresolved non-hydrogen dihedrals: 962 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 16, 'TRP:plan': 4, 'ASP:plan': 19, 'PHE:plan': 9, 'GLU:plan': 35, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 617 Chain: "l" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2572 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 10, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 719 Unresolved non-hydrogen angles: 906 Unresolved non-hydrogen dihedrals: 569 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 16, 'TYR:plan': 6, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 22, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 374 Chain: "m" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2421 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 365} Unresolved non-hydrogen bonds: 697 Unresolved non-hydrogen angles: 885 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 14, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 426 Chain: "n" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1030 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 658 Unresolved non-hydrogen angles: 851 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 14, 'TRP:plan': 3, 'ASP:plan': 16, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 370 Chain: "o" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 377 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 115 Chain: "p" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 504 Classifications: {'peptide': 101} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 85} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 116 Chain: "q" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1311 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 247} Chain breaks: 2 Unresolved non-hydrogen bonds: 755 Unresolved non-hydrogen angles: 961 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 12, 'TYR:plan': 8, 'ASN:plan1': 13, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 404 Chain: "r" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "s" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "t" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {'6V9': 1, '6VA': 1, '7C9': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'7C9:plan-1': 2, '6V9:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "u" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Unusual residues: {'6V9': 1, '6VA': 1, '7C9': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'7C9:plan-1': 2, '6V9:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "c" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 32.90, per 1000 atoms: 0.43 Number of scatterers: 76085 At special positions: 0 Unit cell: (186.69, 172.72, 304.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 400 16.00 P 12 15.00 O 14554 8.00 N 13346 7.00 C 47773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 61 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 43 " - pdb=" SG CYS Z 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 54 " - pdb=" SG CYS Z 61 " distance=2.02 Simple disulfide: pdb=" SG CYS c 236 " - pdb=" SG CYS c 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM75945 O3A ADP c 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM76026 O3A ADP g 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75948 O5' ADP c 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM76026 O3A ADP g 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75945 O3A ADP c 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75945 O3A ADP c 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75947 O4' ADP c 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75999 O3A ADP e 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75975 O5' ADP d 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75975 O5' ADP d 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM75974 O4' ADP d 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 26.06 Conformation dependent library (CDL) restraints added in 11.4 seconds 20684 Ramachandran restraints generated. 10342 Oldfield, 0 Emsley, 10342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 339 helices and 83 sheets defined 34.8% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 79 through 100 removed outlier: 3.860A pdb=" N ARG A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.667A pdb=" N LYS A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.756A pdb=" N ALA B 24 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 29 " --> pdb=" O MET B 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.784A pdb=" N ASN B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 230 through 238 removed outlier: 3.557A pdb=" N GLU B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 14 No H-bonds generated for 'chain 'C' and resid 12 through 14' Processing helix chain 'C' and resid 17 through 27 Processing helix chain 'C' and resid 50 through 53 No H-bonds generated for 'chain 'C' and resid 50 through 53' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 80 through 97 Processing helix chain 'C' and resid 104 through 118 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 222 through 234 removed outlier: 3.569A pdb=" N GLU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 28 Processing helix chain 'D' and resid 86 through 103 Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.845A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 231 through 240 removed outlier: 3.726A pdb=" N ASP D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 7 No H-bonds generated for 'chain 'E' and resid 5 through 7' Processing helix chain 'E' and resid 24 through 30 Processing helix chain 'E' and resid 78 through 97 Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 118 through 121 No H-bonds generated for 'chain 'E' and resid 118 through 121' Processing helix chain 'E' and resid 165 through 172 Processing helix chain 'E' and resid 184 through 195 removed outlier: 4.154A pdb=" N LYS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA E 194 " --> pdb=" O HIS E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 31 removed outlier: 3.673A pdb=" N ALA F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 102 Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.983A pdb=" N THR F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 178 removed outlier: 4.733A pdb=" N THR F 174 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 200 removed outlier: 3.852A pdb=" N ALA F 194 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 233 No H-bonds generated for 'chain 'F' and resid 231 through 233' Processing helix chain 'F' and resid 236 through 238 No H-bonds generated for 'chain 'F' and resid 236 through 238' Processing helix chain 'G' and resid 25 through 32 removed outlier: 3.518A pdb=" N ALA G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 105 removed outlier: 4.085A pdb=" N ARG G 88 " --> pdb=" O THR G 84 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN G 90 " --> pdb=" O ASP G 86 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG G 93 " --> pdb=" O SER G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.557A pdb=" N CYS G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 181 Processing helix chain 'G' and resid 198 through 205 removed outlier: 4.276A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 240 Processing helix chain 'H' and resid 49 through 70 removed outlier: 3.999A pdb=" N ASP H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 132 through 138 removed outlier: 4.512A pdb=" N ALA H 136 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE H 138 " --> pdb=" O ALA H 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 132 through 138' Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'I' and resid 56 through 76 Processing helix chain 'I' and resid 83 through 94 Processing helix chain 'I' and resid 142 through 145 No H-bonds generated for 'chain 'I' and resid 142 through 145' Processing helix chain 'I' and resid 147 through 152 Processing helix chain 'I' and resid 159 through 175 Processing helix chain 'J' and resid 53 through 71 removed outlier: 3.681A pdb=" N ALA J 57 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU J 58 " --> pdb=" O VAL J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 90 Processing helix chain 'J' and resid 135 through 139 removed outlier: 3.710A pdb=" N LEU J 138 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR J 139 " --> pdb=" O ALA J 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 135 through 139' Processing helix chain 'J' and resid 142 through 145 No H-bonds generated for 'chain 'J' and resid 142 through 145' Processing helix chain 'J' and resid 153 through 169 Processing helix chain 'K' and resid 51 through 70 Processing helix chain 'K' and resid 76 through 89 Processing helix chain 'K' and resid 133 through 142 Processing helix chain 'K' and resid 149 through 166 Processing helix chain 'K' and resid 192 through 199 Processing helix chain 'L' and resid 58 through 76 Processing helix chain 'L' and resid 85 through 98 Processing helix chain 'L' and resid 142 through 151 removed outlier: 3.523A pdb=" N GLN L 146 " --> pdb=" O SER L 142 " (cutoff:3.500A) Proline residue: L 147 - end of helix removed outlier: 3.524A pdb=" N ASN L 151 " --> pdb=" O PRO L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 185 removed outlier: 3.852A pdb=" N LYS L 176 " --> pdb=" O MET L 172 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL L 178 " --> pdb=" O LEU L 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 77 removed outlier: 3.884A pdb=" N LEU M 77 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 102 removed outlier: 3.582A pdb=" N HIS M 89 " --> pdb=" O PRO M 85 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS M 102 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 156 removed outlier: 5.744A pdb=" N ALA M 146 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN M 147 " --> pdb=" O TYR M 144 " (cutoff:3.500A) Proline residue: M 148 - end of helix removed outlier: 3.731A pdb=" N ARG M 151 " --> pdb=" O PRO M 148 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU M 152 " --> pdb=" O LEU M 149 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU M 154 " --> pdb=" O ARG M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 179 Processing helix chain 'N' and resid 50 through 70 removed outlier: 3.683A pdb=" N ALA N 54 " --> pdb=" O ALA N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 88 Processing helix chain 'N' and resid 136 through 142 Processing helix chain 'N' and resid 149 through 166 Processing helix chain 'O' and resid 19 through 29 Processing helix chain 'O' and resid 79 through 100 removed outlier: 3.860A pdb=" N ARG O 83 " --> pdb=" O GLY O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 116 Processing helix chain 'O' and resid 119 through 121 No H-bonds generated for 'chain 'O' and resid 119 through 121' Processing helix chain 'O' and resid 166 through 175 Processing helix chain 'O' and resid 185 through 194 Processing helix chain 'O' and resid 222 through 230 removed outlier: 3.667A pdb=" N LYS O 226 " --> pdb=" O PRO O 222 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP O 227 " --> pdb=" O THR O 223 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 30 removed outlier: 3.755A pdb=" N ALA P 24 " --> pdb=" O GLN P 20 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY P 29 " --> pdb=" O MET P 