Starting phenix.real_space_refine on Fri Dec 15 10:17:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flc_29274/12_2023/8flc_29274_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flc_29274/12_2023/8flc_29274.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flc_29274/12_2023/8flc_29274_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flc_29274/12_2023/8flc_29274_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flc_29274/12_2023/8flc_29274_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flc_29274/12_2023/8flc_29274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flc_29274/12_2023/8flc_29274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flc_29274/12_2023/8flc_29274_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flc_29274/12_2023/8flc_29274_neut_updated.pdb" } resolution = 2.76 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= 0.052 sd= 0.177 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 3650 5.49 5 Mg 88 5.21 5 S 269 5.16 5 C 73505 2.51 5 N 26267 2.21 5 O 35809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L7 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LW TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NK TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NR GLU 118": "OE1" <-> "OE2" Residue "SD GLU 68": "OE1" <-> "OE2" Residue "SD PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 139595 Number of models: 1 Model: "" Number of chains: 65 Chain: "BA" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 449 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 86} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 126 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: 72412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3373, 72412 Classifications: {'RNA': 3373} Modifications used: {'rna2p': 5, 'rna2p_pur': 330, 'rna2p_pyr': 207, 'rna3p': 81, 'rna3p_pur': 1491, 'rna3p_pyr': 1241} Link IDs: {'rna2p': 541, 'rna3p': 2831} Chain breaks: 28 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 33 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: "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: "NR" Number of atoms: 1299 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1292 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 4, 'TRANS': 147} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 152, 1292 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 4, 'TRANS': 147} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1304 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: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 650 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 449 Unresolved non-hydrogen angles: 565 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 260 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: "VB" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Chain: "L1" 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: "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: "LN" 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: 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: "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: "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 A05JA SG CYSLR 46 84.825 183.133 78.216 1.00 57.37 S ATOM A05JR SG CYSLR 49 83.589 186.392 79.870 1.00 63.10 S ATOM A05R2 SG CYSLR 83 81.604 184.870 77.077 1.00 57.33 S ATOM A05RM SG CYSLR 86 84.966 186.363 76.287 1.00 58.50 S ATOM A083Y SG CYSLV 12 187.885 115.749 113.656 1.00 34.20 S ATOM A084M SG CYSLV 15 191.074 114.874 111.786 1.00 37.05 S ATOM A08HN SG CYSLV 72 189.905 118.592 112.184 1.00 31.61 S ATOM A08IO SG CYSLV 77 188.006 116.068 109.989 1.00 37.26 S ATOM A08SY SG CYSLW 19 93.119 128.140 98.122 1.00 43.60 S ATOM A08TQ SG CYSLW 22 93.762 125.371 100.553 1.00 43.44 S ATOM A08W9 SG CYSLW 34 95.910 128.569 100.621 1.00 40.06 S ATOM A08WS SG CYSLW 37 96.349 126.097 97.806 1.00 42.19 S ATOM A09GZ SG CYSLX 39 95.444 194.525 86.819 1.00 54.89 S ATOM A09HM SG CYSLX 42 92.087 196.130 86.374 1.00 58.62 S ATOM A09L0 SG CYSLX 57 92.376 193.203 88.725 1.00 55.02 S ATOM A09LG SG CYSLX 60 92.722 192.545 85.032 1.00 58.37 S ATOM A0BBC SG CYSNP 63 74.203 202.490 157.223 1.00 59.36 S ATOM A0BBV SG CYSNP 66 73.684 198.806 156.817 1.00 60.68 S ATOM A0T8C SG CYSSV 6 62.964 182.960 177.697 1.00 52.53 S ATOM A0T95 SG CYSSV 9 59.371 181.694 177.494 1.00 49.65 S ATOM A0TE9 SG CYSSV 32 61.970 179.255 178.452 1.00 49.16 S ATOM A0TF3 SG CYSSV 36 62.048 180.547 174.936 1.00 46.26 S Time building chain proxies: 54.31, per 1000 atoms: 0.39 Number of scatterers: 139595 At special positions: 0 Unit cell: (256.208, 243.344, 278.72, 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 269 16.00 P 3650 15.00 Mg 88 11.99 O 35809 8.00 N 26267 7.00 C 73505 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: 50.83 