Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 12:59:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl9_29271/08_2023/8fl9_29271_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl9_29271/08_2023/8fl9_29271.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl9_29271/08_2023/8fl9_29271_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl9_29271/08_2023/8fl9_29271_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl9_29271/08_2023/8fl9_29271_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl9_29271/08_2023/8fl9_29271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl9_29271/08_2023/8fl9_29271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl9_29271/08_2023/8fl9_29271_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl9_29271/08_2023/8fl9_29271_neut_updated.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.051 sd= 0.175 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 6 6.06 5 P 3637 5.49 5 Mg 88 5.21 5 S 277 5.16 5 C 73755 2.51 5 N 26289 2.21 5 O 35826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L6 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LM TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LW TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LY TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NK TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 139879 Number of models: 1 Model: "" Number of chains: 65 Chain: "BA" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 786 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 9, 'TRANS': 150} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 553 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 199 Chain: "L1" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3278 Classifications: {'RNA': 154} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p': 3, 'rna3p_pur': 61, 'rna3p_pyr': 64} Link IDs: {'rna2p': 25, 'rna3p': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "L3" Number of atoms: 72147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3361, 72147 Classifications: {'RNA': 3361} Modifications used: {'rna2p': 5, 'rna2p_pur': 325, 'rna2p_pyr': 205, 'rna3p': 80, 'rna3p_pur': 1487, 'rna3p_pyr': 1241} Link IDs: {'rna2p': 534, 'rna3p': 2826} Chain breaks: 31 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 32 Chain: "L4" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2561 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 54, 'rna3p_pyr': 54} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "L5" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1349 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "L6" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain: "L7" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1650 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 191} Chain: "L8" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "L9" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "LA" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "LB" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1512 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "LC" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1461 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain: "LD" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1289 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "LE" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1264 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain breaks: 1 Chain: "LF" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 842 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "LG" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1034 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "LH" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 958 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "LI" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LJ" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "LK" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "LL" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "LM" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 699 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "LN" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3239 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 386} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "LO" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 738 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "LP" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 879 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "LQ" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "LR" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 888 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "LS" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "LT" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "LU" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "LV" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "LW" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 82} Chain: "LX" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "LY" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "LZ" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "NC" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 219 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "NF" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 626 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "NK" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 581 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "NP" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 847 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "SA" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2853 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 339} Chain: "SB" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2243 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain: "SC" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 202} Chain breaks: 2 Chain: "SD" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "SE" Number of atoms: 1869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1861 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 231, 1861 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 bond proxies already assigned to first conformer: 1883 Chain: "SF" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1876 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 230} Chain: "SG" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "SK" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1852 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "SQ" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "SR" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4932 Classifications: {'peptide': 601} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 2 Chain: "SV" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1184 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "L1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L3" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Unusual residues: {' MG': 74} Classifications: {'undetermined': 74} Link IDs: {None: 73} Chain: "L4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "LG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LW" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "LX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "NP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "SA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SR" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' K': 1, ' MG': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "SV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A05LA SG CYSLR 46 86.896 179.792 79.244 1.00 63.89 S ATOM A05LR SG CYSLR 49 85.779 183.232 80.744 1.00 70.59 S ATOM A05T2 SG CYSLR 83 83.705 181.768 78.224 1.00 61.61 S ATOM A05TM SG CYSLR 86 87.117 182.781 77.069 1.00 61.63 S ATOM A085Y SG CYSLV 12 190.032 112.560 114.804 1.00 37.55 S ATOM A086M SG CYSLV 15 193.239 111.779 112.994 1.00 43.47 S ATOM A08JN SG CYSLV 72 192.215 115.494 113.629 1.00 39.46 S ATOM A08KO SG CYSLV 77 190.276 113.245 111.226 1.00 47.61 S ATOM A08UY SG CYSLW 19 95.289 125.004 98.966 1.00 39.75 S ATOM A08VQ SG CYSLW 22 95.927 122.193 101.425 1.00 40.60 S ATOM A08Y9 SG CYSLW 34 97.924 125.383 101.689 1.00 34.58 S ATOM A08YS SG CYSLW 37 98.605 123.055 98.861 1.00 37.07 S ATOM A09IZ SG CYSLX 39 97.705 191.212 87.651 1.00 59.37 S ATOM A09JM SG CYSLX 42 94.347 192.889 87.414 1.00 62.35 S ATOM A09N0 SG CYSLX 57 94.695 189.828 89.612 1.00 57.13 S ATOM A09NG SG CYSLX 60 94.902 189.384 85.890 1.00 58.56 S ATOM A0C0T SG CYSNP 63 76.423 198.981 157.956 1.00 66.61 S ATOM A0C1C SG CYSNP 66 74.922 195.568 157.929 1.00 67.38 S ATOM A0TSV SG CYSSV 6 65.233 179.688 178.837 1.00 51.20 S ATOM A0TTO SG CYSSV 9 61.587 178.523 178.246 1.00 47.91 S ATOM A0TYS SG CYSSV 32 64.114 176.119 179.621 1.00 47.41 S ATOM A0TZM SG CYSSV 36 64.422 177.245 176.063 1.00 45.39 S Time building chain proxies: 50.63, per 1000 atoms: 0.36 Number of scatterers: 139879 At special positions: 0 Unit cell: (257.28, 240.128, 279.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 K 1 19.00 S 277 16.00 P 3637 15.00 Mg 88 11.99 O 35826 8.00 N 26289 7.00 C 73755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 52.48 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLR 500 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 83 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 86 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 49 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 46 " pdb=" ZNLV 200 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 77 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 12 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 72 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 15 " pdb=" ZNLW 101 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 22 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 19 " pdb=" ZNLX 500 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 39 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 57 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 60 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 42 " pdb=" ZNNP 500 " pdb="ZN ZNNP 500 " - pdb=" NE2 HISNP 79 " pdb="ZN ZNNP 500 " - pdb=" ND1 HISNP 85 " pdb="ZN ZNNP 500 " - pdb=" SG CYSNP 63 " pdb="ZN ZNNP 500 " - pdb=" SG CYSNP 66 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 31 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14394 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 279 helices and 75 sheets defined 44.9% alpha, 13.0% beta 1125 base pairs and 1773 stacking pairs defined. Time for finding SS restraints: 71.13 Creating SS restraints... Processing helix chain 'BA' and resid 24 through 33 Proline residue: BA 30 - end of helix Processing helix chain 