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS P 30 " --> pdb=" O GLU P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 101 removed outlier: 3.785A pdb=" N ASN P 84 " --> pdb=" O THR P 80 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL P 85 " --> pdb=" O SER P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 123 Processing helix chain 'P' and resid 175 through 177 No H-bonds generated for 'chain 'P' and resid 175 through 177' Processing helix chain 'P' and resid 186 through 199 Processing helix chain 'P' and resid 230 through 238 removed outlier: 3.558A pdb=" N GLU P 234 " --> pdb=" O GLN P 230 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS P 238 " --> pdb=" O GLU P 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 14 No H-bonds generated for 'chain 'Q' and resid 12 through 14' Processing helix chain 'Q' and resid 17 through 27 Processing helix chain 'Q' and resid 56 through 58 No H-bonds generated for 'chain 'Q' and resid 56 through 58' Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 104 through 118 Processing helix chain 'Q' and resid 166 through 174 Processing helix chain 'Q' and resid 185 through 196 Processing helix chain 'Q' and resid 222 through 235 Processing helix chain 'R' and resid 22 through 28 Processing helix chain 'R' and resid 86 through 103 Processing helix chain 'R' and resid 112 through 117 Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.845A pdb=" N GLU R 183 " --> pdb=" O SER R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 204 Processing helix chain 'R' and resid 231 through 240 removed outlier: 3.727A pdb=" N ASP R 240 " --> pdb=" O GLU R 236 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 7 No H-bonds generated for 'chain 'S' and resid 5 through 7' Processing helix chain 'S' and resid 24 through 30 Processing helix chain 'S' and resid 79 through 97 Processing helix chain 'S' and resid 105 through 115 Processing helix chain 'S' and resid 118 through 121 No H-bonds generated for 'chain 'S' and resid 118 through 121' Processing helix chain 'S' and resid 165 through 172 Processing helix chain 'S' and resid 184 through 195 removed outlier: 4.155A pdb=" N LYS S 189 " --> pdb=" O ASP S 185 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS S 190 " --> pdb=" O GLU S 186 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA S 194 " --> pdb=" O HIS S 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 31 removed outlier: 3.673A pdb=" N ALA T 26 " --> pdb=" O GLN T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 102 Processing helix chain 'T' and resid 108 through 123 removed outlier: 3.983A pdb=" N THR T 123 " --> pdb=" O VAL T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 178 removed outlier: 4.731A pdb=" N THR T 174 " --> pdb=" O GLN T 170 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU T 175 " --> pdb=" O ALA T 171 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE T 176 " --> pdb=" O ALA T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 187 through 200 removed outlier: 3.852A pdb=" N ALA T 194 " --> pdb=" O VAL T 190 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS T 195 " --> pdb=" O LYS T 191 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 233 No H-bonds generated for 'chain 'T' and resid 231 through 233' Processing helix chain 'T' and resid 236 through 238 No H-bonds generated for 'chain 'T' and resid 236 through 238' Processing helix chain 'U' and resid 25 through 32 removed outlier: 3.518A pdb=" N ALA U 31 " --> pdb=" O TYR U 27 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE U 32 " --> pdb=" O ALA U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 105 removed outlier: 4.085A pdb=" N ARG U 88 " --> pdb=" O THR U 84 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER U 89 " --> pdb=" O ALA U 85 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN U 90 " --> pdb=" O ASP U 86 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 125 removed outlier: 3.557A pdb=" N CYS U 115 " --> pdb=" O VAL U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 181 Processing helix chain 'U' and resid 198 through 205 removed outlier: 4.277A pdb=" N LEU U 202 " --> pdb=" O ALA U 198 " (cutoff:3.500A) Processing helix chain 'U' and resid 232 through 240 Processing helix chain 'V' and resid 49 through 70 removed outlier: 3.999A pdb=" N ASP V 53 " --> pdb=" O ALA V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 88 Processing helix chain 'V' and resid 132 through 138 removed outlier: 4.513A pdb=" N ALA V 136 " --> pdb=" O LEU V 132 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL V 137 " --> pdb=" O ALA V 133 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE V 138 " --> pdb=" O ALA V 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 132 through 138' Processing helix chain 'V' and resid 148 through 163 Processing helix chain 'W' and resid 56 through 76 Processing helix chain 'W' and resid 83 through 94 Processing helix chain 'W' and resid 142 through 145 No H-bonds generated for 'chain 'W' and resid 142 through 145' Processing helix chain 'W' and resid 147 through 152 Processing helix chain 'W' and resid 159 through 175 Processing helix chain 'X' and resid 53 through 71 removed outlier: 3.681A pdb=" N ALA X 57 " --> pdb=" O THR X 53 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU X 58 " --> pdb=" O VAL X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 90 Processing helix chain 'X' and resid 135 through 139 removed outlier: 3.710A pdb=" N LEU X 138 " --> pdb=" O GLY X 135 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR X 139 " --> pdb=" O ALA X 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 135 through 139' Processing helix chain 'X' and resid 142 through 145 No H-bonds generated for 'chain 'X' and resid 142 through 145' Processing helix chain 'X' and resid 153 through 169 Processing helix chain 'Y' and resid 51 through 70 Processing helix chain 'Y' and resid 76 through 89 Processing helix chain 'Y' and resid 133 through 142 Processing helix chain 'Y' and resid 149 through 166 Processing helix chain 'Y' and resid 192 through 199 Processing helix chain 'Z' and resid 58 through 76 Processing helix chain 'Z' and resid 85 through 98 Processing helix chain 'Z' and resid 142 through 151 removed outlier: 3.523A pdb=" N GLN Z 146 " --> pdb=" O SER Z 142 " (cutoff:3.500A) Proline residue: Z 147 - end of helix removed outlier: 3.525A pdb=" N ASN Z 151 " --> pdb=" O PRO Z 147 " (cutoff:3.500A) Processing helix chain 'Z' and resid 172 through 185 removed outlier: 3.852A pdb=" N LYS Z 176 " --> pdb=" O MET Z 172 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP Z 177 " --> pdb=" O ARG Z 173 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL Z 178 " --> pdb=" O LEU Z 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 77 removed outlier: 3.885A pdb=" N LEU a 77 " --> pdb=" O ASP a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 102 removed outlier: 3.581A pdb=" N HIS a 89 " --> pdb=" O PRO a 85 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS a 102 " --> pdb=" O SER a 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 140 through 156 removed outlier: 5.744A pdb=" N ALA a 146 " --> pdb=" O ALA a 143 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLN a 147 " --> pdb=" O TYR a 144 " (cutoff:3.500A) Proline residue: a 148 - end of helix removed outlier: 3.730A pdb=" N ARG a 151 " --> pdb=" O PRO a 148 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU a 152 " --> pdb=" O LEU a 149 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL a 153 " --> pdb=" O LEU a 150 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU a 154 " --> pdb=" O ARG a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 162 through 179 Processing helix chain 'b' and resid 50 through 70 removed outlier: 3.683A pdb=" N ALA b 54 " --> pdb=" O ALA b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 136 through 142 Processing helix chain 'b' and resid 149 through 166 Processing helix chain 'c' and resid 159 through 161 No H-bonds generated for 'chain 'c' and resid 159 through 161' Processing helix chain 'c' and resid 183 through 191 removed outlier: 3.515A pdb=" N LEU c 187 " --> pdb=" O GLN c 183 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL c 190 " --> pdb=" O LYS c 186 " (cutoff:3.500A) Processing helix chain 'c' and resid 196 through 203 removed outlier: 3.946A pdb=" N VAL c 202 " --> pdb=" O GLU c 199 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 231 Processing helix chain 'c' and resid 252 through 265 Processing helix chain 'c' and resid 277 through 279 No H-bonds generated for 'chain 'c' and resid 277 through 279' Processing helix chain 'c' and resid 293 through 305 Processing helix chain 'c' and resid 348 through 358 removed outlier: 3.965A pdb=" N THR c 352 " --> pdb=" O LEU c 348 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS c 353 " --> pdb=" O GLU c 349 " (cutoff:3.500A) Processing helix chain 'c' and resid 370 through 376 Processing helix chain 'c' and resid 385 through 398 Processing helix chain 'c' and resid 409 through 416 Processing helix chain 'c' and resid 429 through 432 No H-bonds generated for 'chain 'c' and resid 429 through 432' Processing helix chain 'd' and resid 95 through 98 No H-bonds generated for 'chain 'd' and resid 95 through 98' Processing helix chain 'd' and resid 184 through 187 No H-bonds generated for 'chain 'd' and resid 184 through 187' Processing helix chain 'd' and resid 192 through 206 Proline residue: d 204 - end of helix Processing helix chain 'd' and resid 208 through 214 removed outlier: 3.761A pdb=" N TYR d 211 " --> pdb=" O PRO d 208 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLU d 212 " --> pdb=" O GLU d 209 " (cutoff:3.500A) Processing helix chain 'd' and resid 238 through 241 No H-bonds generated for 'chain 'd' and resid 238 through 241' Processing helix chain 'd' and resid 251 through 255 Processing helix chain 'd' and resid 270 through 277 removed outlier: 3.690A pdb=" N HIS d 277 " --> pdb=" O VAL d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 302 through 316 Processing helix chain 'd' and resid 358 through 371 removed outlier: 3.918A pdb=" N ILE d 367 " --> pdb=" O ARG d 363 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS d 368 " --> pdb=" O ILE d 364 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR d 369 " --> pdb=" O PHE d 365 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER d 370 " --> pdb=" O GLN d 366 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG d 371 " --> pdb=" O ILE d 367 " (cutoff:3.500A) Processing helix chain 'd' and resid 392 through 405 removed outlier: 3.505A pdb=" N LYS d 396 " --> pdb=" O GLY d 392 " (cutoff:3.500A) Processing helix chain 'd' and resid 418 through 426 Processing helix chain 'e' and resid 56 through 73 removed outlier: 3.637A pdb=" N TYR e 60 " --> pdb=" O VAL e 56 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS e 62 " --> pdb=" O GLU e 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP e 63 " --> pdb=" O GLU e 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 78 through 81 removed outlier: 3.841A pdb=" N ARG e 81 " --> pdb=" O GLU e 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 78 through 81' Processing helix chain 'e' and resid 172 through 180 Processing helix chain 'e' and resid 183 through 186 No H-bonds generated for 'chain 'e' and resid 183 through 186' Processing helix