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLR 202 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 83 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 86 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 49 " pdb="ZN ZNLR 202 " - 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 15 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 72 " pdb=" ZNLW 101 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 22 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 37 " pdb=" ZNLX 500 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 57 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 42 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 39 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 60 " 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 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 31 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14286 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 280 helices and 70 sheets defined 45.6% alpha, 13.0% beta 1128 base pairs and 1707 stacking pairs defined. Time for finding SS restraints: 78.71 Creating SS restraints... Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.752A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 4.806A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.576A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 Processing helix chain 'L5' and resid 30 through 45 Processing helix chain 'L5' and resid 76 through 91 Processing helix chain 'L5' and resid 111 through 116 removed outlier: 4.438A pdb=" N LEUL5 115 " --> pdb=" O GLUL5 111 " (cutoff:3.500A) removed outlier: 4.280A 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: 4.679A 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: 4.228A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 3.994A 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 Processing helix chain 'L6' and resid 77 through 85 Processing helix chain 'L6' and resid 87 through 95 removed outlier: 4.068A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.160A 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: 3.803A pdb=" N LEUL6 146 " --> pdb=" O GLUL6 142 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALAL6 147 " --> pdb=" O GLUL6 143 " (cutoff:3.500A) Processing helix chain 'L6' and resid 170 through 177 removed outlier: 5.743A pdb=" N LYSL6 177 " --> pdb=" O GLUL6 173 " (cutoff:3.500A) Processing helix chain 'L6' and resid 178 through 192 Processing helix chain 'L6' and resid 193 through 211 removed outlier: 3.569A pdb=" N GLUL6 208 " --> pdb=" O GLUL6 204 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.538A pdb=" N LYSL7 25 " --> pdb=" O ALAL7 21 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 61 removed outlier: 3.524A pdb=" N ARGL7 59 " --> pdb=" O LEUL7 55 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARGL7 61 " --> pdb=" O PHEL7 57 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 removed outlier: 3.572A 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: 3.643A pdb=" N METL7 87 " --> pdb=" O THRL7 83 " (cutoff:3.500A) removed outlier: 3.547A 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: 3.852A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.920A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.374A 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: 3.652A pdb=" N ILEL7 166 " --> pdb=" O GLUL7 162 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VALL7 185 " --> pdb=" O ALAL7 181 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.514A pdb=" N VALL7 195 " --> pdb=" O LYSL7 191 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLYL7 200 " --> pdb=" O LEUL7 196 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.846A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.234A 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: 3.604A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.584A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 4.017A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 removed outlier: 3.547A pdb=" N LEUL8 136 " --> pdb=" O LYSL8 132 " (cutoff:3.500A) Processing helix chain 'L9' and resid 2 through 14 removed outlier: 4.041A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARGL9 12 " --> pdb=" O GLNL9 8 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 3.748A pdb=" N GLNL9 32 " --> pdb=" O TRPL9 28 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEUL9 33 " --> pdb=" O GLNL9 29 " (cutoff:3.500A) removed outlier: 5.218A 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: 3.925A pdb=" N HISL9 87 " --> pdb=" O LYSL9 83 " (cutoff:3.500A) removed outlier: 5.032A 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: 3.707A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.572A pdb=" N ASNL9 145 " --> pdb=" O ALAL9 141 " (cutoff:3.500A) Proline residue: L9 146 - end of helix Processing helix chain 'L9' and resid 147 through 153 removed outlier: 6.211A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYSL9 153 " --> pdb=" O GLNL9 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 147 through 153' Processing helix chain 'L9' and resid 158 through 163 removed outlier: 3.615A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 3.533A pdb=" N LYSL9 170 " --> pdb=" O SERL9 166 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 3.887A 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 removed outlier: 3.558A pdb=" N ALALA 35 " --> pdb=" O GLULA 31 " (cutoff:3.500A) Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 72 through 77 removed outlier: 4.828A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.191A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.654A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.717A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 removed outlier: 3.546A pdb=" N LEULB 128 " --> pdb=" O ASPLB 124 " (cutoff:3.500A) Processing helix chain 'LB' and resid 146 through 153 removed outlier: 4.473A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLYLB 153 " --> pdb=" O TYRLB 149 " (cutoff:3.500A) Processing helix chain 'LB' and resid 171 through 176 removed outlier: 5.543A pdb=" N GLULB 175 " --> pdb=" O GLYLB 171 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARGLB 176 " --> pdb=" O ARGLB 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 171 through 176' Processing helix chain 'LB' and resid 7 through 12 removed outlier: 4.792A pdb=" N ARGLB 11 " --> pdb=" O ASNLB 8 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LYSLB 12 " --> pdb=" O LYSLB 9 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 removed outlier: 3.916A pdb=" N GLNLC 50 " --> pdb=" O TYRLC 46 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEULC 51 " --> pdb=" O PHELC 47 " (cutoff:3.500A) Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.954A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.606A 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: 4.641A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.311A 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: 3.740A pdb=" N VALLD 22 " --> pdb=" O GLYLD 18 " (cutoff:3.500A) removed outlier: 5.865A 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 35 removed outlier: 3.598A pdb=" N ASNLD 34 " --> pdb=" O ASNLD 30 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALALD 35 " --> pdb=" O GLULD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 37 through 48 removed outlier: 3.612A pdb=" N LYSLD 43 " --> pdb=" O GLNLD 39 " (cutoff:3.500A) Processing helix chain 'LD' and resid 60 through 73 Processing helix chain 'LD' and resid 77 through 82 removed outlier: 6.065A pdb=" N LYSLD 82 " --> pdb=" O ILELD 78 " (cutoff:3.500A) Processing helix chain 'LD' and resid 84 through 113 Proline residue: LD 90 - end of helix removed outlier: 6.829A pdb=" N VALLD 93 " --> pdb=" O METLD 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THRLD 94 " --> pdb=" O PROLD 90 " (cutoff:3.500A) Processing helix chain 'LD' and resid 116 through 130 removed outlier: 4.588A pdb=" N ASNLD 130 " --> pdb=" O LYSLD 126 " (cutoff:3.500A) Processing helix chain 'LD' and resid 134 through 155 Processing helix chain 'LE' and resid 26 through 32 removed outlier: 4.584A pdb=" N TYRLE 30 " --> pdb=" O PROLE 26 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARGLE 32 " --> pdb=" O ALALE 28 " (cutoff:3.500A) Processing helix chain 'LE' and resid 54 through 59 removed outlier: 3.746A pdb=" N HISLE 58 " --> pdb=" O HISLE 54 " (cutoff:3.500A) removed outlier: 6.058A 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: 4.178A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.303A 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: 3.522A pdb=" N ASPLE 103 " --> pdb=" O SERLE 99 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYSLE 120 " --> pdb=" O LYSLE 116 " (cutoff:3.500A) Processing helix chain 'LF' and resid 25 through 32 removed outlier: 3.560A pdb=" N ASPLF 31 " --> pdb=" O HISLF 27 " (cutoff:3.500A) Processing helix chain 'LF' and resid 35 through 47 Processing helix chain 'LF' and resid 55 through 60 removed outlier: 3.624A pdb=" N GLYLF 59 " --> pdb=" O ASNLF 55 " (cutoff:3.500A) 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: 3.552A pdb=" N LYSLF 84 " --> pdb=" O LYSLF 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 69 through 74 removed outlier: 3.609A pdb=" N ARGLG 73 " --> pdb=" O LYSLG 69 " (cutoff:3.500A) removed outlier: 5.525A 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: 3.749A 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 136 removed outlier: 4.582A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) 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: 