'BA' and resid 38 through 51 Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.602A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 4.961A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 Processing helix chain 'BA' and resid 147 through 158 Processing helix chain 'L5' and resid 30 through 45 removed outlier: 3.570A pdb=" N THRL5 34 " --> pdb=" O GLYL5 30 " (cutoff:3.500A) Processing helix chain 'L5' and resid 76 through 91 removed outlier: 3.612A pdb=" N GLUL5 80 " --> pdb=" O GLYL5 76 " (cutoff:3.500A) Processing helix chain 'L5' and resid 111 through 116 removed outlier: 4.175A pdb=" N LEUL5 115 " --> pdb=" O GLUL5 111 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLYL5 116 " --> pdb=" O HISL5 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L5' and resid 111 through 116' Processing helix chain 'L5' and resid 139 through 144 removed outlier: 4.535A pdb=" N ASPL5 143 " --> pdb=" O PHEL5 139 " (cutoff:3.500A) Processing helix chain 'L5' and resid 158 through 170 Processing helix chain 'L6' and resid 17 through 22 removed outlier: 4.087A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VALL6 22 " --> pdb=" O TRPL6 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L6' and resid 17 through 22' Processing helix chain 'L6' and resid 27 through 47 removed outlier: 3.643A pdb=" N ALAL6 47 " --> pdb=" O ALAL6 43 " (cutoff:3.500A) Processing helix chain 'L6' and resid 77 through 85 Processing helix chain 'L6' and resid 87 through 95 removed outlier: 4.153A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 Processing helix chain 'L6' and resid 140 through 147 removed outlier: 3.516A pdb=" N LYSL6 145 " --> pdb=" O ALAL6 141 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEUL6 146 " --> pdb=" O GLUL6 142 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALAL6 147 " --> pdb=" O GLUL6 143 " (cutoff:3.500A) Processing helix chain 'L6' and resid 170 through 176 removed outlier: 3.654A pdb=" N PHEL6 176 " --> pdb=" O GLUL6 172 " (cutoff:3.500A) Processing helix chain 'L6' and resid 177 through 192 Processing helix chain 'L6' and resid 193 through 211 Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.540A pdb=" N LYSL7 25 " --> pdb=" O ALAL7 21 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 61 removed outlier: 3.714A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ARGL7 61 " --> pdb=" O PHEL7 57 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 removed outlier: 3.743A pdb=" N GLYL7 69 " --> pdb=" O ASNL7 65 " (cutoff:3.500A) Proline residue: L7 70 - end of helix No H-bonds generated for 'chain 'L7' and resid 65 through 70' Processing helix chain 'L7' and resid 75 through 89 removed outlier: 3.763A pdb=" N METL7 87 " --> pdb=" O THRL7 83 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEUL7 88 " --> pdb=" O VALL7 84 " (cutoff:3.500A) Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 3.562A pdb=" N ARGL7 101 " --> pdb=" O ALAL7 97 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.926A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LYSL7 116 " --> pdb=" O TYRL7 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L7' and resid 110 through 116' Processing helix chain 'L7' and resid 124 through 129 Processing helix chain 'L7' and resid 137 through 146 Processing helix chain 'L7' and resid 151 through 190 removed outlier: 5.436A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.506A pdb=" N VALL7 195 " --> pdb=" O LYSL7 191 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.995A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLNL8 56 " --> pdb=" O PHEL8 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'L8' and resid 51 through 56' Processing helix chain 'L8' and resid 69 through 81 removed outlier: 3.525A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.626A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.984A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 removed outlier: 3.728A pdb=" N LEUL8 136 " --> pdb=" O LYSL8 132 " (cutoff:3.500A) Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.950A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARGL9 12 " --> pdb=" O GLNL9 8 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 3.745A pdb=" N GLNL9 32 " --> pdb=" O TRPL9 28 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEUL9 33 " --> pdb=" O GLNL9 29 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SERL9 34 " --> pdb=" O TYRL9 30 " (cutoff:3.500A) Processing helix chain 'L9' and resid 44 through 52 Processing helix chain 'L9' and resid 83 through 88 removed outlier: 3.756A pdb=" N HISL9 87 " --> pdb=" O LYSL9 83 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLYL9 88 " --> pdb=" O PROL9 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 83 through 88' Processing helix chain 'L9' and resid 97 through 111 removed outlier: 3.557A pdb=" N HISL9 109 " --> pdb=" O ARGL9 105 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.697A pdb=" N ASNL9 145 " --> pdb=" O ALAL9 141 " (cutoff:3.500A) Proline residue: L9 146 - end of helix Processing helix chain 'L9' and resid 148 through 153 removed outlier: 4.272A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYSL9 153 " --> pdb=" O GLNL9 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 148 through 153' Processing helix chain 'L9' and resid 158 through 163 removed outlier: 3.556A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 3.641A pdb=" N LYSL9 170 " --> pdb=" O SERL9 166 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLYL9 173 " --> pdb=" O ARGL9 169 " (cutoff:3.500A) Processing helix chain 'L9' and resid 187 through 197 Processing helix chain 'LA' and resid 25 through 37 Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 70 through 77 removed outlier: 4.496A pdb=" N LYSLA 74 " --> pdb=" O CYSLA 70 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLNLA 75 " --> pdb=" O ALALA 71 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) Processing helix chain 'LA' and resid 84 through 106 removed outlier: 3.718A pdb=" N HISLA 93 " --> pdb=" O GLULA 89 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N METLA 94 " --> pdb=" O PHELA 90 " (cutoff:3.500A) Processing helix chain 'LB' and resid 22 through 39 removed outlier: 3.571A pdb=" N PHELB 34 " --> pdb=" O LYSLB 30 " (cutoff:3.500A) Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.331A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VALLB 46 " --> pdb=" O THRLB 42 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.507A pdb=" N ALALB 116 " --> pdb=" O ARGLB 112 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 removed outlier: 3.502A pdb=" N LEULB 128 " --> pdb=" O ASPLB 124 " (cutoff:3.500A) Processing helix chain 'LB' and resid 146 through 153 removed outlier: 4.419A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLYLB 153 " --> pdb=" O TYRLB 149 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 removed outlier: 3.511A pdb=" N TRPLC 45 " --> pdb=" O LYSLC 41 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLNLC 50 " --> pdb=" O TYRLC 46 " (cutoff:3.500A) Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 4.044A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLNLC 125 " --> pdb=" O ALALC 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 120 through 125' Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.923A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASPLC 147 " --> pdb=" O LYSLC 143 " (cutoff:3.500A) Processing helix chain 'LC' and resid 161 through 166 Proline residue: LC 165 - end of helix No H-bonds generated for 'chain 'LC' and resid 161 through 166' Processing helix chain 'LD' and resid 4 through 16 Processing helix chain 'LD' and resid 18 through 23 removed outlier: 3.673A pdb=" N VALLD 22 " --> pdb=" O GLYLD 18 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TRPLD 23 " --> pdb=" O LYSLD 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 18 through 23' Processing helix chain 'LD' and resid 28 through 36 removed outlier: 3.581A pdb=" N ASNLD 34 " --> pdb=" O ASNLD 30 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALALD 35 " --> pdb=" O GLULD 31 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASNLD 36 " --> pdb=" O ILELD 32 " (cutoff:3.500A) Processing helix chain 'LD' and resid 37 through 48 Processing helix chain 'LD' and resid 60 through 73 Processing helix chain 'LD' and resid 84 through 113 Proline residue: LD 90 - end of helix removed outlier: 6.769A pdb=" N VALLD 93 " --> pdb=" O METLD 89 " (cutoff:3.500A) Processing helix chain 'LD' and resid 116 through 130 removed outlier: 4.556A pdb=" N ASNLD 130 " --> pdb=" O LYSLD 126 " (cutoff:3.500A) Processing helix chain 'LD' and resid 134 through 155 removed outlier: 3.534A pdb=" N LEULD 138 " --> pdb=" O ASNLD 134 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HISLD 143 " --> pdb=" O METLD 139 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYSLD 144 " --> pdb=" O GLULD 140 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEULD 145 " --> pdb=" O HISLD 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALALD 150 " --> pdb=" O LYSLD 146 " (cutoff:3.500A) Processing helix chain 'LE' and resid 11 through 16 removed outlier: 4.351A pdb=" N PHELE 15 " --> pdb=" O THRLE 11 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SERLE 16 " --> pdb=" O ARGLE 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 11 through 16' Processing helix chain 'LE' and resid 26 through 32 removed outlier: 4.510A pdb=" N TYRLE 30 " --> pdb=" O PROLE 26 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARGLE 32 " --> pdb=" O ALALE 28 " (cutoff:3.500A) Processing helix chain 'LE' and resid 54 through 59 removed outlier: 3.731A pdb=" N HISLE 58 " --> pdb=" O HISLE 54 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLYLE 59 " --> pdb=" O LYSLE 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 54 through 59' Processing helix chain 'LE' and resid 92 through 97 removed outlier: 4.063A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LYSLE 97 " --> pdb=" O ILELE 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 92 through 97' Processing helix chain 'LE' and resid 99 through 121 removed outlier: 4.422A pdb=" N ASPLE 103 " --> pdb=" O SERLE 99 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SERLE 104 " --> pdb=" O LYSLE 100 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYSLE 110 " --> pdb=" O LEULE 106 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLULE 121 " --> pdb=" O LYSLE 117 " (cutoff:3.500A) Processing helix chain 'LF' and resid 25 through 32 Processing helix chain 'LF' and resid 35 through 47 Processing helix chain 'LF' and resid 55 through 60 Processing helix chain 'LF' and resid 79 through 95 removed outlier: 3.940A pdb=" N LEULF 83 " --> pdb=" O SERLF 79 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYSLF 84 " --> pdb=" O LYSLF 