chain 'e' and resid 191 through 194 No H-bonds generated for 'chain 'e' and resid 191 through 194' Processing helix chain 'e' and resid 243 through 255 Processing helix chain 'e' and resid 267 through 269 No H-bonds generated for 'chain 'e' and resid 267 through 269' Processing helix chain 'e' and resid 285 through 298 removed outlier: 4.030A pdb=" N LEU e 290 " --> pdb=" O GLN e 286 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU e 291 " --> pdb=" O ARG e 287 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP e 297 " --> pdb=" O LEU e 293 " (cutoff:3.500A) Processing helix chain 'e' and resid 338 through 350 removed outlier: 3.651A pdb=" N ARG e 342 " --> pdb=" O ARG e 338 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU e 343 " --> pdb=" O ARG e 339 " (cutoff:3.500A) Processing helix chain 'e' and resid 361 through 364 No H-bonds generated for 'chain 'e' and resid 361 through 364' Processing helix chain 'e' and resid 373 through 386 Processing helix chain 'e' and resid 397 through 406 Processing helix chain 'f' and resid 34 through 50 removed outlier: 4.686A pdb=" N SER f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASN f 45 " --> pdb=" O GLU f 41 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP f 46 " --> pdb=" O LYS f 42 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU f 47 " --> pdb=" O SER f 43 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS f 48 " --> pdb=" O GLU f 44 " (cutoff:3.500A) Processing helix chain 'f' and resid 89 through 91 No H-bonds generated for 'chain 'f' and resid 89 through 91' Processing helix chain 'f' and resid 139 through 154 Proline residue: f 152 - end of helix Processing helix chain 'f' and resid 156 through 162 removed outlier: 4.242A pdb=" N GLN f 160 " --> pdb=" O GLU f 157 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG f 161 " --> pdb=" O LEU f 158 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 188 Processing helix chain 'f' and resid 210 through 224 Processing helix chain 'f' and resid 251 through 254 No H-bonds generated for 'chain 'f' and resid 251 through 254' Processing helix chain 'f' and resid 256 through 264 Processing helix chain 'f' and resid 282 through 284 No H-bonds generated for 'chain 'f' and resid 282 through 284' Processing helix chain 'f' and resid 307 through 316 Processing helix chain 'f' and resid 328 through 334 Processing helix chain 'f' and resid 340 through 357 Processing helix chain 'f' and resid 364 through 374 removed outlier: 3.807A pdb=" N ARG f 372 " --> pdb=" O MET f 368 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS f 373 " --> pdb=" O LYS f 369 " (cutoff:3.500A) Processing helix chain 'g' and resid 64 through 80 removed outlier: 3.528A pdb=" N ALA g 68 " --> pdb=" O HIS g 64 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET g 69 " --> pdb=" O GLU g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 170 through 173 No H-bonds generated for 'chain 'g' and resid 170 through 173' Processing helix chain 'g' and resid 192 through 202 Processing helix chain 'g' and resid 210 through 215 Processing helix chain 'g' and resid 233 through 240 Processing helix chain 'g' and resid 262 through 277 removed outlier: 3.708A pdb=" N VAL g 268 " --> pdb=" O GLY g 264 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG g 269 " --> pdb=" O ALA g 265 " (cutoff:3.500A) Processing helix chain 'g' and resid 290 through 292 No H-bonds generated for 'chain 'g' and resid 290 through 292' Processing helix chain 'g' and resid 305 through 315 removed outlier: 4.242A pdb=" N ASN g 315 " --> pdb=" O LEU g 311 " (cutoff:3.500A) Processing helix chain 'g' and resid 340 through 343 Processing helix chain 'g' and resid 361 through 371 removed outlier: 3.641A pdb=" N SER g 370 " --> pdb=" O MET g 366 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG g 371 " --> pdb=" O GLN g 367 " (cutoff:3.500A) Processing helix chain 'g' and resid 381 through 386 Processing helix chain 'g' and resid 394 through 410 Processing helix chain 'g' and resid 417 through 424 Processing helix chain 'h' and resid 39 through 63 Processing helix chain 'h' and resid 65 through 67 No H-bonds generated for 'chain 'h' and resid 65 through 67' Processing helix chain 'h' and resid 101 through 103 No H-bonds generated for 'chain 'h' and resid 101 through 103' Processing helix chain 'h' and resid 133 through 139 Processing helix chain 'h' and resid 156 through 163 Processing helix chain 'h' and resid 167 through 170 No H-bonds generated for 'chain 'h' and resid 167 through 170' Processing helix chain 'h' and resid 199 through 205 removed outlier: 3.667A pdb=" N ALA h 204 " --> pdb=" O ALA h 200 " (cutoff:3.500A) Processing helix chain 'h' and resid 233 through 241 Processing helix chain 'h' and resid 267 through 278 removed outlier: 3.808A pdb=" N LEU h 276 " --> pdb=" O THR h 272 " (cutoff:3.500A) Processing helix chain 'h' and resid 322 through 335 Processing helix chain 'h' and resid 344 through 350 Processing helix chain 'h' and resid 357 through 371 removed outlier: 4.096A pdb=" N VAL h 362 " --> pdb=" O GLU h 358 " (cutoff:3.500A) Processing helix chain 'h' and resid 381 through 387 Processing helix chain 'i' and resid 476 through 480 Processing helix chain 'i' and resid 492 through 501 Processing helix chain 'i' and resid 507 through 520 Processing helix chain 'i' and resid 526 through 533 Processing helix chain 'i' and resid 543 through 558 removed outlier: 6.874A pdb=" N VAL i 550 " --> pdb=" O ARG i 546 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY i 551 " --> pdb=" O GLY i 547 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE i 552 " --> pdb=" O LEU i 548 " (cutoff:3.500A) Processing helix chain 'i' and resid 561 through 572 removed outlier: 4.532A pdb=" N GLU i 568 " --> pdb=" O ASP i 564 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N SER i 569 " --> pdb=" O ALA i 565 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU i 570 " --> pdb=" O LEU i 566 " (cutoff:3.500A) Processing helix chain 'i' and resid 576 through 585 Processing helix chain 'i' and resid 596 through 607 Processing helix chain 'i' and resid 614 through 624 Processing helix chain 'i' and resid 633 through 641 removed outlier: 3.801A pdb=" N LEU i 639 " --> pdb=" O SER i 635 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU i 640 " --> pdb=" O VAL i 636 " (cutoff:3.500A) Processing helix chain 'i' and resid 648 through 660 removed outlier: 4.477A pdb=" N CYS i 659 " --> pdb=" O ALA i 655 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS i 660 " --> pdb=" O LEU i 656 " (cutoff:3.500A) Processing helix chain 'i' and resid 670 through 673 No H-bonds generated for 'chain 'i' and resid 670 through 673' Processing helix chain 'i' and resid 681 through 692 removed outlier: 3.610A pdb=" N GLN i 685 " --> pdb=" O ASN i 681 " (cutoff:3.500A) Processing helix chain 'i' and resid 757 through 764 removed outlier: 4.022A pdb=" N VAL i 763 " --> pdb=" O SER i 759 " (cutoff:3.500A) Processing helix chain 'j' and resid 158 through 163 Processing helix chain 'j' and resid 178 through 190 Processing helix chain 'j' and resid 201 through 203 No H-bonds generated for 'chain 'j' and resid 201 through 203' Processing helix chain 'j' and resid 210 through 220 Processing helix chain 'j' and resid 223 through 230 removed outlier: 4.296A pdb=" N GLN j 228 " --> pdb=" O ALA j 224 " (cutoff:3.500A) Processing helix chain 'j' and resid 247 through 255 removed outlier: 4.204A pdb=" N VAL j 253 " --> pdb=" O LEU j 249 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE j 254 " --> pdb=" O ARG j 250 " (cutoff:3.500A) Processing helix chain 'j' and resid 322 through 337 removed outlier: 3.910A pdb=" N ALA j 326 " --> pdb=" O GLU j 322 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE j 327 " --> pdb=" O PRO j 323 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG j 330 " --> pdb=" O ALA j 326 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE j 331 " --> pdb=" O PHE j 327 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER j 332 " --> pdb=" O HIS j 328 " (cutoff:3.500A) Processing helix chain 'j' and resid 339 through 343 Processing helix chain 'k' and resid 40 through 53 removed outlier: 4.514A pdb=" N LYS k 52 " --> pdb=" O LEU k 48 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN k 53 " --> pdb=" O SER k 49 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 64 removed outlier: 3.918A pdb=" N SER k 64 " --> pdb=" O MET k 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 60 through 64' Processing helix chain 'k' and resid 66 through 73 Processing helix chain 'k' and resid 105 through 114 removed outlier: 4.430A pdb=" N TYR k 111 " --> pdb=" O GLN k 107 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU k 113 " --> pdb=" O CYS k 109 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU k 114 " --> pdb=" O THR k 110 " (cutoff:3.500A) Processing helix chain 'k' and resid 127 through 129 No H-bonds generated for 'chain 'k' and resid 127 through 129' Processing helix chain 'k' and resid 139 through 149 Processing helix chain 'k' and resid 153 through 155 No H-bonds generated for 'chain 'k' and resid 153 through 155' Processing helix chain 'k' and resid 163 through 165 No H-bonds generated for 'chain 'k' and resid 163 through 165' Processing helix chain 'k' and resid 184 through 188 Processing helix chain 'k' and resid 191 through 194 No H-bonds generated for 'chain 'k' and resid 191 through 194' Processing helix chain 'k' and resid 229 through 233 Processing helix chain 'k' and resid 269 through 275 Processing helix chain 'k' and resid 281 through 288 removed outlier: 3.746A pdb=" N HIS k 288 " --> pdb=" O SER k 284 " (cutoff:3.500A) Processing helix chain 'k' and resid 294 through 297 No H-bonds generated for 'chain 'k' and resid 294 through 297' Processing helix chain 'k' and resid 304 through 309 Processing helix chain 'k' and resid 319 through 322 No H-bonds generated for 'chain 'k' and resid 319 through 322' Processing helix chain 'k' and resid 347 through 369 removed outlier: 3.525A pdb=" N TRP k 351 " --> pdb=" O GLY k 347 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS k 361 " --> pdb=" O ARG k 357 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN k 362 " --> pdb=" O VAL k 358 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG k 364 " --> pdb=" O GLU k 360 " (cutoff:3.500A) Processing helix chain 'k' and resid 375 through 381 Processing helix chain 'k' and resid 387 through 398 Processing helix chain 'k' and resid 423 through 431 Processing helix chain 'l' and resid 10 through 16 removed outlier: 4.292A pdb=" N SER l 14 " --> pdb=" O ARG l 11 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU l 15 " --> pdb=" O ALA l 12 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU l 16 " --> pdb=" O GLN l 13 " (cutoff:3.500A) Processing helix chain 'l' and resid 27 through 31 Processing helix chain 'l' and resid 42 through 60 Processing helix chain 'l' and resid 63 through 70 Processing helix chain 'l' and resid 83 through 98 Processing helix chain 'l' and resid 106 through 119 removed outlier: 3.750A pdb=" N CYS l 113 " --> pdb=" O LEU l 109 " (cutoff:3.500A) Processing helix chain 'l' and resid 123 through 139 removed outlier: 3.668A pdb=" N GLN l 127 " --> pdb=" O THR l 123 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP l 139 " --> pdb=" O SER l 135 " (cutoff:3.500A) Processing