4.759A 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: 3.796A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.349A 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: 4.061A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.328A 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 removed outlier: 3.608A pdb=" N ILELI 118 " --> pdb=" O ASPLI 114 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 58 through 67 removed outlier: 3.671A pdb=" N LYSLJ 67 " --> pdb=" O ALALJ 63 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 81 removed outlier: 3.551A pdb=" N LEULJ 80 " --> pdb=" O ASNLJ 76 " (cutoff:3.500A) removed outlier: 5.190A 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: 3.824A pdb=" N ASNLJ 97 " --> pdb=" O LYSLJ 93 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 99 through 104 removed outlier: 4.536A 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 99 through 104' Processing helix chain 'LJ' and resid 105 through 125 removed outlier: 3.575A pdb=" N GLULJ 120 " --> pdb=" O VALLJ 116 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLYLJ 125 " --> pdb=" O ARGLJ 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 127 through 133 removed outlier: 3.819A pdb=" N PHELJ 131 " --> pdb=" O ASNLJ 127 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYSLJ 133 " --> pdb=" O TRPLJ 129 " (cutoff:3.500A) Processing helix chain 'LK' and resid 6 through 12 removed outlier: 4.260A pdb=" N LYSLK 10 " --> pdb=" O ARGLK 6 " (cutoff:3.500A) Processing helix chain 'LK' and resid 41 through 48 Processing helix chain 'LK' and resid 64 through 69 removed outlier: 4.191A pdb=" N SERLK 68 " --> pdb=" O LYSLK 64 " (cutoff:3.500A) removed outlier: 3.922A 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: 4.445A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THRLK 80 " --> pdb=" O ASPLK 76 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEULK 81 " --> pdb=" O LYSLK 77 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VALLK 82 " --> pdb=" O LEULK 78 " (cutoff:3.500A) removed outlier: 5.484A 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: 3.593A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 removed outlier: 3.501A pdb=" N VALLK 140 " --> pdb=" O LYSLK 136 " (cutoff:3.500A) Processing helix chain 'LL' and resid 2 through 13 removed outlier: 3.501A pdb=" N VALLL 9 " --> pdb=" O LEULL 5 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.805A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 4.387A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARGLL 119 " --> pdb=" O SERLL 115 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LM' and resid 11 through 20 removed outlier: 4.514A pdb=" N LYSLM 15 " --> pdb=" O ASNLM 11 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASNLM 19 " --> pdb=" O LYSLM 15 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLYLM 20 " --> pdb=" O TRPLM 16 " (cutoff:3.500A) Processing helix chain 'LM' and resid 36 through 55 removed outlier: 3.506A pdb=" N ASNLM 50 " --> pdb=" O ALALM 46 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYSLM 51 " --> pdb=" O LYSLM 47 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYSLM 52 " --> pdb=" O LYSLM 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLYLM 53 " --> pdb=" O HISLM 49 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEULM 54 " --> pdb=" O ASNLM 50 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYSLM 55 " --> pdb=" O LYSLM 51 " (cutoff:3.500A) Processing helix chain 'LM' and resid 56 through 66 Processing helix chain 'LM' and resid 91 through 101 Processing helix chain 'LM' and resid 105 through 116 removed outlier: 3.513A pdb=" N ALALM 110 " --> pdb=" O LYSLM 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILELM 112 " --> pdb=" O ALALM 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALALM 113 " --> pdb=" O ARGLM 109 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLYLM 115 " --> pdb=" O ARGLM 111 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEULM 116 " --> pdb=" O ILELM 112 " (cutoff:3.500A) Processing helix chain 'LN' and resid 13 through 18 removed outlier: 4.491A 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: 4.053A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 4.409A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 156 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 4.189A 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 Processing helix chain 'LN' and resid 206 through 211 removed outlier: 4.222A 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: 4.914A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.080A 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: 4.054A 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: 3.505A pdb=" N GLYLO 82 " --> pdb=" O ASNLO 78 " (cutoff:3.500A) Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.817A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HISLP 34 " --> pdb=" O HISLP 30 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 57 removed outlier: 3.569A pdb=" N LEULP 46 " --> pdb=" O ALALP 42 " (cutoff:3.500A) Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.532A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 5.074A 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 89 removed outlier: 4.085A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.560A pdb=" N GLNLQ 117 " --> pdb=" O GLULQ 113 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 68 removed outlier: 3.679A pdb=" N LEULR 64 " --> pdb=" O ARGLR 60 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N METLR 65 " --> pdb=" O PROLR 61 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARGLR 66 " --> pdb=" O LYSLR 62 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEULR 67 " --> pdb=" O VALLR 63 " (cutoff:3.500A) removed outlier: 5.587A 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: 3.740A pdb=" N GLULR 98 " --> pdb=" O ALALR 94 " (cutoff:3.500A) Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.726A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 removed outlier: 3.604A pdb=" N LEULS 17 " --> pdb=" O LYSLS 13 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.699A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VALLS 49 " --> pdb=" O SERLS 45 " (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 94 removed outlier: 3.504A pdb=" N ARGLS 94 " --> pdb=" O ALALS 90 " (cutoff:3.500A) Processing helix chain 'LS' and resid 96 through 102 removed outlier: 3.713A pdb=" N LEULS 102 " --> pdb=" O HISLS 98 " (cutoff:3.500A) Processing helix chain 'LS' and resid 104 through 114 Processing helix chain 'LT' and resid 35 through 40 removed outlier: 3.818A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.687A 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: 4.025A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.173A 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: 3.774A 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 46 Processing helix chain 'LW' and resid 4 through 11 removed outlier: 3.767A pdb=" N GLYLW 9 " --> pdb=" O THRLW 5 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYSLW 10 " --> pdb=" O SERLW 6 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARGLW 11 " --> pdb=" O SERLW 7 " (cutoff:3.500A) Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.565A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.167A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLYLW 77 " --> pdb=" O ARGLW 73 " (cutoff:3.500A) Processing helix chain 'LX' and resid 19 through 34 removed outlier: 3.903A pdb=" N LYSLX 28 " --> pdb=" O LYSLX 24 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILELX 29 " --> pdb=" O METLX 25 " (cutoff:3.500A) Processing helix chain 'LX' and resid 73 through 92 removed outlier: 3.713A pdb=" N GLULX 88 " --> pdb=" O ARGLX 84 " (cutoff:3.500A) Processing helix chain 'LY' and resid 7 through 17 Processing helix chain 'LY' and resid 49 through 60 removed outlier: 3.593A pdb=" N LYSLY 55 " --> pdb=" O GLULY 51 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLNLY 58 " --> pdb=" O GLULY 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEULY 60 " --> pdb=" O LEULY 56 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 6 through 21 removed outlier: 5.234A pdb=" N ARGLZ 21 " --> pdb=" O GLNLZ 17 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 24 through 31 removed outlier: 4.729A pdb=" N ARGLZ 28 " --> pdb=" O PROLZ 24 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N METLZ 29 " --> pdb=" O GLNLZ 25 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYSLZ 30 " --> pdb=" O TRPLZ 26 " (cutoff:3.500A) removed outlier: 5.674A 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 'NK' and resid 12 through 33 removed outlier: 3.555A 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: 3.753A pdb=" N LYSNK 108 " --> pdb=" O ARGNK 104 " (cutoff:3.500A) Processing helix chain 'NP' and resid 15 through 21 removed outlier: 4.270A pdb=" N METNP 19 " --> pdb=" O LEUNP 15 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALANP 21 " --> pdb=" O ARGNP 17 " (cutoff:3.500A) Processing helix chain 'NP' and resid 27 through 36 removed outlier: 3.617A pdb=" N ILENP 31 " --> pdb=" O ASPNP 27 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HISNP 32 " --> pdb=" O LEUNP 28 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARGNP 33 " --> pdb=" O ASPNP 29 " (cutoff:3.500A) Processing helix chain 'NP' and resid 72 through 82 removed outlier: 3.753A pdb=" N ARGNP 81 " --> pdb=" O LYSNP 77 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SERNP 82 " --> pdb=" O THRNP 78 " (cutoff:3.500A) Processing helix chain 'NP' and resid 83 through 