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 69 through 74 removed outlier: 3.591A pdb=" N ARGLG 73 " --> pdb=" O LYSLG 69 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LYSLG 74 " --> pdb=" O PROLG 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 69 through 74' Processing helix chain 'LG' and resid 122 through 130 removed outlier: 3.809A pdb=" N LEULG 128 " --> pdb=" O GLULG 124 " (cutoff:3.500A) Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 137 removed outlier: 4.300A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALALG 136 " --> pdb=" O ILELG 132 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLYLG 137 " --> pdb=" O ALALG 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 131 through 137' Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.699A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 92 Processing helix chain 'LH' and resid 105 through 117 Processing helix chain 'LH' and resid 145 through 154 Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 3.701A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SERLI 31 " --> pdb=" O ARGLI 27 " (cutoff:3.500A) Processing helix chain 'LI' and resid 35 through 43 Processing helix chain 'LI' and resid 100 through 105 removed outlier: 4.167A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VALLI 105 " --> pdb=" O PROLI 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 100 through 105' Processing helix chain 'LI' and resid 112 through 134 Processing helix chain 'LJ' and resid 58 through 67 removed outlier: 3.980A pdb=" N LYSLJ 67 " --> pdb=" O ALALJ 63 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 81 removed outlier: 3.616A pdb=" N LEULJ 80 " --> pdb=" O ASNLJ 76 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N METLJ 81 " --> pdb=" O TYRLJ 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 76 through 81' Processing helix chain 'LJ' and resid 92 through 97 removed outlier: 3.871A pdb=" N ASNLJ 97 " --> pdb=" O LYSLJ 93 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 98 through 104 removed outlier: 4.505A pdb=" N ARGLJ 102 " --> pdb=" O LYSLJ 98 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASPLJ 103 " --> pdb=" O ASPLJ 99 " (cutoff:3.500A) Proline residue: LJ 104 - end of helix No H-bonds generated for 'chain 'LJ' and resid 98 through 104' Processing helix chain 'LJ' and resid 105 through 125 removed outlier: 3.836A pdb=" N THRLJ 124 " --> pdb=" O GLULJ 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLYLJ 125 " --> pdb=" O ARGLJ 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 127 through 133 removed outlier: 3.830A pdb=" N PHELJ 131 " --> pdb=" O ASNLJ 127 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYSLJ 133 " --> pdb=" O TRPLJ 129 " (cutoff:3.500A) Processing helix chain 'LK' and resid 2 through 7 removed outlier: 3.980A pdb=" N ARGLK 6 " --> pdb=" O PROLK 2 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYSLK 7 " --> pdb=" O SERLK 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 2 through 7' Processing helix chain 'LK' and resid 41 through 48 Processing helix chain 'LK' and resid 64 through 69 removed outlier: 4.341A pdb=" N SERLK 68 " --> pdb=" O LYSLK 64 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHELK 69 " --> pdb=" O ARGLK 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 64 through 69' Processing helix chain 'LK' and resid 74 through 83 removed outlier: 4.418A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N THRLK 80 " --> pdb=" O ASPLK 76 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEULK 81 " --> pdb=" O LYSLK 77 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VALLK 82 " --> pdb=" O LEULK 78 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 93 Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.690A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 removed outlier: 3.576A pdb=" N VALLK 140 " --> pdb=" O LYSLK 136 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLYLK 141 " --> pdb=" O ILELK 137 " (cutoff:3.500A) Processing helix chain 'LL' and resid 2 through 13 removed outlier: 3.541A pdb=" N METLL 8 " --> pdb=" O HISLL 4 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.735A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 4.453A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LM' and resid 11 through 20 removed outlier: 4.095A pdb=" N LYSLM 15 " --> pdb=" O ASNLM 11 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASNLM 19 " --> pdb=" O LYSLM 15 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLYLM 20 " --> pdb=" O TRPLM 16 " (cutoff:3.500A) Processing helix chain 'LM' and resid 36 through 54 removed outlier: 3.587A pdb=" N ASNLM 50 " --> pdb=" O ALALM 46 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYSLM 51 " --> pdb=" O LYSLM 47 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYSLM 52 " --> pdb=" O LYSLM 48 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLYLM 53 " --> pdb=" O HISLM 49 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEULM 54 " --> pdb=" O ASNLM 50 " (cutoff:3.500A) Processing helix chain 'LM' and resid 55 through 66 Processing helix chain 'LM' and resid 91 through 101 Processing helix chain 'LM' and resid 105 through 116 removed outlier: 3.534A pdb=" N ILELM 112 " --> pdb=" O ALALM 108 " (cutoff:3.500A) Processing helix chain 'LN' and resid 13 through 18 removed outlier: 4.501A pdb=" N LEULN 17 " --> pdb=" O SERLN 13 " (cutoff:3.500A) Proline residue: LN 18 - end of helix No H-bonds generated for 'chain 'LN' and resid 13 through 18' Processing helix chain 'LN' and resid 111 through 120 removed outlier: 4.134A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 139 removed outlier: 3.528A pdb=" N CYSLN 134 " --> pdb=" O PHELN 130 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) Processing helix chain 'LN' and resid 140 through 156 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 4.123A pdb=" N LEULN 171 " --> pdb=" O GLNLN 167 " (cutoff:3.500A) Proline residue: LN 172 - end of helix No H-bonds generated for 'chain 'LN' and resid 167 through 172' Processing helix chain 'LN' and resid 189 through 201 removed outlier: 3.523A pdb=" N GLULN 199 " --> pdb=" O ASPLN 195 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARGLN 200 " --> pdb=" O TRPLN 196 " (cutoff:3.500A) Processing helix chain 'LN' and resid 206 through 211 removed outlier: 4.008A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 230 through 235 Processing helix chain 'LN' and resid 356 through 361 removed outlier: 4.770A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLULN 361 " --> pdb=" O ARGLN 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 356 through 361' Processing helix chain 'LN' and resid 381 through 390 Processing helix chain 'LN' and resid 392 through 403 Processing helix chain 'LO' and resid 13 through 25 removed outlier: 3.984A pdb=" N ARGLO 17 " --> pdb=" O SERLO 13 " (cutoff:3.500A) Processing helix chain 'LO' and resid 30 through 41 Processing helix chain 'LO' and resid 53 through 68 Processing helix chain 'LO' and resid 77 through 86 removed outlier: 3.601A pdb=" N GLYLO 86 " --> pdb=" O GLYLO 82 " (cutoff:3.500A) Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.876A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HISLP 34 " --> pdb=" O HISLP 30 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 58 removed outlier: 4.196A pdb=" N GLYLP 58 " --> pdb=" O METLP 54 " (cutoff:3.500A) Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.640A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 24 through 29' Processing helix chain 'LQ' and resid 43 through 48 Processing helix chain 'LQ' and resid 81 through 90 removed outlier: 4.174A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.889A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 68 removed outlier: 3.684A pdb=" N LEULR 64 " --> pdb=" O ARGLR 60 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N METLR 65 " --> pdb=" O PROLR 61 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ARGLR 66 " --> pdb=" O LYSLR 62 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEULR 67 " --> pdb=" O VALLR 63 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SERLR 68 " --> pdb=" O LEULR 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'LR' and resid 60 through 68' Processing helix chain 'LR' and resid 83 through 113 removed outlier: 3.505A pdb=" N VALLR 104 " --> pdb=" O GLNLR 100 " (cutoff:3.500A) Processing helix chain 'LS' and resid 5 through 10 removed outlier: 3.507A pdb=" N LEULS 9 " --> pdb=" O LYSLS 5 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARGLS 10 " --> pdb=" O ALALS 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'LS' and resid 5 through 10' Processing helix chain 'LS' and resid 13 through 38 removed outlier: 3.504A pdb=" N ASPLS 23 " --> pdb=" O LYSLS 19 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEULS 24 " --> pdb=" O GLNLS 20 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.646A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VALLS 49 " --> pdb=" O SERLS 45 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALALS 55 " --> pdb=" O ARGLS 51 " (cutoff:3.500A) Processing helix chain 'LS' and resid 80 through 85 Proline residue: LS 85 - end of helix Processing helix chain 'LS' and resid 88 through 95 removed outlier: 3.509A pdb=" N ARGLS 94 " --> pdb=" O ALALS 90 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEULS 95 " --> pdb=" O METLS 91 " (cutoff:3.500A) Processing helix chain 'LS' and resid 96 through 102 Processing helix chain 'LS' and resid 104 through 114 Processing helix chain 'LT' and resid 35 through 40 removed outlier: 3.850A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLULT 40 " --> pdb=" O ARGLT 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 35 through 40' Processing helix chain 'LU' and resid 25 through 30 removed outlier: 4.261A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARGLU 30 " --> pdb=" O HISLU 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 25 through 30' Processing helix chain 'LU' and resid 34 through 49 Processing helix chain 'LU' and resid 51 through 64 removed outlier: 3.612A pdb=" N VALLU 63 " --> pdb=" O GLULU 59 " (cutoff:3.500A) Processing helix chain 'LU' and resid 65 through 78 Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LV' and resid 35 through 47 removed outlier: 5.939A pdb=" N GLYLV 47 " --> pdb=" O ARGLV 43 " (cutoff:3.500A) Processing helix chain 'LW' and resid 4 through 11 removed outlier: 3.984A pdb=" N GLYLW 9 " --> pdb=" O THRLW 5 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYSLW 10 " --> pdb=" O SERLW 6 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARGLW 11 " --> pdb=" O SERLW 7 " (cutoff:3.500A) Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.640A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.416A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) Processing