helix chain 'l' and resid 146 through 159 removed outlier: 3.946A pdb=" N ARG l 155 " --> pdb=" O SER l 151 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU l 156 " --> pdb=" O GLN l 152 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS l 159 " --> pdb=" O ARG l 155 " (cutoff:3.500A) Processing helix chain 'l' and resid 166 through 178 removed outlier: 4.132A pdb=" N HIS l 178 " --> pdb=" O SER l 174 " (cutoff:3.500A) Processing helix chain 'l' and resid 188 through 195 Processing helix chain 'l' and resid 204 through 219 Processing helix chain 'l' and resid 230 through 232 No H-bonds generated for 'chain 'l' and resid 230 through 232' Processing helix chain 'l' and resid 236 through 238 No H-bonds generated for 'chain 'l' and resid 236 through 238' Processing helix chain 'l' and resid 244 through 258 Processing helix chain 'l' and resid 264 through 271 removed outlier: 3.875A pdb=" N GLN l 268 " --> pdb=" O GLU l 265 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA l 269 " --> pdb=" O ASP l 266 " (cutoff:3.500A) Processing helix chain 'l' and resid 282 through 296 Processing helix chain 'l' and resid 299 through 303 removed outlier: 3.826A pdb=" N GLU l 303 " --> pdb=" O ALA l 300 " (cutoff:3.500A) Processing helix chain 'l' and resid 311 through 313 No H-bonds generated for 'chain 'l' and resid 311 through 313' Processing helix chain 'l' and resid 320 through 339 removed outlier: 3.993A pdb=" N ALA l 324 " --> pdb=" O SER l 320 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS l 325 " --> pdb=" O THR l 321 " (cutoff:3.500A) Processing helix chain 'l' and resid 347 through 352 Processing helix chain 'l' and resid 359 through 365 Processing helix chain 'l' and resid 396 through 421 removed outlier: 3.903A pdb=" N SER l 408 " --> pdb=" O ILE l 404 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS l 409 " --> pdb=" O GLN l 405 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 27 removed outlier: 3.531A pdb=" N SER m 27 " --> pdb=" O ARG m 23 " (cutoff:3.500A) Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.569A pdb=" N ALA m 44 " --> pdb=" O GLU m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 51 through 59 removed outlier: 5.179A pdb=" N ALA m 56 " --> pdb=" O PRO m 52 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS m 58 " --> pdb=" O TYR m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 70 through 88 removed outlier: 4.001A pdb=" N ASP m 85 " --> pdb=" O LEU m 81 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU m 86 " --> pdb=" O LYS m 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU m 87 " --> pdb=" O ARG m 83 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU m 88 " --> pdb=" O LEU m 84 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 110 Processing helix chain 'm' and resid 121 through 128 removed outlier: 3.681A pdb=" N ARG m 125 " --> pdb=" O LEU m 121 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS m 126 " --> pdb=" O THR m 122 " (cutoff:3.500A) Processing helix chain 'm' and resid 139 through 151 removed outlier: 4.023A pdb=" N ILE m 147 " --> pdb=" O TYR m 143 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE m 150 " --> pdb=" O ARG m 146 " (cutoff:3.500A) Processing helix chain 'm' and resid 154 through 162 Processing helix chain 'm' and resid 177 through 188 Processing helix chain 'm' and resid 194 through 202 removed outlier: 4.018A pdb=" N ALA m 198 " --> pdb=" O PHE m 194 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU m 199 " --> pdb=" O LYS m 195 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU m 200 " --> pdb=" O GLN m 196 " (cutoff:3.500A) Processing helix chain 'm' and resid 219 through 224 Processing helix chain 'm' and resid 227 through 230 No H-bonds generated for 'chain 'm' and resid 227 through 230' Processing helix chain 'm' and resid 237 through 241 Processing helix chain 'm' and resid 254 through 260 Processing helix chain 'm' and resid 268 through 278 removed outlier: 4.568A pdb=" N GLN m 273 " --> pdb=" O SER m 269 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL m 278 " --> pdb=" O SER m 274 " (cutoff:3.500A) Processing helix chain 'm' and resid 289 through 310 removed outlier: 3.510A pdb=" N GLU m 309 " --> pdb=" O SER m 305 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER m 310 " --> pdb=" O GLN m 306 " (cutoff:3.500A) Processing helix chain 'm' and resid 316 through 320 Processing helix chain 'm' and resid 328 through 340 Processing helix chain 'm' and resid 362 through 383 removed outlier: 4.251A pdb=" N TYR m 366 " --> pdb=" O LYS m 362 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS m 371 " --> pdb=" O GLN m 367 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 25 Processing helix chain 'n' and resid 72 through 81 Processing helix chain 'n' and resid 103 through 110 Processing helix chain 'n' and resid 169 through 173 removed outlier: 3.938A pdb=" N GLU n 173 " --> pdb=" O VAL n 170 " (cutoff:3.500A) Processing helix chain 'n' and resid 228 through 231 No H-bonds generated for 'chain 'n' and resid 228 through 231' Processing helix chain 'n' and resid 244 through 284 removed outlier: 3.598A pdb=" N LEU n 265 " --> pdb=" O TYR n 261 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE n 266 " --> pdb=" O LEU n 262 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG n 267 " --> pdb=" O ALA n 263 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER n 268 " --> pdb=" O SER n 264 " (cutoff:3.500A) Processing helix chain 'o' and resid 92 through 100 Processing helix chain 'o' and resid 113 through 118 removed outlier: 3.557A pdb=" N ALA o 117 " --> pdb=" O PHE o 113 " (cutoff:3.500A) Processing helix chain 'o' and resid 128 through 136 Processing helix chain 'p' and resid 28 through 34 Processing helix chain 'p' and resid 69 through 75 removed outlier: 3.619A pdb=" N LEU p 75 " --> pdb=" O ILE p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 86 through 98 Processing helix chain 'p' and resid 127 through 133 removed outlier: 4.408A pdb=" N LEU p 131 " --> pdb=" O LEU p 127 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS p 132 " --> pdb=" O ALA p 128 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LYS p 133 " --> pdb=" O LYS p 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 127 through 133' Processing helix chain 'q' and resid 36 through 47 Processing helix chain 'q' and resid 84 through 86 No H-bonds generated for 'chain 'q' and resid 84 through 86' Processing helix chain 'q' and resid 90 through 101 Processing helix chain 'q' and resid 123 through 136 removed outlier: 4.461A pdb=" N ILE q 127 " --> pdb=" O SER q 123 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN q 128 " --> pdb=" O GLY q 124 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLN q 131 " --> pdb=" O ILE q 127 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER q 132 " --> pdb=" O ASN q 128 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE q 133 " --> pdb=" O THR q 129 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU q 134 " --> pdb=" O GLN q 130 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA q 135 " --> pdb=" O GLN q 131 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU q 136 " --> pdb=" O SER q 132 " (cutoff:3.500A) Processing helix chain 'q' and resid 191 through 200 removed outlier: 4.468A pdb=" N HIS q 199 " --> pdb=" O GLY q 195 " (cutoff:3.500A) Processing helix chain 'q' and resid 211 through 217 Processing helix chain 'q' and resid 236 through 239 No H-bonds generated for 'chain 'q' and resid 236 through 239' Processing helix chain 'q' and resid 244 through 262 Processing helix chain 'q' and resid 268 through 273 Processing helix chain 'q' and resid 282 through 292 removed outlier: 3.648A pdb=" N LEU q 291 " --> pdb=" O HIS q 287 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET q 292 " --> pdb=" O VAL q 288 " (cutoff:3.500A) Processing helix chain 'q' and resid 297 through 302 Processing helix chain 's' and resid 51 through 62 Processing sheet with id= A, first strand: chain 'A' and resid 42 through 47 Processing sheet with id= B, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.579A pdb=" N LEU A 133 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= D, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= E, first strand: chain 'C' and resid 32 through 37 removed outlier: 3.510A pdb=" N VAL C 41 " --> pdb=" O MET C 211 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA C 209 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU C 208 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 220 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 167 through 169 removed outlier: 4.343A pdb=" N THR D 36 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 67 through 69 removed outlier: 3.558A pdb=" N LEU D 142 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 159 through 161 Processing sheet with id= I, first strand: chain 'E' and resid 133 through 136 removed outlier: 4.306A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 36 through 41 Processing sheet with id= K, first strand: chain 'F' and resid 66 through 68 removed outlier: 3.562A pdb=" N PHE F 67 " --> pdb=" O MET F 75 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 149 through 151 Processing sheet with id= M, first strand: chain 'G' and resid 39 through 44 Processing sheet with id= N, first strand: chain 'G' and resid 76 through 80 removed outlier: 3.636A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS G 154 " --> pdb=" O MET G 138 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= P, first strand: chain 'H' and resid 41 through 43 removed outlier: 4.589A pdb=" N LEU H 110 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU H 122 " --> pdb=" O LEU H 110 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 175 through 178 removed outlier: 3.621A pdb=" N LEU H 186 " --> pdb=" O LEU H 175 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.430A pdb=" N ALA I 9 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 41 through 43 Processing sheet with id= T, first strand: chain 'J' and resid 129 through 131 removed outlier: 3.534A pdb=" N ASP J 184 " --> pdb=" O GLY J 187 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 43 through 48 removed outlier: 3.628A pdb=" N VAL J 47 " --> pdb=" O ASN J 101 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 3 through 7 removed outlier: 4.037A pdb=" N LEU K 176 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER K 188 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N HIS K 178 " --> pdb=" O ARG K 186 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG K 186 " --> pdb=" O HIS K 178 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 98 through 101 Processing sheet with id= X, first strand: chain 'K' and resid 20 through 22 removed outlier: 3.841A pdb=" N SER K 28 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA K 22 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE K 26 " --> pdb=" O ALA K 22 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 14 through 16 Processing sheet with id= Z, first strand: chain 'L' and resid 43 through 45 Processing sheet with id= AA, first strand: chain 'L' and resid 121 through 123 removed outlier: 3.992A pdb=" N VAL L 121 " --> pdb=" O ASP L 133 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN L 131 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 29 through 31 removed outlier: 3.871A pdb=" N