94 removed outlier: 3.807A pdb=" N LEUNP 89 " --> pdb=" O HISNP 85 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYSNP 90 " --> pdb=" O LYSNP 86 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SERNP 93 " --> pdb=" O LEUNP 89 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VALNP 94 " --> pdb=" O LYSNP 90 " (cutoff:3.500A) Processing helix chain 'NP' and resid 98 through 107 Processing helix chain 'NR' and resid 21 through 62 removed outlier: 3.579A pdb=" N ALANR 25 " --> pdb=" O SERNR 21 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEUNR 62 " --> pdb=" O PHENR 58 " (cutoff:3.500A) Processing helix chain 'NR' and resid 70 through 98 removed outlier: 3.599A pdb=" N ARGNR 84 " --> pdb=" O ARGNR 80 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHENR 85 " --> pdb=" O TYRNR 81 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SERNR 86 " --> pdb=" O LEUNR 82 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SERNR 87 " --> pdb=" O ASNNR 83 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLUNR 88 " --> pdb=" O ARGNR 84 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILENR 98 " --> pdb=" O LEUNR 94 " (cutoff:3.500A) Processing helix chain 'NR' and resid 106 through 126 Processing helix chain 'NR' and resid 136 through 146 Processing helix chain 'NR' and resid 149 through 157 removed outlier: 4.089A pdb=" N LEUNR 153 " --> pdb=" O ASPNR 149 " (cutoff:3.500A) Proline residue: NR 154 - end of helix removed outlier: 5.307A pdb=" N LYSNR 157 " --> pdb=" O LEUNR 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'NR' and resid 149 through 157' Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.391A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.788A 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: 3.951A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.549A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.792A 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: 3.777A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.518A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 156 through 161' Processing helix chain 'SA' and resid 163 through 175 removed outlier: 3.595A pdb=" N ALASA 167 " --> pdb=" O LYSSA 163 " (cutoff:3.500A) Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.724A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.741A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.777A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.754A 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: 4.077A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.449A pdb=" N LEUSA 322 " --> pdb=" O PROSA 318 " (cutoff:3.500A) Processing helix chain 'SA' and resid 323 through 329 Processing helix chain 'SA' and resid 330 through 361 removed outlier: 4.460A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SB' and resid 9 through 16 Processing helix chain 'SB' and resid 20 through 26 Processing helix chain 'SB' and resid 29 through 37 removed outlier: 3.822A pdb=" N ARGSB 35 " --> pdb=" O TYRSB 31 " (cutoff:3.500A) Processing helix chain 'SB' and resid 79 through 87 removed outlier: 4.406A 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: 3.764A pdb=" N GLUSB 120 " --> pdb=" O ASPSB 116 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 170 removed outlier: 3.923A pdb=" N GLYSB 161 " --> pdb=" O ASNSB 157 " (cutoff:3.500A) Processing helix chain 'SB' and resid 191 through 201 Processing helix chain 'SB' and resid 202 through 215 removed outlier: 3.576A 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: 4.543A pdb=" N ASNSB 229 " --> pdb=" O GLNSB 225 " (cutoff:3.500A) Processing helix chain 'SB' and resid 232 through 251 removed outlier: 4.908A pdb=" N GLUSB 237 " --> pdb=" O PROSB 233 " (cutoff:3.500A) removed outlier: 5.097A 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: 3.573A pdb=" N ALASC 67 " --> pdb=" O TYRSC 63 " (cutoff:3.500A) Processing helix chain 'SC' and resid 132 through 137 removed outlier: 6.072A pdb=" N VALSC 137 " --> pdb=" O PHESC 133 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.848A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.666A 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: 3.867A 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: 5.228A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.249A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.617A 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: 3.659A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.744A 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: 4.287A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.613A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.266A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 239 through 248 removed outlier: 3.594A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.576A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 