helix chain 'LX' and resid 20 through 35 removed outlier: 4.014A pdb=" N LYSLX 28 " --> pdb=" O LYSLX 24 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILELX 29 " --> pdb=" O METLX 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HISLX 34 " --> pdb=" O GLULX 30 " (cutoff:3.500A) Processing helix chain 'LX' and resid 73 through 92 removed outlier: 3.888A pdb=" N GLULX 88 " --> pdb=" O ARGLX 84 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEULX 89 " --> pdb=" O ARGLX 85 " (cutoff:3.500A) Processing helix chain 'LY' and resid 7 through 17 removed outlier: 3.511A pdb=" N ARGLY 17 " --> pdb=" O LEULY 13 " (cutoff:3.500A) Processing helix chain 'LY' and resid 49 through 60 removed outlier: 3.638A pdb=" N LYSLY 55 " --> pdb=" O GLULY 51 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLNLY 58 " --> pdb=" O GLULY 54 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEULY 60 " --> pdb=" O LEULY 56 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 6 through 21 removed outlier: 5.372A pdb=" N ARGLZ 21 " --> pdb=" O GLNLZ 17 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 24 through 31 removed outlier: 4.641A pdb=" N ARGLZ 28 " --> pdb=" O PROLZ 24 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N METLZ 29 " --> pdb=" O GLNLZ 25 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYSLZ 30 " --> pdb=" O TRPLZ 26 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N THRLZ 31 " --> pdb=" O ILELZ 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 24 through 31' Processing helix chain 'NC' and resid 133 through 138 removed outlier: 4.648A pdb=" N THRNC 137 " --> pdb=" O HISNC 133 " (cutoff:3.500A) Processing helix chain 'NC' and resid 139 through 144 Processing helix chain 'NC' and resid 159 through 174 removed outlier: 3.807A pdb=" N GLUNC 165 " --> pdb=" O GLNNC 161 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASNNC 166 " --> pdb=" O SERNC 162 " (cutoff:3.500A) Processing helix chain 'NF' and resid 5 through 14 removed outlier: 3.992A pdb=" N LEUNF 9 " --> pdb=" O GLUNF 5 " (cutoff:3.500A) Processing helix chain 'NF' and resid 21 through 34 removed outlier: 4.019A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HISNF 33 " --> pdb=" O SERNF 29 " (cutoff:3.500A) Processing helix chain 'NF' and resid 44 through 72 Processing helix chain 'NK' and resid 9 through 33 removed outlier: 3.520A pdb=" N LYSNK 20 " --> pdb=" O GLUNK 16 " (cutoff:3.500A) Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 98 through 112 removed outlier: 3.685A pdb=" N ARGNK 104 " --> pdb=" O ARGNK 100 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYSNK 108 " --> pdb=" O ARGNK 104 " (cutoff:3.500A) Processing helix chain 'NP' and resid 15 through 21 removed outlier: 4.566A pdb=" N METNP 19 " --> pdb=" O LEUNP 15 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALANP 21 " --> pdb=" O ARGNP 17 " (cutoff:3.500A) Processing helix chain 'NP' and resid 27 through 36 removed outlier: 3.614A pdb=" N ARGNP 33 " --> pdb=" O ASPNP 29 " (cutoff:3.500A) Processing helix chain 'NP' and resid 72 through 83 removed outlier: 3.517A pdb=" N PHENP 80 " --> pdb=" O LEUNP 76 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARGNP 81 " --> pdb=" O LYSNP 77 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SERNP 82 " --> pdb=" O THRNP 78 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYSNP 83 " --> pdb=" O HISNP 79 " (cutoff:3.500A) Processing helix chain 'NP' and resid 84 through 94 removed outlier: 3.742A pdb=" N LEUNP 89 " --> pdb=" O HISNP 85 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSNP 90 " --> pdb=" O LYSNP 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SERNP 93 " --> pdb=" O LEUNP 89 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VALNP 94 " --> pdb=" O LYSNP 90 " (cutoff:3.500A) Processing helix chain 'NP' and resid 98 through 107 removed outlier: 3.627A pdb=" N ALANP 106 " --> pdb=" O ALANP 102 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLYNP 107 " --> pdb=" O GLUNP 103 " (cutoff:3.500A) Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.761A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALASA 30 " --> pdb=" O ALASA 26 " (cutoff:3.500A) Proline residue: SA 31 - end of helix No H-bonds generated for 'chain 'SA' and resid 25 through 31' Processing helix chain 'SA' and resid 33 through 49 removed outlier: 3.815A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.629A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEUSA 133 " --> pdb=" O ALASA 129 " (cutoff:3.500A) Proline residue: SA 134 - end of helix Processing helix chain 'SA' and resid 135 through 141 removed outlier: 3.538A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 155 through 161 removed outlier: 4.857A pdb=" N GLUSA 159 " --> pdb=" O GLUSA 155 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 155 through 161' Processing helix chain 'SA' and resid 163 through 175 removed outlier: 3.791A pdb=" N ALASA 167 " --> pdb=" O LYSSA 163 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUSA 170 " --> pdb=" O GLUSA 166 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEUSA 171 " --> pdb=" O ALASA 167 " (cutoff:3.500A) Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.721A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.821A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASNSA 198 " --> pdb=" O GLYSA 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 193 through 198' Processing helix chain 'SA' and resid 216 through 222 Processing helix chain 'SA' and resid 236 through 242 Proline residue: SA 242 - end of helix Processing helix chain 'SA' and resid 253 through 265 removed outlier: 3.790A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 Processing helix chain 'SA' and resid 296 through 303 removed outlier: 4.054A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 321 through 329 removed outlier: 3.695A pdb=" N METSA 325 " --> pdb=" O ASNSA 321 " (cutoff:3.500A) Processing helix chain 'SA' and resid 330 through 361 removed outlier: 4.621A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N METSA 335 " --> pdb=" O TYRSA 331 " (cutoff:3.500A) Processing helix chain 'SB' and resid 9 through 16 Processing helix chain 'SB' and resid 20 through 26 removed outlier: 3.654A pdb=" N GLYSB 26 " --> pdb=" O ARGSB 22 " (cutoff:3.500A) Processing helix chain 'SB' and resid 29 through 37 removed outlier: 3.922A pdb=" N ARGSB 35 " --> pdb=" O TYRSB 31 " (cutoff:3.500A) Processing helix chain 'SB' and resid 79 through 87 removed outlier: 4.089A pdb=" N LEUSB 83 " --> pdb=" O TYRSB 79 " (cutoff:3.500A) Proline residue: SB 84 - end of helix Processing helix chain 'SB' and resid 94 through 114 Processing helix chain 'SB' and resid 115 through 120 removed outlier: 3.534A pdb=" N GLUSB 120 " --> pdb=" O ASPSB 116 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 170 removed outlier: 3.639A pdb=" N GLYSB 161 " --> pdb=" O ASNSB 157 " (cutoff:3.500A) Processing helix chain 'SB' and resid 191 through 201 removed outlier: 3.503A pdb=" N HISSB 195 " --> pdb=" O ASNSB 191 " (cutoff:3.500A) Processing helix chain 'SB' and resid 202 through 215 removed outlier: 3.747A pdb=" N GLUSB 213 " --> pdb=" O ARGSB 209 " (cutoff:3.500A) Processing helix chain 'SB' and resid 216 through 224 Processing helix chain 'SB' and resid 225 through 230 removed outlier: 4.499A pdb=" N ASNSB 229 " --> pdb=" O GLNSB 225 " (cutoff:3.500A) Processing helix chain 'SB' and resid 232 through 251 removed outlier: 3.745A pdb=" N METSB 236 " --> pdb=" O THRSB 232 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLUSB 237 " --> pdb=" O PROSB 233 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLUSB 238 " --> pdb=" O ASPSB 234 " (cutoff:3.500A) Proline residue: SB 251 - end of helix Processing helix chain 'SB' and resid 272 through 280 Processing helix chain 'SC' and resid 58 through 67 removed outlier: 3.566A pdb=" N ALASC 67 " --> pdb=" O TYRSC 63 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.826A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILESC 195 " --> pdb=" O GLNSC 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 190 through 195' Processing helix chain 'SC' and resid 213 through 218 Processing helix chain 'SC' and resid 243 through 262 removed outlier: 3.624A pdb=" N GLNSC 256 " --> pdb=" O ALASC 252 " (cutoff:3.500A) Proline residue: SC 259 - end of helix Processing helix chain 'SC' and resid 266 through 274 removed outlier: 5.417A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.346A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.712A pdb=" N GLUSD 68 " --> pdb=" O METSD 64 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) Processing helix chain 'SD' and resid 102 through 113 Processing helix chain 'SD' and resid 126 through 137 removed outlier: 3.534A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VALSD 136 " --> pdb=" O METSD 132 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.241A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 4.065A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.207A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 239 through 248 removed outlier: 3.593A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.775A pdb=" N ALASE 68 " --> pdb=" O GLNSE 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.737A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.621A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 121 removed outlier: 3.695A pdb=" N GLNSE 112 " --> pdb=" O GLNSE 108 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALASE 118 " --> pdb=" O LEUSE 114 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLUSE 119 " --> pdb=" O LEUSE 115 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYSSE 120 " --> pdb=" O ALASE 116 " (cutoff:3.500A) Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 164 through 178 removed outlier: 4.914A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEUSE 170 " --> pdb=" O LEUSE 166 " (cutoff:3.500A) Proline residue: SE 171 - end of helix Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.564A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 226 removed outlier: 4.432A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THRSE 224 " --> pdb=" O GLUSE 220 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASNSE 225 " --> pdb=" O ALASE 221 " (cutoff:3.500A) Processing helix chain 'SE' and resid 229 through 236 removed outlier: 3.680A pdb=" N ARGSE 235 " --> pdb=" O ASPSE 231 " (cutoff:3.500A) Processing helix chain 'SE' and resid 243 through 266 removed outlier: 5.098A pdb=" N GLYSE 266 " --> pdb=" O ALASE 262 " (cutoff:3.500A) Processing helix chain 'SF' and resid 5 through 13 removed outlier: 3.613A pdb=" N ARGSF 9 " --> pdb=" O ILESF 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYSSF 10 " --> pdb=" O ARGSF 6 