LEU L 29 " --> pdb=" O THR L 37 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR L 37 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU L 31 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'M' and resid 11 through 15 Processing sheet with id= AD, first strand: chain 'M' and resid 110 through 115 Processing sheet with id= AE, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.705A pdb=" N GLY N 11 " --> pdb=" O PHE N 8 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 99 through 103 removed outlier: 4.218A pdb=" N VAL N 111 " --> pdb=" O GLN N 123 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 174 through 178 removed outlier: 3.979A pdb=" N ILE N 174 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA N 178 " --> pdb=" O GLU N 185 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'O' and resid 42 through 47 Processing sheet with id= AI, first strand: chain 'O' and resid 133 through 135 removed outlier: 3.580A pdb=" N LEU O 133 " --> pdb=" O SER O 148 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'P' and resid 35 through 37 Processing sheet with id= AK, first strand: chain 'P' and resid 72 through 75 Processing sheet with id= AL, first strand: chain 'Q' and resid 32 through 37 removed outlier: 3.510A pdb=" N VAL Q 41 " --> pdb=" O MET Q 211 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA Q 209 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU Q 208 " --> pdb=" O LEU Q 220 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU Q 220 " --> pdb=" O LEU Q 208 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'R' and resid 167 through 169 removed outlier: 4.343A pdb=" N THR R 36 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'R' and resid 67 through 69 removed outlier: 3.558A pdb=" N LEU R 142 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'S' and resid 159 through 161 Processing sheet with id= AP, first strand: chain 'S' and resid 133 through 136 removed outlier: 4.305A pdb=" N ILE S 144 " --> pdb=" O CYS S 156 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'T' and resid 36 through 41 Processing sheet with id= AR, first strand: chain 'T' and resid 66 through 68 removed outlier: 3.562A pdb=" N PHE T 67 " --> pdb=" O MET T 75 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'T' and resid 149 through 151 Processing sheet with id= AT, first strand: chain 'U' and resid 39 through 41 Processing sheet with id= AU, first strand: chain 'U' and resid 76 through 80 removed outlier: 3.637A pdb=" N GLY U 77 " --> pdb=" O ILE U 141 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS U 154 " --> pdb=" O MET U 138 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'V' and resid 3 through 7 Processing sheet with id= AW, first strand: chain 'V' and resid 41 through 43 removed outlier: 4.589A pdb=" N LEU V 110 " --> pdb=" O LEU V 122 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU V 122 " --> pdb=" O LEU V 110 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'V' and resid 175 through 178 removed outlier: 3.620A pdb=" N LEU V 186 " --> pdb=" O LEU V 175 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'W' and resid 135 through 139 removed outlier: 5.430A pdb=" N ALA W 9 " --> pdb=" O ASP W 24 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'W' and resid 41 through 43 Processing sheet with id= BA, first strand: chain 'X' and resid 129 through 131 Processing sheet with id= BB, first strand: chain 'X' and resid 43 through 48 removed outlier: 3.628A pdb=" N VAL X 47 " --> pdb=" O ASN X 101 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'Y' and resid 3 through 7 removed outlier: 4.036A pdb=" N LEU Y 176 " --> pdb=" O SER Y 188 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER Y 188 " --> pdb=" O LEU Y 176 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS Y 178 " --> pdb=" O ARG Y 186 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG Y 186 " --> pdb=" O HIS Y 178 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'Y' and resid 98 through 101 Processing sheet with id= BE, first strand: chain 'Y' and resid 20 through 22 removed outlier: 3.841A pdb=" N SER Y 28 " --> pdb=" O ALA Y 20 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA Y 22 " --> pdb=" O ILE Y 26 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE Y 26 " --> pdb=" O ALA Y 22 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'Z' and resid 14 through 16 Processing sheet with id= BG, first strand: chain 'Z' and resid 43 through 45 Processing sheet with id= BH, first strand: chain 'Z' and resid 121 through 123 removed outlier: 3.992A pdb=" N VAL Z 121 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN Z 131 " --> pdb=" O SER Z 123 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Z' and resid 29 through 31 removed outlier: 3.872A pdb=" N LEU Z 29 " --> pdb=" O THR Z 37 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR Z 37 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU Z 31 " --> pdb=" O ILE Z 35 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE Z 35 " --> pdb=" O GLU Z 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'a' and resid 11 through 15 Processing sheet with id= BK, first strand: chain 'a' and resid 110 through 115 Processing sheet with id= BL, first strand: chain 'b' and resid 125 through 129 removed outlier: 6.705A pdb=" N GLY b 11 " --> pdb=" O PHE b 8 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'b' and resid 99 through 103 removed outlier: 4.218A pdb=" N VAL b 111 " --> pdb=" O GLN b 123 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'b' and resid 174 through 178 removed outlier: 3.978A pdb=" N ILE b 174 " --> pdb=" O LEU b 189 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA b 178 " --> pdb=" O GLU b 185 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'c' and resid 93 through 97 removed outlier: 4.334A pdb=" N ARG c 139 " --> pdb=" O LEU c 153 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE c 151 " --> pdb=" O GLY c 141 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP c 143 " --> pdb=" O ILE c 149 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE c 149 " --> pdb=" O ASP c 143 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'c' and resid 340 through 343 removed outlier: 6.518A pdb=" N LEU c 213 " --> pdb=" O ILE c 341 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE c 343 " --> pdb=" O LEU c 213 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE c 215 " --> pdb=" O PHE c 343 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N LEU c 214 " --> pdb=" O VAL c 317 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET c 319 " --> pdb=" O LEU c 214 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLY c 216 " --> pdb=" O MET c 319 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR c 321 " --> pdb=" O GLY c 216 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE c 272 " --> pdb=" O LYS c 316 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE c 238 " --> pdb=" O PHE c 273 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP c 275 " --> pdb=" O ILE c 238 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL c 240 " --> pdb=" O ASP c 275 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'd' and resid 108 through 111 Processing sheet with id= BR, first strand: chain 'd' and resid 120 through 124 Processing sheet with id= BS, first strand: chain 'd' and resid 223 through 225 removed outlier: 6.427A pdb=" N MET d 329 " --> pdb=" O LEU d 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'd' and resid 246 through 249 Processing sheet with id= BU, first strand: chain 'e' and resid 89 through 91 removed outlier: 3.636A pdb=" N VAL e 130 " --> pdb=" O GLY e 90 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'e' and resid 331 through 333 removed outlier: 8.516A pdb=" N VAL e 202 " --> pdb=" O VAL e 305 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL e 307 " --> pdb=" O VAL e 202 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N MET e 204 " --> pdb=" O VAL e 307 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET e 309 " --> pdb=" O MET e 204 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLY e 206 " --> pdb=" O MET e 309 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR e 311 " --> pdb=" O GLY e 206 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA e 260 " --> pdb=" O LYS e 306 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE e 308 " --> pdb=" O ALA e 260 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE e 262 " --> pdb=" O ILE e 308 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ALA e 310 " --> pdb=" O ILE e 262 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE e 264 " --> pdb=" O ALA e 310 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA e 226 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE e 263 " --> pdb=" O ALA e 226 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE e 228 " --> pdb=" O PHE e 263 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ASP e 265 " --> pdb=" O ILE e 228 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL e 230 " --> pdb=" O ASP e 265 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'f' and resid 97 through 100 Processing sheet with id= BX, first strand: chain 'f' and resid 195 through 199 removed outlier: 6.675A pdb=" N ILE f 229 " --> pdb=" O LEU f 196 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL f 198 " --> pdb=" O ILE f 229 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N PHE f 231 " --> pdb=" O VAL f 198 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS f 274 " --> pdb=" O ILE f 230 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N MET f 232 " --> pdb=" O LYS f 274 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE f 276 " --> pdb=" O MET f 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= BX Processing sheet with id= BY, first strand: chain 'g' and resid 130 through 135 removed outlier: 3.595A pdb=" N CYS g 121 " --> pdb=" O LEU g 97 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU g 95 " --> pdb=" O VAL g 123 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS g 125 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL g 93 " --> pdb=" O LYS g 125 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'g' and resid 351 through 354 removed outlier: 6.456A pdb=" N LEU g 224 " --> pdb=" O ILE g 352 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE g 354 " --> pdb=" O LEU g 224 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR g 226 " --> pdb=" O PHE g 354 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY g 227 " --> pdb=" O THR g 332 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR g 247 " --> pdb=" O ILE g 282 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N PHE g 284 " --> pdb=" O THR g 247 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU g 249 " --> pdb=" O PHE g 284 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASP g 286 " --> pdb=" O LEU g 249 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'h' and resid 292 through 295 removed outlier: 6.238A pdb=" N VAL h 186 " --> pdb=" O MET h 293 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR h 295 " --> pdb=" O VAL h 186 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU h 188 " --> pdb=" O THR h 295 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG h 313 " --> pdb=" O LEU h 187 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TYR h 189 " --> pdb=" O ARG h 313 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE h 315 " --> pdb=" O TYR h 189 " (cutoff:3.500A) No H-bonds generated for sheet with id= CA Processing sheet with id= CB, first strand: chain 'h' and resid 244 through 246 Processing sheet with id= CC, first strand: chain 'm' and resid 313 through 315 Processing sheet with id= CD, first strand: chain 'q' and resid 143 through 146 removed outlier: 3.558A pdb=" N VAL q 144 " --> pdb=" O ASP q 158 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP q 158 " --> pdb=" O VAL q 144 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP q 146 " --> pdb=" O VAL q 156 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL q 156 " --> pdb=" O ASP q 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= CD Processing sheet with id= CE, first strand: chain 'q' and resid 108 through 112 removed outlier: 6.843A pdb=" N MET q 57 " --> pdb=" O VAL q 109 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP q 111 " --> pdb=" O GLY q 55 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY q 55 " --> pdb=" O TRP q 111 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP q 71 " --> pdb=" O LEU q 58 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLU q 60 " --> pdb=" O VAL q 69 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL q 69 " --> pdb=" O GLU q 60 " (cutoff:3.500A) 2716 hydrogen bonds defined for protein. 