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLYSF 11 " --> pdb=" O GLYSF 7 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALASF 12 " --> pdb=" O GLNSF 8 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLYSF 13 " --> pdb=" O ARGSF 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'SF' and resid 5 through 13' Processing helix chain 'SF' and resid 33 through 39 Processing helix chain 'SF' and resid 103 through 108 removed outlier: 3.703A pdb=" N METSF 107 " --> pdb=" O PROSF 103 " (cutoff:3.500A) Proline residue: SF 108 - end of helix No H-bonds generated for 'chain 'SF' and resid 103 through 108' Processing helix chain 'SF' and resid 181 through 193 removed outlier: 3.575A pdb=" N ALASF 191 " --> pdb=" O HISSF 187 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYSSF 192 " --> pdb=" O LYSSF 188 " (cutoff:3.500A) Processing helix chain 'SF' and resid 200 through 205 removed outlier: 3.914A pdb=" N METSF 204 " --> pdb=" O ARGSF 200 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASNSF 205 " --> pdb=" O GLYSF 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'SF' and resid 200 through 205' Processing helix chain 'SG' and resid 63 through 86 removed outlier: 3.955A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 4.055A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 5.099A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 4.068A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.564A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLUSK 41 " --> pdb=" O VALSK 37 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 3.855A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 88 Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.912A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N METSK 197 " --> pdb=" O ILESK 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'SK' and resid 192 through 197' Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.398A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 4.183A pdb=" N SERSK 235 " --> pdb=" O THRSK 231 " (cutoff:3.500A) Processing helix chain 'SK' and resid 238 through 244 Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.397A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 50 through 61 removed outlier: 4.561A pdb=" N LYSSQ 54 " --> pdb=" O ASNSQ 50 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASPSQ 55 " --> pdb=" O SERSQ 51 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 96 removed outlier: 4.034A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.480A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 149 through 157 removed outlier: 3.595A pdb=" N LEUSQ 156 " --> pdb=" O GLNSQ 152 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 183 through 194 Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 70 removed outlier: 3.570A pdb=" N LYSSR 50 " --> pdb=" O PHESR 46 " (cutoff:3.500A) Proline residue: SR 70 - end of helix Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 120 removed outlier: 3.824A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 145 removed outlier: 3.619A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) Processing helix chain 'SR' and resid 146 through 161 removed outlier: 3.540A pdb=" N GLNSR 153 " --> pdb=" O GLUSR 149 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARGSR 160 " --> pdb=" O GLNSR 156 " (cutoff:3.500A) Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.675A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VALSR 188 " --> pdb=" O PHESR 184 " (cutoff:3.500A) Processing helix chain 'SR' and resid 235 through 247 removed outlier: 4.123A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 Proline residue: SR 277 - end of helix removed outlier: 3.849A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 290 through 295 removed outlier: 3.583A pdb=" N LYSSR 294 " --> pdb=" O LYSSR 290 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARGSR 295 " --> pdb=" O CYSSR 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 290 through 295' Processing helix chain 'SR' and resid 300 through 314 removed outlier: 3.546A pdb=" N ILESR 306 " --> pdb=" O ASPSR 302 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLYSR 314 " --> pdb=" O LEUSR 310 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 3.556A pdb=" N THRSR 346 " --> pdb=" O HISSR 342 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 4.099A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUSR 357 " --> pdb=" O VALSR 353 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HISSR 361 " --> pdb=" O LEUSR 357 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 352 through 362' Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.376A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 417 removed outlier: 5.260A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 417' Processing helix chain 'SR' and resid 421 through 426 removed outlier: 4.212A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N HISSR 426 " --> pdb=" O LEUSR 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 421 through 426' Processing helix chain 'SR' and resid 437 through 442 removed outlier: 3.991A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 442' Processing helix chain 'SR' and resid 445 through 464 removed outlier: 3.691A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SR' and resid 474 through 503 removed outlier: 4.929A pdb=" N LEUSR 478 " --> pdb=" O ASPSR 474 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLNSR 486 " --> pdb=" O GLNSR 482 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THRSR 503 " --> pdb=" O LYSSR 499 " (cutoff:3.500A) Processing helix chain 'SR' and resid 509 through 514 removed outlier: 4.048A pdb=" N LYSSR 513 " --> pdb=" O PROSR 509 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYSSR 514 " --> pdb=" O ARGSR 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 509 through 514' Processing helix chain 'SR' and resid 516 through 528 removed outlier: 3.622A pdb=" N LEUSR 520 " --> pdb=" O GLNSR 516 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEUSR 527 " --> pdb=" O GLUSR 523 " (cutoff:3.500A) Processing helix chain 'SR' and resid 537 through 551 removed outlier: 3.740A pdb=" N SERSR 548 " --> pdb=" O ARGSR 544 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILESR 549 " --> pdb=" O ARGSR 545 " (cutoff:3.500A) Processing helix chain 'SR' and resid 574 through 579 removed outlier: 4.158A pdb=" N GLYSR 579 " --> pdb=" O ARGSR 575 " (cutoff:3.500A) Processing helix chain 'SR' and resid 582 through 604 removed outlier: 3.531A pdb=" N GLNSR 597 " --> pdb=" O METSR 593 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYSSR 598 " --> pdb=" O LYSSR 594 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYSSR 599 " --> pdb=" O ASNSR 595 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N METSR 600 " --> pdb=" O ALASR 596 " (cutoff:3.500A) Processing helix chain 'SR' and resid 618 through 623 Processing helix chain 'SV' and resid 33 through 43 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.700A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 removed outlier: 3.511A pdb=" N ARGSV 56 " --> pdb=" O THRSV 52 " (cutoff:3.500A) Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.463A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 71' Processing helix chain 'SV' and resid 82 through 135 removed outlier: 4.339A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASNSV 87 " --> pdb=" O ARGSV 83 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASPSV 91 " --> pdb=" O ASNSV 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARGSV 111 " --> pdb=" O PHESV 107 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYSSV 125 " --> pdb=" O VALSV 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILESV 131 " --> pdb=" O VALSV 127 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILESV 134 " --> pdb=" O ASNSV 130 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'BA' and resid 11 through 17 removed outlier: 4.086A pdb=" N THRBA 59 " --> pdb=" O VALBA 74 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'L5' and resid 48 through 51 removed outlier: 3.585A pdb=" N ALAL5 69 " --> pdb=" O SERL5 51 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILEL5 68 " --> pdb=" O VALL5 26 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYSL5 19 " --> pdb=" O VALL5 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASNL5 23 " --> pdb=" O ASPL5 129 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASPL5 129 " --> pdb=" O ASNL5 23 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYSL5 25 " --> pdb=" O GLYL5 127 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N GLYL5 127 " --> pdb=" O CYSL5 25 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'L5' and resid 92 through 95 Processing sheet with id= 4, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 5, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 6, first strand: chain 'L8' and resid 11 through 15 removed outlier: 4.609A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L8' and resid 28 through 31 removed outlier: 6.529A pdb=" N ARGL8 35 " --> pdb=" O ILEL8 31 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLYL8 40 " --> pdb=" O ARGL8 46 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ARGL8 46 " --> pdb=" O GLYL8 40 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.438A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.833A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LA' and resid 14 through 20 removed outlier: 6.747A pdb=" N ILELA 149 " --> pdb=" O GLULA 115 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LA' and resid 57 through 60 removed outlier: 5.483A pdb=" N GLNLA 80 " --> pdb=" O PHELA 60 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LA' and resid 116 through 122 Processing sheet with id= 13, first strand: chain 'LA' and resid 124 through 131 removed outlier: 3.666A pdb=" N METLA 125 " --> pdb=" O SERLA 141 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARGLA 127 " --> pdb=" O TYRLA 139 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARGLA 135 " --> pdb=" O ARGLA 131 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LB' and resid 118 through 121 removed outlier: 3.528A pdb=" N ALALB 102 " --> pdb=" O LEULB 121 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYSLB 99 " --> pdb=" O LYSLB 78 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.419A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.239A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.598A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LE' and resid 39 through 42 removed outlier: 4.005A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 20, first strand: chain 'LF' and resid 61 through 65 removed outlier: 6.005A pdb=" N GLULF 108 " --> pdb=" O LYSLF 20 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TRPLF 99 " --> pdb=" O PHELF 115 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LG' and resid 82 through 85 removed outlier: 3.596A pdb=" N ARGLG 83 " --> pdb=" O ALALG 102 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASNLG 101 " --> pdb=" O VALLG 25 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N METLG 62 " --> pdb=" O ILELG 40 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASPLG 59 " --> pdb=" O VALLG 81 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LG' and resid 87 through 90 removed outlier: 3.775A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LG' and resid 78 through 81 Processing sheet with id= 24, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.978A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYSLH 123 " --> pdb=" O ARGLH 139 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.881A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LI' and resid 72 through 75 removed outlier: 3.640A pdb=" N GLNLI 72 " --> pdb=" O TYRLI 81 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.357A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LJ' and resid 10 through 14 removed outlier: 4.262A pdb=" N ARGLJ 21 " --> pdb=" O VALLJ 13 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LJ' and resid 27 through 30 removed outlier: 6.210A pdb=" N HISLJ 40 " --> pdb=" O ILELJ 29 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 31, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.501A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LN' and resid 45 through 50 removed outlier: 4.897A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LN' and resid 53 through 59 removed outlier: 4.047A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.591A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LN' and resid 179 through 185 removed outlier: 4.764A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILELN 160 " --> pdb=" O VALLN 185 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LN' and resid 88 through 93 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain 'LO' and resid 26 through 29 removed outlier: 6.488A pdb=" N LYSLO 26 " --> pdb=" O ILELO 97 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLYLO 70 " --> pdb=" O LYSLO 44 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.852A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 40, first strand: chain 'LR' and resid 20 through 24 Processing sheet with id= 41, first strand: chain 'LT' and resid 56 through 60 removed outlier: 5.854A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THRLT 59 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LT' and resid 8 through 12 removed outlier: 5.910A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LT' and resid 6 through 10 Processing sheet with id= 44, first strand: chain 'LV' and resid 7 through 10 removed outlier: 5.614A pdb=" N VALLV 67 " --> pdb=" O TYRLV 26 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LX' and resid 47 through 50 removed outlier: 6.924A pdb=" N ILELX 54 " --> pdb=" O ARGLX 50 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLYLX 53 " --> pdb=" O GLYLX 66 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYSLX 62 " --> pdb=" O CYSLX 57 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LY' and resid 2 through 5 removed outlier: 3.563A pdb=" N ARGLY 3 " --> pdb=" O LEULY 42 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VALLY 46 " --> pdb=" O ILELY 5 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SERLY 22 " --> pdb=" O ARGLY 37 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYSLY 27 " --> pdb=" O LEULY 69 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'NP' and resid 61 through 64 removed outlier: 4.582A pdb=" N HISNP 61 " --> pdb=" O PHENP 70 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARGNP 68 " --> pdb=" O CYSNP 63 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'SA' and resid 7 through 10 removed outlier: 4.743A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SA' and resid 226 through 231 removed outlier: 5.704A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'SB' and resid 60 through 66 removed outlier: 3.586A pdb=" N VALSB 53 " --> pdb=" O ASPSB 147 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SC' and resid 91 through 95 Processing sheet with id= 52, first strand: chain 'SC' and resid 148 through 153 removed outlier: 4.646A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 54, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.794A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SE' and resid 180 through 185 removed outlier: 3.679A pdb=" N LEUSE 154 " --> pdb=" O PHESE 204 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SF' and resid 47 through 50 removed outlier: 3.634A pdb=" N ASPSF 47 " --> pdb=" O LYSSF 60 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYSSF 60 " --> pdb=" O LYSSF 46 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLNSF 86 " --> pdb=" O VALSF 45 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SF' and resid 110 through 114 removed outlier: 4.023A pdb=" N THRSF 111 " --> pdb=" O VALSF 136 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARGSF 147 " --> pdb=" O ILESF 137 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYSSF 145 " --> pdb=" O ASNSF 140 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SF' and resid 58 through 65 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'SF' and resid 146 through 150 removed outlier: 4.275A pdb=" N SERSF 154 " --> pdb=" O LEUSF 150 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.481A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 62, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.675A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.842A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'SK' and resid 1 through 5 removed outlier: 3.556A pdb=" N ALASK 204 " --> pdb=" O METSK 1 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 66, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 67, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 68, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 69, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 4.939A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.777A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 72, first strand: chain 'SQ' and resid 213 through 217 Processing sheet with id= 73, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.297A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'SR' and resid 205 through 211 removed outlier: 5.400A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SV' and resid 18 through 22 No H-bonds generated for sheet with id= 75 2429 hydrogen bonds defined for protein. 7227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2976 hydrogen bonds 5084 hydrogen bond angles 0 basepair planarities 1125 basepair parallelities 1773 stacking parallelities Total time for adding SS restraints: 193.81 Time building geometry restraints manager: 57.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 14404 1.31 - 1.43: 62053 1.43 - 1.56: 65931 1.56 - 1.69: 7259 1.69 - 1.81: 451 Bond restraints: 150098 Sorted by residual: bond pdb=" C2' A2ML32401 " pdb=" C1' A2ML32401 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C2' A2ML33867 " pdb=" C1' A2ML33867 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C2' A2ML32815 " pdb=" C1' A2ML32815 " ideal model delta sigma weight residual 1.305 1.550 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C2' A2ML33825 " pdb=" C1' A2ML33825 " ideal model delta sigma weight residual 1.305 1.549 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C2' A2ML33724 " pdb=" C1' A2ML33724 " ideal model delta sigma weight residual 1.305 1.548 -0.243 2.00e-02 2.50e+03 1.48e+02 ... (remaining 150093 not shown) Histogram of bond angle deviations from ideal: 86.99 - 97.46: 14 97.46 - 107.93: 32339 107.93 - 118.40: 105850 118.40 - 128.87: 78053 128.87 - 139.33: 3828 Bond angle restraints: 220084 Sorted by residual: angle pdb=" C1' A2ML34590 " pdb=" N9 A2ML34590 " pdb=" C8 A2ML34590 " ideal model delta sigma weight residual 88.50 129.15 -40.65 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C1' A2ML32787 " pdb=" N9 A2ML32787 " pdb=" C8 A2ML32787 " ideal model delta sigma weight residual 88.50 127.01 -38.51 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C1' A2ML31524 " pdb=" N9 A2ML31524 " pdb=" C8 A2ML31524 " ideal model delta sigma weight residual 88.50 126.69 -38.19 3.00e+00 1.11e-01 1.62e+02 angle pdb=" C1' A2ML33718 " pdb=" N9 A2ML33718 " pdb=" C8 A2ML33718 " ideal model delta sigma weight residual 88.50 126.53 -38.03 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C1' A2ML3 398 " pdb=" N9 A2ML3 398 " pdb=" C8 A2ML3 398 " ideal model delta sigma weight residual 88.50 126.50 -38.00 3.00e+00 1.11e-01 1.60e+02 ... (remaining 220079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 80199 35.51 - 71.02: 2064 71.02 - 106.53: 224 106.53 - 142.05: 14 142.05 - 177.56: 11 Dihedral angle restraints: 82512 sinusoidal: 60221 harmonic: 22291 Sorted by residual: dihedral pdb=" C5' GL34305 " pdb=" C4' GL34305 " pdb=" C3' GL34305 " pdb=" O3' GL34305 " ideal model delta sinusoidal sigma weight residual 147.00 73.67 73.33 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C4' GL34305 " pdb=" C3' GL34305 " pdb=" C2' GL34305 " pdb=" C1' GL34305 " ideal model delta sinusoidal sigma weight residual -35.00 35.04 -70.04 1 8.00e+00 1.56e-02 9.88e+01 dihedral pdb=" C4' CL3 502 " pdb=" C3' CL3 502 " pdb=" C2' CL3 502 " pdb=" C1' CL3 502 " ideal model delta sinusoidal sigma weight residual -35.00 34.01 -69.01 1 8.00e+00 1.56e-02 9.63e+01 ... (remaining 82509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 26005 0.087 - 0.173: 962 0.173 - 0.260: 48 0.260 - 0.346: 4 0.346 - 0.433: 18 Chirality restraints: 27037 Sorted by residual: chirality pdb=" C2' A2ML31871 " pdb=" C3' A2ML31871 " pdb=" O2' A2ML31871 " pdb=" C1' A2ML31871 " both_signs ideal model delta sigma weight residual False -2.39 -2.82 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" C3' GL34305 " pdb=" C4' GL34305 " pdb=" O3' GL34305 " pdb=" C2' GL34305 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C2' A2ML34571 " pdb=" C3' A2ML34571 " pdb=" O2' A2ML34571 " pdb=" C1' A2ML34571 " both_signs ideal model delta sigma weight residual False -2.39 -2.79 0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 27034 not shown) Planarity restraints: 14366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34228 " 0.912 2.00e-02 2.50e+03 6.17e-01 8.57e+03 pdb=" C4' OMGL34228 " -0.210 2.00e-02 2.50e+03 pdb=" O4' OMGL34228 " -0.690 2.00e-02 2.50e+03 pdb=" C3' OMGL34228 " 0.179 2.00e-02 2.50e+03 pdb=" O3' OMGL34228 " -0.994 2.00e-02 2.50e+03 pdb=" C2' OMGL34228 " 0.623 2.00e-02 2.50e+03 pdb=" O2' OMGL34228 " 0.680 2.00e-02 2.50e+03 pdb=" C1' OMGL34228 " -0.449 2.00e-02 2.50e+03 