7791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 32.35 Time building geometry restraints manager: 28.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.95: 1 0.95 - 1.27: 13149 1.27 - 1.59: 63421 1.59 - 1.91: 684 1.91 - 2.23: 2 Bond restraints: 77257 Sorted by residual: bond pdb=" C SER B 168 " pdb=" N VAL B 172 " ideal model delta sigma weight residual 1.332 2.148 -0.816 1.36e-02 5.41e+03 3.60e+03 bond pdb=" C THR N 201 " pdb=" N PRO N 202 " ideal model delta sigma weight residual 1.341 2.234 -0.893 1.60e-02 3.91e+03 3.12e+03 bond pdb=" C VAL Q 45 " pdb=" N GLU Q 46 " ideal model delta sigma weight residual 1.332 0.632 0.700 1.40e-02 5.10e+03 2.50e+03 bond pdb=" C CYS Q 63 " pdb=" N ALA Q 64 " ideal model delta sigma weight residual 1.331 1.550 -0.219 1.34e-02 5.57e+03 2.67e+02 bond pdb=" CA GLU S 237 " pdb=" C GLU S 237 " ideal model delta sigma weight residual 1.523 1.439 0.085 1.34e-02 5.57e+03 3.98e+01 ... (remaining 77252 not shown) Histogram of bond angle deviations from ideal: 62.68 - 77.63: 3 77.63 - 92.59: 4 92.59 - 107.54: 3259 107.54 - 122.49: 90796 122.49 - 137.45: 10828 Bond angle restraints: 104890 Sorted by residual: angle pdb=" O CYS Q 63 " pdb=" C CYS Q 63 " pdb=" N ALA Q 64 " ideal model delta sigma weight residual 123.16 98.84 24.32 1.26e+00 6.30e-01 3.72e+02 angle pdb=" C ARG e 323 " pdb=" N PRO e 324 " pdb=" CD PRO e 324 " ideal model delta sigma weight residual 125.00 62.68 62.32 4.10e+00 5.95e-02 2.31e+02 angle pdb=" C GLU d 145 " pdb=" N PRO d 146 " pdb=" CD PRO d 146 " ideal model delta sigma weight residual 125.00 63.65 61.35 4.10e+00 5.95e-02 2.24e+02 angle pdb=" C PRO g 228 " pdb=" N PRO g 229 " pdb=" CD PRO g 229 " ideal model delta sigma weight residual 125.00 71.32 53.68 4.10e+00 5.95e-02 1.71e+02 angle pdb=" CA HIS P 240 " pdb=" C HIS P 240 " pdb=" N GLU P 241 " ideal model delta sigma weight residual 119.80 102.63 17.17 1.34e+00 5.57e-01 1.64e+02 ... (remaining 104885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 45953 35.12 - 70.24: 652 70.24 - 105.36: 50 105.36 - 140.49: 11 140.49 - 175.61: 6 Dihedral angle restraints: 46672 sinusoidal: 16328 harmonic: 30344 Sorted by residual: dihedral pdb=" CA LEU n 70 " pdb=" C LEU n 70 " pdb=" N ASP n 71 " pdb=" CA ASP n 71 " ideal model delta harmonic sigma weight residual 180.00 46.29 133.71 0 5.00e+00 4.00e-02 7.15e+02 dihedral pdb=" CA ALA i 661 " pdb=" C ALA i 661 " pdb=" N GLY i 662 " pdb=" CA GLY i 662 " ideal model delta harmonic sigma weight residual 180.00 60.98 119.02 0 5.00e+00 4.00e-02 5.67e+02 dihedral pdb=" CA ALA h 242 " pdb=" C ALA h 242 " pdb=" N PRO h 243 " pdb=" CA PRO h 243 " ideal model delta harmonic sigma weight residual 180.00 80.97 99.03 0 5.00e+00 4.00e-02 3.92e+02 ... (remaining 46669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 12030 0.198 - 0.397: 197 0.397 - 0.595: 10 0.595 - 0.794: 1 0.794 - 0.992: 1 Chirality restraints: 12239 Sorted by residual: chirality pdb=" CA GLU d 254 " pdb=" N GLU d 254 " pdb=" C GLU d 254 " pdb=" CB GLU d 254 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA ASN i 665 " pdb=" N ASN i 665 " pdb=" C ASN i 665 " pdb=" CB ASN i 665 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.13e+00 chirality pdb=" CG LEU d 163 " pdb=" CB LEU d 163 " pdb=" CD1 LEU d 163 " pdb=" CD2 LEU d 163 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.20e+00 ... (remaining 12236 not shown) Planarity restraints: 13718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 168 " 0.098 2.00e-02 2.50e+03 1.75e-01 3.07e+02 pdb=" C SER B 168 " -0.300 2.00e-02 2.50e+03 pdb=" O SER B 168 " 0.139 2.00e-02 2.50e+03 pdb=" N VAL B 172 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER P 168 " 0.086 2.00e-02 2.50e+03 1.69e-01 2.86e+02 pdb=" C SER P 168 " -0.292 2.00e-02 2.50e+03 pdb=" O SER P 168 " 0.117 2.00e-02 2.50e+03 pdb=" N ALA P 169 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU S 236 " -0.072 2.00e-02 2.50e+03 1.57e-01 2.48e+02 pdb=" C LEU S 236 " 0.272 2.00e-02 2.50e+03 pdb=" O LEU S 236 " -0.113 2.00e-02 2.50e+03 pdb=" N GLU S 237 " -0.087 2.00e-02 2.50e+03 ... (remaining 13715 not shown) Histogram of nonbonded interaction distances: 0.19 - 1.13: 77 1.13 - 2.07: 400 2.07 - 3.01: 42721 3.01 - 3.96: 205001 3.96 - 4.90: 364431 Warning: very small nonbonded interaction distances. Nonbonded interactions: 612630 Sorted by model distance: nonbonded pdb=" CD1 LEU m 134 " pdb=" OE1 GLU m 169 " model vdw 0.185 3.460 nonbonded pdb=" NE ARG e 326 " pdb=" NZ LYS h 142 " model vdw 0.188 3.200 nonbonded pdb=" CZ ARG d 343 " pdb=" O3A ADP c 501 " model vdw 0.217 2.616 nonbonded pdb=" OE1 GLN c 165 " pdb=" CA PHE c 237 " model vdw 0.275 3.470 nonbonded pdb=" CZ ARG h 117 " pdb=" CE1 TYR h 121 " model vdw 0.310 3.570 ... (remaining 612625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 50 or (resid 51 through 52 and (nam \ e N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )) or resid 55 through 163 or (r \ esid 164 and (name N or name CA or name C or name O or name CB )) or resid 165 t \ hrough 173 or (resid 174 through 175 and (name N or name CA or name C or name O \ or name CB )) or resid 176 or (resid 177 and (name N or name CA or name C or nam \ e O or name CB )) or resid 178 through 232)) selection = (chain 'O' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 51 or (resid 52 and (name N or name CA or name C or name O \ or name CB )) or resid 53 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 139 or (resid 140 and (name N or \ name CA or name C or name O or name CB )) or resid 141 through 148 or (resid 149 \ and (name N or name CA or name C or name O or name CB )) or resid 150 through 1 \ 98 or (resid 199 and (name N or name CA or name C or name O or name CB )) or res \ id 200 or (resid 201 and (name N or name CA or name C or name O or name CB )) or \ resid 202 through 232)) } ncs_group { reference = (chain 'B' and (resid 2 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 228 or (resid 229 and (name N or na \ me CA or name C or name O or name CB )) or resid 230 through 231 or (resid 232 a \ nd (name N or name CA or name C or name O or name CB )) or resid 233 through 237 \ or (resid 238 through 243 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'P' and (resid 2 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )) or resid 55 through 168 or resid 172 through 200 or res \ id 206 through 209 or (resid 210 and (name N or name CA or name C or name O or n \ ame CB )) or resid 211 through 243)) } ncs_group { reference = (chain 'C' and (resid 2 through 47 or (resid 49 through 52 and (name N or name C \ A or name C or name O or name CB )) or resid 53 through 181 or (resid 182 and (n \ ame N or name CA or name C or name O or name CB )) or resid 183 through 188 or ( \ resid 189 and (name N or name CA or name C or name O or name CB )) or resid 190 \ through 199 or resid 201 through 230 or (resid 231 through 235 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'Q' and (resid 2 through 46 or (resid 47 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 165 or (resid 166 and (name N or na \ me CA or name C or name O or name CB )) or resid 167 through 169 or (resid 170 a \ nd (name N or name CA or name C or name O or name CB )) or resid 171 through 173 \ or (resid 174 and (name N or name CA or name C or name O or name CB )) or resid \ 175 through 198 or (resid 199 and (name N or name CA or name C or name O or nam \ e CB )) or resid 201 through 203 or (resid 204 and (name N or name CA or name C \ or name O or name CB )) or resid 205 or (resid 206 through 207 and (name N or na \ me CA or name C or name O or name CB )) or resid 208 through 214 or (resid 215 a \ nd (name N or name CA or name C or name O or name CB )) or resid 216 through 222 \ or (resid 223 through 224 and (name N or name CA or name C or name O or name CB \ )) or resid 225 through 235)) } ncs_group { reference = (chain 'D' and (resid 9 through 126 or (resid 127 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 174 or (resid 175 an \ d (name N or name CA or name C or name O or name CB )) or resid 176 through 241) \ ) selection = (chain 'R' and (resid 9 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 171 or (resid 172 through 173 an \ d (name N or name CA or name C or name O or name CB )) or resid 174 through 186 \ or (resid 187 and (name N or name CA or name C or name O or name CB )) or resid \ 188 through 195 or (resid 196 and (name N or name CA or name C or name O or name \ CB )) or resid 197 through 208 or (resid 209 and (name N or name CA or name C o \ r name O or name CB )) or resid 210 through 240 or (resid 241 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)))) } ncs_group { reference = (chain 'E' and (resid 4 through 188 or (resid 189 and (name N or name CA or name \ C or name O or name CB )) or resid 190 through 216 or (resid 217 through 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 235 \ or (resid 236 through 237 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'S' and (resid 4 through 50 or (resid 51 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 201 or (resid 202 throug \ h 203 and (name N or name CA or name C or name O or name CB )) or resid 204 thro \ ugh 207 or (resid 208 and (name N or name CA or name C or name O or name CB )) o \ r resid 209 through 237)) } ncs_group { reference = (chain 'F' and (resid 6 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 through 241)) selection = (chain 'T' and (resid 6 through 203 or resid 208 through 241)) } ncs_group { reference = (chain 'G' and (resid 8 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 58 or (resid 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 144 or (resid 145 thro \ ugh 147 and (name N or name CA or name C or name O or name CB )) or resid 148 th \ rough 169 or (resid 170 through 171 and (name N or name CA or name C or name O o \ r name CB )) or resid 172 through 208 or (resid 209 and (name N or name CA or na \ me C or name O or name CB )) or resid 210 through 225 or (resid 226 and (name N \ or name CA or name C or name O or name CB )) or resid 227 through 242)) selection = (chain 'U' and (resid 8 through 187 or resid 192 through 195 or (resid 196 and ( \ name N or name CA or name C or name O or name CB )) or resid 197 through 242)) } ncs_group { reference = (chain 'H' and (resid 1 through 103 or resid 105 through 181 or (resid 182 and ( \ name N or name CA or name C or name O or name CB )) or resid 183 through 193 or \ (resid 194 through 195 and (name N or name CA or name C or name O or name CB )) \ or resid 196 through 200 or (resid 201 and (name N or name CA or name C or name \ O or name CB )) or resid 202 or (resid 203 through 206 and (name N or name CA or \ name C or name O or name CB )) or resid 207 through 219 or (resid 220 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'V' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 103 or resid 105 through 220)) } ncs_group { reference = (chain 'I' and (resid 1 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB )) or resid 162 through 204)) selection = (chain 'W' and (resid 1 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)))) } ncs_group { reference = (chain 'J' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 196)) selection = (chain 'X' and (resid 1 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB )) or resid 25 through 153 or (resid 154 and (name N or na \ me CA or name C or name O or name CB )) or resid 155 through 196)) } ncs_group { reference = chain 'K' selection = (chain 'Y' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 105 or (resid 106 and (name N or name \ CA or name C or name O or name CB )) or resid 107 through 200)) } ncs_group { reference = (chain 'L' and (resid 1 through 2 or resid 4 through 160 or (resid 161 through 1 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 163 through \ 213)) selection = (chain 'Z' and (resid 1 through 2 or resid 4 through 172 or (resid 173 and (name \ N or name CA or name C or name O or name CB )) or resid 174 through 199 or (res \ id 200 and (name N or name CA or name C or name O or name CB )) or resid 201 thr \ ough 213)) } ncs_group { reference = (chain 'M' and (resid 1 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or resid 157 through 205 or (resid 206 and (name N or \ name CA or name C or name O or name CB )) or resid 207 through 216)) selection = chain 'a' } ncs_group { reference = (chain 'N' and (resid 1 through 198 or (resid 199 through 200 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 202)) selection = (chain 'b' and (resid 1 through 201 or resid 203)) } ncs_group { reference = chain 't' selection = chain 'u' } 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 12.620 Check model and map are aligned: 0.840 Set scattering table: 0.500 Process input model: 161.850 Find NCS groups from input model: 6.590 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.009 0.893 77257 Z= 0.656 Angle : 1.467 62.323 104890 Z= 0.809 Chirality : 0.072 0.992 12239 Planarity : 0.011 0.261 13718 Dihedral : 13.187 175.607 27097 Min Nonbonded Distance : 0.185 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 1.71 % Allowed : 14.37 % Favored : 83.92 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.04 % Twisted Proline : 5.67 % Twisted General : 1.04 % 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: -5.42 (0.06), residues: 10342 helix: -3.45 (0.05), residues: 3900 sheet: -3.02 (0.11), residues: 1571 loop : -3.92 (0.07), residues: 4871 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20684 Ramachandran restraints generated. 10342 Oldfield, 0 Emsley, 10342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20684 Ramachandran restraints generated. 10342 Oldfield, 0 Emsley, 10342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1701 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1482 time to evaluate : 7.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR e 417 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 109 residues processed: 1657 average time/residue: 0.8024 time to fit residues: 2231.2084 Evaluate side-chains 972 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 863 time to evaluate : 6.964 Switching outliers to nearest non-outliers 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 TARDY: cannot create tardy model for: "TYR e 417 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 26 residues processed: 109 average time/residue: 0.6791 time to fit residues: 140.1449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 872 optimal weight: 20.0000 chunk 782 optimal weight: 1.9990 chunk 434 optimal weight: 0.9980 chunk 267 optimal weight: 0.9980 chunk 528 optimal weight: 2.9990 chunk 418 optimal weight: 6.9990 chunk 809 optimal weight: 7.9990 chunk 313 optimal weight: 0.7980 chunk 492 optimal weight: 1.9990 chunk 602 optimal weight: 1.9990 chunk 938 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 94 GLN A 95 GLN B 69 ASN B 84 ASN B 177 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 122 ASN D 99 HIS D 122 GLN E 59 HIS E 143 HIS E 183 ASN E 190 HIS F 105 ASN F 201 HIS H 66 HIS ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN J 193 ASN L 8 ASN M 38 ASN M 104 ASN N 53 GLN ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 GLN O 188 HIS P 40 ASN P 84 ASN P 88 ASN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 142 HIS P 198 ASN Q 122 ASN R 99 HIS R 186 HIS R 204 GLN ** S 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 22 GLN T 97 ASN T 105 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 ASN U 12 HIS U 33 ASN V 66 HIS X 71 ASN Y 62 GLN a 47 ASN ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 GLN b 53 GLN c 145 ASN ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 433 ASN d 153 ASN d 154 HIS ** d 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 133 HIS e 380 GLN e 414 HIS f 254 GLN f 262 ASN f 316 HIS f 339 ASN f 345 ASN g 130 GLN h 332 HIS ** h 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 77257 Z= 0.269 Angle : 0.890 32.237 104890 Z= 0.453 Chirality : 0.049 0.479 12239 Planarity : 0.007 0.170 13718 Dihedral : 9.571 175.583 11340 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.73 % Allowed : 12.47 % Favored : 86.79 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 3.39 % Twisted General : 0.53 % 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: -4.21 (0.07), residues: 10345 helix: -1.96 (0.07), residues: 4006 sheet: -2.57 (0.12), residues: 1538 loop : -3.63 (0.08), residues: 4801 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1004 time to evaluate : 7.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 253 outliers final: 116 residues processed: 1187 average time/residue: 0.7150 time to fit residues: 1464.6093 Evaluate side-chains 936 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 820 time to evaluate : 6.972 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 0 residues processed: 116 average time/residue: 0.5860 time to fit residues: 135.7136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 521 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 780 optimal weight: 0.9980 chunk 638 optimal weight: 10.0000 chunk 258 optimal weight: 0.0010 chunk 939 optimal weight: 7.9990 chunk 1015 optimal weight: 10.0000 chunk 836 optimal weight: 30.0000 chunk 931 optimal weight: 20.0000 chunk 320 optimal weight: 3.9990 chunk 753 optimal weight: 3.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 198 ASN C 54 GLN E 43 HIS ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN I 161 HIS L 77 HIS O 62 HIS O 111 GLN ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN S 121 GLN S 152 ASN T 97 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 GLN W 156 ASN X 61 GLN Z 77 HIS ** Z 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 47 ASN a 69 GLN ** b 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 154 HIS d 242 GLN d 314 ASN ** d 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 77257 Z= 0.326 Angle : 0.817 16.943 104890 Z= 0.420 Chirality : 0.048 0.325 12239 Planarity : 0.006 0.163 13718 Dihedral : 8.760 170.294 11340 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.57 % Allowed : 12.83 % Favored : 86.60 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.82 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.08), residues: 10345 helix: -1.01 (0.08), residues: 4071 sheet: -2.40 (0.12), residues: 1607 loop : -3.45 (0.08), residues: 4667 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 921 time to evaluate : 7.493 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 221 outliers final: 97 residues processed: 1097 average time/residue: 0.7059 time to fit residues: 1347.4718 Evaluate side-chains 892 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 795 time to evaluate : 7.605 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.5836 time to fit residues: 116.2591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 928 optimal weight: 50.0000 chunk 706 optimal weight: 1.9990 chunk 487 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 448 optimal weight: 10.0000 chunk 631 optimal weight: 0.0040 chunk 943 optimal weight: 0.0010 chunk 998 optimal weight: 30.0000 chunk 492 optimal weight: 0.8980 chunk 893 optimal weight: 50.0000 chunk 269 optimal weight: 0.6980 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 GLN Q 54 GLN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 HIS S 68 ASN S 86 ASN S 121 GLN S 152 ASN T 97 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 GLN ** W 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 ASN Z 8 ASN ** Z 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 GLN d 154 HIS d 314 ASN f 262 ASN g 323 ASN h 296 ASN ** h 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 77257 Z= 0.183 Angle : 0.738 12.564 104890 Z= 0.375 Chirality : 0.045 0.258 12239 Planarity : 0.006 0.137 13718 Dihedral : 8.230 173.817 11340 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.21 % Favored : 88.25 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.82 % Twisted General : 0.30 % 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: -2.93 (0.08), residues: 10345 helix: -0.46 (0.08), residues: 4074 sheet: -2.04 (0.12), residues: 1494 loop : -3.34 (0.08), residues: 4777 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 967 time to evaluate : 7.130 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 61 residues processed: 1103 average time/residue: 0.7055 time to fit residues: 1355.6669 Evaluate side-chains 868 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 807 time to evaluate : 7.077 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.5770 time to fit residues: 76.7345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 831 optimal weight: 20.0000 chunk 566 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 743 optimal weight: 6.9990 chunk 411 optimal weight: 2.9990 chunk 852 optimal weight: 40.0000 chunk 690 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 509 optimal weight: 5.9990 chunk 896 optimal weight: 50.0000 chunk 251 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 21 GLN G 90 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 HIS ** O 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 157 ASN b 53 GLN ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 GLN c 353 HIS d 154 HIS ** d 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 86 GLN ** f 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.133 77257 Z= 