pdb=" N9 OMGL34228 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34618 " 0.058 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' OMGL34618 " 0.434 2.00e-02 2.50e+03 pdb=" O4' OMGL34618 " 0.646 2.00e-02 2.50e+03 pdb=" C3' OMGL34618 " -0.601 2.00e-02 2.50e+03 pdb=" O3' OMGL34618 " -0.632 2.00e-02 2.50e+03 pdb=" C2' OMGL34618 " -0.182 2.00e-02 2.50e+03 pdb=" O2' OMGL34618 " 0.975 2.00e-02 2.50e+03 pdb=" C1' OMGL34618 " 0.216 2.00e-02 2.50e+03 pdb=" N9 OMGL34618 " -0.915 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCL33887 " 0.013 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' OMCL33887 " 0.468 2.00e-02 2.50e+03 pdb=" O4' OMCL33887 " 0.828 2.00e-02 2.50e+03 pdb=" C3' OMCL33887 " -0.580 2.00e-02 2.50e+03 pdb=" O3' OMCL33887 " -0.541 2.00e-02 2.50e+03 pdb=" C2' OMCL33887 " -0.263 2.00e-02 2.50e+03 pdb=" O2' OMCL33887 " 0.836 2.00e-02 2.50e+03 pdb=" C1' OMCL33887 " 0.187 2.00e-02 2.50e+03 pdb=" N1 OMCL33887 " -0.948 2.00e-02 2.50e+03 ... (remaining 14363 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.56: 917 2.56 - 3.20: 118963 3.20 - 3.85: 309453 3.85 - 4.49: 439483 4.49 - 5.14: 599274 Nonbonded interactions: 1468090 Sorted by model distance: nonbonded pdb=" OP2 GL32584 " pdb="MG MGL35101 " model vdw 1.913 2.170 nonbonded pdb=" OP2 AL31337 " pdb="MG MGL35110 " model vdw 1.922 2.170 nonbonded pdb=" OP2 AL31917 " pdb="MG MGL35122 " model vdw 1.947 2.170 nonbonded pdb=" OP1 AL34378 " pdb="MG MGL35153 " model vdw 1.947 2.170 nonbonded pdb=" OP1 CL32393 " pdb="MG MGL35143 " model vdw 1.949 2.170 ... (remaining 1468085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.170 Extract box with map and model: 30.290 Check model and map are aligned: 1.530 Set scattering table: 0.910 Process input model: 486.200 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 540.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.008 0.246 150098 Z= 0.449 Angle : 0.786 40.650 220084 Z= 0.344 Chirality : 0.038 0.433 27037 Planarity : 0.027 0.617 14366 Dihedral : 13.833 177.556 68118 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.89 % Favored : 98.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 7576 helix: 0.83 (0.10), residues: 2766 sheet: 0.55 (0.16), residues: 1022 loop : 0.02 (0.10), residues: 3788 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1567 time to evaluate : 7.353 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 outliers start: 0 outliers final: 4 residues processed: 1567 average time/residue: 2.2582 time to fit residues: 4971.8545 Evaluate side-chains 1041 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1037 time to evaluate : 7.288 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 3 average time/residue: 1.0849 time to fit residues: 14.5384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 938 optimal weight: 6.9990 chunk 842 optimal weight: 5.9990 chunk 467 optimal weight: 0.0270 chunk 287 optimal weight: 10.0000 chunk 568 optimal weight: 7.9990 chunk 449 optimal weight: 7.9990 chunk 870 optimal weight: 3.9990 chunk 336 optimal weight: 0.7980 chunk 529 optimal weight: 0.9990 chunk 648 optimal weight: 2.9990 chunk 1008 optimal weight: 6.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 42 GLN L5 112 HIS L6 115 GLN L6 175 ASN L7 5 GLN ** L8 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 8 GLN L9 86 HIS L9 117 ASN LB 160 HIS LC 122 HIS LE 58 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 107 HIS LH 111 GLN LI 91 ASN LJ 127 ASN LK 17 HIS LK 66 ASN LL 12 ASN LM 49 HIS LN 42 HIS LN 175 GLN LN 271 GLN LN 322 HIS LN 328 ASN LO 33 GLN ** LP 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 121 ASN ** LQ 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 15 HIS LU 36 HIS LV 90 HIS NK 99 GLN ** NP 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NP 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 38 ASN ** SA 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 24 ASN SD 56 HIS SE 82 GLN SE 149 ASN ** SF 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 162 GLN SG 188 GLN SK 83 HIS SK 225 ASN SQ 106 ASN ** SQ 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 37 HIS SR 91 HIS SR 100 ASN SR 146 GLN SR 157 HIS SR 209 HIS SR 274 ASN SV 39 ASN SV 104 GLN SV 115 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 150098 Z= 0.200 Angle : 0.733 19.279 220084 Z= 0.390 Chirality : 0.035 0.373 27037 Planarity : 0.007 0.132 14366 Dihedral : 13.588 178.175 51994 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.76 % Favored : 98.23 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 7576 helix: 1.59 (0.10), residues: 2792 sheet: 0.63 (0.16), residues: 1010 loop : 0.12 (0.10), residues: 3774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1101 time to evaluate : 7.392 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 outliers start: 200 outliers final: 85 residues processed: 1191 average time/residue: 2.1222 time to fit residues: 3661.6700 Evaluate side-chains 1072 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 987 time to evaluate : 7.293 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 45 residues processed: 43 average time/residue: 1.2823 time to fit residues: 103.6307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 560 optimal weight: 8.9990 chunk 313 optimal weight: 30.0000 chunk 839 optimal weight: 5.9990 chunk 687 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 1010 optimal weight: 3.9990 chunk 1091 optimal weight: 8.9990 chunk 900 optimal weight: 7.9990 chunk 1002 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 810 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 23 ASN ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 87 HIS L9 117 ASN LA 34 GLN LB 93 GLN LE 131 GLN ** LF 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 91 ASN LK 25 HIS LL 12 ASN LL 83 ASN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 100 ASN LQ 23 HIS ** LQ 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 100 GLN LU 36 HIS LX 56 HIS LX 72 ASN NK 99 GLN NP 13 HIS ** NP 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 116 ASN SB 81 HIS SB 138 GLN SD 206 ASN SE 81 ASN ** SE 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 100 HIS SE 149 ASN SE 159 HIS ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 162 GLN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SQ 155 GLN ** SQ 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 100 ASN SR 260 GLN SR 538 HIS SV 17 HIS SV 115 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.098 150098 Z= 0.428 Angle : 0.809 20.217 220084 Z= 0.424 Chirality : 0.042 0.445 27037 Planarity : 0.008 0.145 14366 Dihedral : 13.824 179.919 51994 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.47 % Favored : 97.52 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 7576 helix: 1.26 (0.10), residues: 2825 sheet: 0.52 (0.16), residues: 1004 loop : -0.23 (0.10), residues: 3747 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1045 time to evaluate : 7.183 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 outliers start: 266 outliers final: 144 residues processed: 1167 average time/residue: 2.0875 time to fit residues: 3539.9725 Evaluate side-chains 1102 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 958 time to evaluate : 7.134 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 73 residues processed: 72 average time/residue: 1.2815 time to fit residues: 168.9976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 998 optimal weight: 6.9990 chunk 759 optimal weight: 5.9990 chunk 524 optimal weight: 0.9980 chunk 111 optimal weight: 30.0000 chunk 482 optimal weight: 5.9990 chunk 678 optimal weight: 1.9990 chunk 1014 optimal weight: 4.9990 chunk 1073 optimal weight: 5.9990 chunk 529 optimal weight: 1.9990 chunk 961 optimal weight: 3.9990 chunk 289 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 175 ASN ** L8 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 117 ASN LA 56 GLN LE 144 ASN LF 119 GLN LG 27 ASN LH 111 GLN LI 91 ASN LK 120 GLN LL 83 ASN LP 100 ASN LQ 126 ASN LR 100 GLN LT 24 HIS LU 36 HIS NK 99 GLN NP 13 HIS SD 206 ASN SE 64 GLN SE 90 GLN SE 159 HIS SE 195 HIS ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 39 ASN SG 162 GLN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SQ 155 GLN ** SQ 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 100 ASN SV 115 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 150098 Z= 0.260 Angle : 0.718 19.636 220084 Z= 0.388 Chirality : 0.036 0.404 27037 Planarity : 0.007 0.135 14366 Dihedral : 13.664 178.890 51994 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.10 % Favored : 97.89 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.09), residues: 7576 helix: 1.47 (0.10), residues: 2809 sheet: 0.55 (0.16), residues: 998 loop : -0.23 (0.10), residues: 3769 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1003 time to evaluate : 7.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 258 outliers final: 140 residues processed: 1146 average time/residue: 2.0512 time to fit residues: 3423.4564 Evaluate side-chains 1087 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 947 time to evaluate : 7.249 Switching outliers to nearest non-outliers outliers start: 140 outliers final: 79 residues processed: 63 average time/residue: 1.2825 time to fit residues: 146.3417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 894 optimal weight: 9.9990 chunk 609 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 799 optimal weight: 6.9990 chunk 443 optimal weight: 5.9990 chunk 916 optimal weight: 0.9980 chunk 742 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 chunk 548 optimal weight: 0.0470 chunk 963 optimal weight: 7.9990 chunk 270 optimal weight: 7.9990 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 175 ASN ** L8 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 117 ASN LE 131 GLN LE 144 ASN LG 27 ASN LI 91 ASN LL 83 ASN LP 100 ASN LR 100 GLN LU 36 HIS LW 57 ASN NP 13 HIS SD 63 GLN SD 206 ASN SE 149 ASN ** SF 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 39 ASN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SQ 155 GLN ** SQ 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 115 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 150098 Z= 0.280 Angle : 0.724 19.706 220084 Z= 0.389 Chirality : 0.037 0.417 27037 Planarity : 0.007 0.137 14366 Dihedral : 13.647 179.088 51994 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.38 % Favored : 97.61 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.09), residues: 7576 helix: 1.50 (0.10), residues: 2810 sheet: 0.50 (0.16), residues: 983 loop : -0.26 (0.10), residues: 3783 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 992 time to evaluate : 7.