0.294 Angle : 0.766 14.200 104890 Z= 0.389 Chirality : 0.046 0.406 12239 Planarity : 0.006 0.309 13718 Dihedral : 8.005 178.089 11340 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 12.25 % Favored : 87.24 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.24 % 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: -2.69 (0.08), residues: 10345 helix: -0.14 (0.08), residues: 4074 sheet: -2.04 (0.12), residues: 1567 loop : -3.27 (0.08), residues: 4704 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 857 time to evaluate : 7.192 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 TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 182 outliers final: 88 residues processed: 998 average time/residue: 0.7399 time to fit residues: 1286.0079 Evaluate side-chains 872 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 784 time to evaluate : 7.070 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 0.5997 time to fit residues: 108.4276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 335 optimal weight: 0.8980 chunk 899 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 586 optimal weight: 0.8980 chunk 246 optimal weight: 3.9990 chunk 999 optimal weight: 8.9990 chunk 829 optimal weight: 30.0000 chunk 462 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 330 optimal weight: 10.0000 chunk 524 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 147 GLN B 240 HIS F 22 GLN G 90 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 118 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 GLN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 154 HIS ** d 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 137 ASN f 262 ASN ** h 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 332 HIS ** h 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 77257 Z= 0.241 Angle : 0.736 12.830 104890 Z= 0.373 Chirality : 0.046 0.318 12239 Planarity : 0.005 0.141 13718 Dihedral : 7.728 145.771 11340 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.74 % Favored : 87.83 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.25 % 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: -2.44 (0.08), residues: 10345 helix: 0.13 (0.08), residues: 4055 sheet: -1.91 (0.12), residues: 1567 loop : -3.19 (0.08), residues: 4723 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 847 time to evaluate : 7.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 62 residues processed: 967 average time/residue: 0.7289 time to fit residues: 1230.3001 Evaluate side-chains 840 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 778 time to evaluate : 7.052 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.5918 time to fit residues: 77.9820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 963 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 569 optimal weight: 8.9990 chunk 729 optimal weight: 0.0970 chunk 565 optimal weight: 2.9990 chunk 841 optimal weight: 6.9990 chunk 558 optimal weight: 0.9990 chunk 995 optimal weight: 0.9990 chunk 623 optimal weight: 2.9990 chunk 607 optimal weight: 5.9990 chunk 459 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN G 90 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 GLN c 183 GLN ** d 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 258 GLN h 69 GLN ** h 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 377 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 77257 Z= 0.209 Angle : 0.721 11.636 104890 Z= 0.364 Chirality : 0.045 0.284 12239 Planarity : 0.005 0.103 13718 Dihedral : 7.545 147.010 11340 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.73 % Favored : 87.87 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % 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: -2.29 (0.08), residues: 10345 helix: 0.28 (0.08), residues: 4054 sheet: -1.78 (0.12), residues: 1558 loop : -3.15 (0.08), residues: 4733 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 848 time to evaluate : 7.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 40 residues processed: 917 average time/residue: 0.7376 time to fit residues: 1183.4481 Evaluate side-chains 827 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 787 time to evaluate : 7.048 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.6252 time to fit residues: 55.5018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 615 optimal weight: 5.9990 chunk 397 optimal weight: 0.0270 chunk 594 optimal weight: 0.0000 chunk 299 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 632 optimal weight: 1.9990 chunk 678 optimal weight: 10.0000 chunk 492 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 782 optimal weight: 3.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 189 HIS ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 172 ASN Z 131 GLN c 183 GLN ** d 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 323 ASN h 69 GLN ** h 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 77257 Z= 0.208 Angle : 0.725 13.048 104890 Z= 0.366 Chirality : 0.045 0.285 12239 Planarity : 0.005 0.099 13718 Dihedral : 7.431 147.882 11340 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.58 % Favored : 88.08 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % 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: -2.17 (0.08), residues: 10345 helix: 0.43 (0.09), residues: 4042 sheet: -1.68 (0.12), residues: 1603 loop : -3.15 (0.08), residues: 4700 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 835 time to evaluate : 7.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 28 residues processed: 878 average time/residue: 0.7399 time to fit residues: 1139.2654 Evaluate side-chains 803 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 775 time to evaluate : 7.132 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.6301 time to fit residues: 41.6792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 905 optimal weight: 5.9990 chunk 953 optimal weight: 9.9990 chunk 870 optimal weight: 20.0000 chunk 927 optimal weight: 10.0000 chunk 558 optimal weight: 0.8980 chunk 404 optimal weight: 6.9990 chunk 728 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 838 optimal weight: 20.0000 chunk 877 optimal weight: 30.0000 chunk 924 optimal weight: 0.4980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 167 ASN B 240 HIS I 71 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 HIS ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 121 GLN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 71 ASN W 172 ASN c 183 GLN d 241 ASN ** d 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 302 ASN ** f 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 HIS ** h 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 170 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 77257 Z= 0.282 Angle : 0.756 12.032 104890 Z= 0.382 Chirality : 0.046 0.219 12239 Planarity : 0.005 0.103 13718 Dihedral : 7.437 148.830 11340 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.41 % Favored : 87.24 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.18 % 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: -2.15 (0.08), residues: 10345 helix: 0.41 (0.08), residues: 4070 sheet: -1.74 (0.12), residues: 1650 loop : -3.09 (0.08), residues: 4625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 811 time to evaluate : 7.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 32 residues processed: 855 average time/residue: 0.7441 time to fit residues: 1112.6912 Evaluate side-chains 800 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 768 time to evaluate : 7.126 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.5851 time to fit residues: 45.1523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 609 optimal weight: 0.3980 chunk 981 optimal weight: 0.0040 chunk 598 optimal weight: 0.2980 chunk 465 optimal weight: 8.9990 chunk 682 optimal weight: 6.9990 chunk 1029 optimal weight: 9.9990 chunk 947 optimal weight: 3.9990 chunk 819 optimal weight: 40.0000 chunk 85 optimal weight: 2.9990 chunk 633 optimal weight: 6.9990 chunk 502 optimal weight: 0.5980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 240 HIS ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 GLN c 247 GLN ** d 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 366 GLN ** f 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 130 GLN g 194 GLN h 69 GLN ** h 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 154 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 77257 Z= 0.195 Angle : 0.737 12.274 104890 Z= 0.370 Chirality : 0.045 0.225 12239 Planarity : 0.005 0.098 13718 Dihedral : 7.255 150.330 11340 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.01 % Favored : 88.70 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.19 % 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: -2.02 (0.08), residues: 10345 helix: 0.57 (0.09), residues: 4044 sheet: -1.64 (0.12), residues: 1612 loop : -3.07 (0.08), residues: 4689 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20690 Ramachandran restraints generated. 10345 Oldfield, 0 Emsley, 10345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 844 time to evaluate : 7.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET j 345 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 857 average time/residue: 0.7520 time to fit residues: 1127.1190 Evaluate side-chains 789 residues out of total 8902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 779 time to evaluate : 7.141 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5936 time to fit residues: 20.7673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1033 random chunks: chunk 650 optimal weight: 0.0970 chunk 872 optimal weight: 0.9990 chunk 251 optimal weight: 0.9980 chunk 755 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 820 optimal weight: 40.0000 chunk 343 optimal weight: 10.0000 chunk 842 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN F 143 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** L 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 172 ASN X 189 HIS Y 85 ASN c 91 GLN c 145 ASN ** c 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 GLN ** d 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 412 GLN ** f 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 130 GLN ** g 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 GLN ** h 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 154 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.089879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.074898 restraints weight = 245528.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077048 restraints weight = 132981.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077629 restraints weight = 87296.439| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 77257 Z= 0.212 Angle : 0.734 11.907 104890 Z= 0.368 Chirality : 0.045 0.281 12239 Planarity : 0.005 0.101 13718 Dihedral : 7.133 151.323 11340 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.40 % Favored : 88.31 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 2.54 % Twisted General : 0.17 % 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: -1.95 (0.08), residues: 10345 helix: 0.62 (0.09), residues: 4048 sheet: -1.56 (0.13), residues: 1607 loop : -3.04 (0.08), residues: 4690 =============================================================================== Job complete usr+sys time: 19420.74 seconds wall clock time: 341 minutes 16.38 seconds (20476.38 seconds total)