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 248 outliers final: 146 residues processed: 1124 average time/residue: 2.0487 time to fit residues: 3373.6091 Evaluate side-chains 1093 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 947 time to evaluate : 7.222 Switching outliers to nearest non-outliers outliers start: 146 outliers final: 88 residues processed: 61 average time/residue: 1.3720 time to fit residues: 149.9347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 361 optimal weight: 10.0000 chunk 967 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 630 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 1074 optimal weight: 7.9990 chunk 892 optimal weight: 0.5980 chunk 497 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 355 optimal weight: 10.0000 chunk 564 optimal weight: 0.0980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 175 ASN ** L8 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 58 HIS LD 143 HIS LE 144 ASN LG 27 ASN LH 111 GLN LI 91 ASN LP 100 ASN LU 36 HIS LW 57 ASN NK 99 GLN SD 63 GLN SE 149 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 39 ASN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SQ 155 GLN ** SQ 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 115 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 150098 Z= 0.271 Angle : 0.719 19.629 220084 Z= 0.387 Chirality : 0.036 0.411 27037 Planarity : 0.007 0.136 14366 Dihedral : 13.631 179.044 51994 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.24 % Favored : 97.74 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 7576 helix: 1.53 (0.10), residues: 2804 sheet: 0.49 (0.16), residues: 974 loop : -0.29 (0.10), residues: 3798 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 992 time to evaluate : 7.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 223 outliers final: 137 residues processed: 1115 average time/residue: 2.0430 time to fit residues: 3349.0055 Evaluate side-chains 1090 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 953 time to evaluate : 7.241 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 88 residues processed: 50 average time/residue: 1.2449 time to fit residues: 118.3351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 1036 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 612 optimal weight: 6.9990 chunk 784 optimal weight: 8.9990 chunk 608 optimal weight: 3.9990 chunk 904 optimal weight: 8.9990 chunk 600 optimal weight: 0.7980 chunk 1070 optimal weight: 10.0000 chunk 670 optimal weight: 6.9990 chunk 652 optimal weight: 0.9990 chunk 494 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 45 GLN LE 131 GLN LE 144 ASN LG 27 ASN LI 91 ASN LL 83 ASN LN 145 GLN LP 100 ASN LR 100 GLN LU 36 HIS LW 57 ASN ** NF 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 9 ASN SD 206 ASN SE 100 HIS SE 149 ASN ** SE 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 159 HIS ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SF 205 ASN SK 93 GLN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SQ 155 GLN SV 115 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 150098 Z= 0.322 Angle : 0.746 19.732 220084 Z= 0.398 Chirality : 0.038 0.432 27037 Planarity : 0.008 0.139 14366 Dihedral : 13.694 179.570 51994 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 3.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 7576 helix: 1.42 (0.10), residues: 2815 sheet: 0.45 (0.16), residues: 965 loop : -0.39 (0.10), residues: 3796 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 965 time to evaluate : 7.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 238 outliers final: 146 residues processed: 1098 average time/residue: 2.0243 time to fit residues: 3281.0510 Evaluate side-chains 1078 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 932 time to evaluate : 7.245 Switching outliers to nearest non-outliers outliers start: 146 outliers final: 92 residues processed: 55 average time/residue: 1.2961 time to fit residues: 132.2594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 662 optimal weight: 8.9990 chunk 427 optimal weight: 0.9980 chunk 639 optimal weight: 0.9980 chunk 322 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 680 optimal weight: 0.5980 chunk 729 optimal weight: 0.8980 chunk 529 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 841 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 115 GLN ** L8 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 117 ASN LE 144 ASN LF 119 GLN LH 111 GLN LI 91 ASN LP 100 ASN LU 36 HIS LW 48 ASN LW 57 ASN NK 89 GLN ** NK 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 93 GLN SK 225 ASN SQ 58 ASN SQ 155 GLN SR 100 ASN SV 115 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 150098 Z= 0.157 Angle : 0.682 19.490 220084 Z= 0.372 Chirality : 0.033 0.411 27037 Planarity : 0.007 0.127 14366 Dihedral : 13.472 178.294 51994 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 7576 helix: 1.67 (0.10), residues: 2810 sheet: 0.40 (0.16), residues: 989 loop : -0.23 (0.10), residues: 3777 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 988 time to evaluate : 7.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 110 residues processed: 1095 average time/residue: 2.0268 time to fit residues: 3288.5445 Evaluate side-chains 1043 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 933 time to evaluate : 7.212 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 85 residues processed: 27 average time/residue: 1.3920 time to fit residues: 72.4646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 974 optimal weight: 6.9990 chunk 1025 optimal weight: 0.5980 chunk 935 optimal weight: 9.9990 chunk 997 optimal weight: 8.9990 chunk 600 optimal weight: 9.9990 chunk 434 optimal weight: 4.9990 chunk 783 optimal weight: 2.9990 chunk 306 optimal weight: 7.9990 chunk 901 optimal weight: 4.9990 chunk 943 optimal weight: 0.9990 chunk 994 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L7 180 GLN ** L8 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 93 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 131 GLN LF 119 GLN LH 69 ASN LH 111 GLN LI 91 ASN LL 83 ASN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 100 ASN LQ 126 ASN LU 36 HIS ** LW 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NK 89 GLN ** NK 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS SD 63 GLN SE 100 HIS SE 149 ASN ** SE 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 163 GLN SK 93 GLN ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SQ 106 ASN SQ 155 GLN SR 100 ASN SV 115 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 150098 Z= 0.274 Angle : 0.720 19.636 220084 Z= 0.386 Chirality : 0.036 0.417 27037 Planarity : 0.007 0.136 14366 Dihedral : 13.522 179.132 51994 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.09), residues: 7576 helix: 1.59 (0.10), residues: 2812 sheet: 0.41 (0.16), residues: 976 loop : -0.31 (0.10), residues: 3788 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 949 time to evaluate : 7.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 115 residues processed: 1047 average time/residue: 2.0166 time to fit residues: 3124.0074 Evaluate side-chains 1037 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 922 time to evaluate : 7.275 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 90 residues processed: 27 average time/residue: 1.3760 time to fit residues: 71.0028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 655 optimal weight: 5.9990 chunk 1055 optimal weight: 9.9990 chunk 644 optimal weight: 0.9980 chunk 500 optimal weight: 0.0770 chunk 733 optimal weight: 2.9990 chunk 1106 optimal weight: 10.0000 chunk 1018 optimal weight: 0.2980 chunk 881 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 680 optimal weight: 0.9980 chunk 540 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 111 GLN L6 115 GLN ** L8 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 44 GLN LA 93 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 119 GLN LH 69 ASN LH 111 GLN LL 31 ASN LL 83 ASN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 100 ASN LR 100 GLN LU 36 HIS LW 48 ASN LW 57 ASN NK 89 GLN ** NK 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 63 GLN ** SE 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 162 GLN SK 225 ASN SQ 58 ASN SQ 155 GLN SR 100 ASN SV 115 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 150098 Z= 0.140 Angle : 0.680 19.495 220084 Z= 0.371 Chirality : 0.032 0.364 27037 Planarity : 0.007 0.126 14366 Dihedral : 13.383 178.104 51994 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 7576 helix: 1.74 (0.10), residues: 2808 sheet: 0.34 (0.16), residues: 1002 loop : -0.17 (0.10), residues: 3766 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15152 Ramachandran restraints generated. 7576 Oldfield, 0 Emsley, 7576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 956 time to evaluate : 7.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 95 residues processed: 1052 average time/residue: 2.0627 time to fit residues: 3213.2974 Evaluate side-chains 1024 residues out of total 6655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 929 time to evaluate : 7.287 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 84 residues processed: 12 average time/residue: 1.3673 time to fit residues: 36.4821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 700 optimal weight: 0.6980 chunk 938 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 812 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 882 optimal weight: 0.0970 chunk 369 optimal weight: 6.9990 chunk 906 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 chunk 162 optimal weight: 10.0000 overall best weight: 3.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 93 HIS LB 125 GLN LC 37 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 131 GLN LF 119 GLN LH 69 ASN LH 111 GLN LI 91 ASN LL 31 ASN LL 83 ASN ** LM 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 145 GLN LP 100 ASN LU 36 HIS ** NF 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NK 89 GLN ** NK 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS SD 63 GLN SE 100 HIS SE 149 ASN ** SE 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SQ 155 GLN SR 100 ASN SV 115 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.091991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067189 restraints weight = 327664.441| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.30 r_work: 0.2977 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 150098 Z= 0.336 Angle : 0.750 19.725 220084 Z= 0.398 Chirality : 0.038 0.430 27037 Planarity : 0.008 0.139 14366 Dihedral : 13.548 179.454 51994 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 7576 helix: 1.51 (0.10), residues: 2816 sheet: 0.34 (0.16), residues: 981 loop : -0.33 (0.10), residues: 3779 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50557.60 seconds wall clock time: 876 minutes 16.13 seconds (52576.13 seconds total)