85 removed outlier: 4.523A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.717A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 123 removed outlier: 3.541A pdb=" N ALASE 118 " --> pdb=" O LEUSE 114 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLUSE 119 " --> pdb=" O LEUSE 115 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYSSE 120 " --> pdb=" O ALASE 116 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALASE 122 " --> pdb=" O ALASE 118 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALASE 123 " --> pdb=" O GLUSE 119 " (cutoff:3.500A) Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 169 through 178 Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.578A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 226 removed outlier: 5.019A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THRSE 224 " --> pdb=" O GLUSE 220 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASNSE 225 " --> pdb=" O ALASE 221 " (cutoff:3.500A) Processing helix chain 'SE' and resid 229 through 236 removed outlier: 3.682A pdb=" N ARGSE 235 " --> pdb=" O ASPSE 231 " (cutoff:3.500A) Processing helix chain 'SE' and resid 243 through 266 removed outlier: 5.076A pdb=" N GLYSE 266 " --> pdb=" O ALASE 262 " (cutoff:3.500A) Processing helix chain 'SF' and resid 5 through 13 removed outlier: 6.409A pdb=" N LYSSF 10 " --> pdb=" O ARGSF 6 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLYSF 11 " --> pdb=" O GLYSF 7 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALASF 12 " --> pdb=" O GLNSF 8 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLYSF 13 " --> pdb=" O ARGSF 9 " (cutoff:3.500A) Processing helix chain 'SF' and resid 33 through 39 Processing helix chain 'SF' and resid 103 through 108 removed outlier: 3.527A 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: 3.898A pdb=" N ALASF 191 " --> pdb=" O HISSF 187 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYSSF 192 " --> pdb=" O LYSSF 188 " (cutoff:3.500A) Processing helix chain 'SF' and resid 200 through 205 removed outlier: 4.009A pdb=" N METSF 204 " --> pdb=" O ARGSF 200 " (cutoff:3.500A) removed outlier: 5.187A 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: 4.207A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.515A pdb=" N THRSG 165 " --> pdb=" O ILESG 161 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.281A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 4.091A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.700A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLUSK 41 " --> pdb=" O VALSK 37 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 3.853A 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: 3.880A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) removed outlier: 3.577A 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: 4.505A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 4.137A 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 20 through 37 removed outlier: 3.570A pdb=" N GLUSQ 28 " --> pdb=" O GLNSQ 24 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 61 removed outlier: 3.503A pdb=" N ILESQ 56 " --> pdb=" O LYSSQ 52 " (cutoff:3.500A) removed outlier: 4.053A 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 97 removed outlier: 4.046A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.217A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 70 removed outlier: 3.529A 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: 3.535A pdb=" N VALSR 109 " --> pdb=" O LEUSR 105 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 146 removed outlier: 3.513A pdb=" N ARGSR 143 " --> pdb=" O THRSR 139 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLNSR 146 " --> pdb=" O LYSSR 142 " (cutoff:3.500A) Processing helix chain 'SR' and resid 147 through 162 removed outlier: 3.881A pdb=" N ARGSR 160 " --> pdb=" O GLNSR 156 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEUSR 161 " --> pdb=" O HISSR 157 " (cutoff:3.500A) Proline residue: SR 162 - end of helix Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.654A pdb=" N ASNSR 186 " --> pdb=" O SERSR 182 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VALSR 188 " --> pdb=" O PHESR 184 " (cutoff:3.500A) Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.728A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 229 through 234' Processing helix chain 'SR' and resid 235 through 247 removed outlier: 3.918A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 removed outlier: 3.545A pdb=" N PHESR 272 " --> pdb=" O GLNSR 268 " (cutoff:3.500A) Proline residue: SR 277 - end of helix removed outlier: 3.955A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 290 through 295 removed outlier: 3.576A pdb=" N LYSSR 294 " --> pdb=" O LYSSR 290 " (cutoff:3.500A) Processing helix chain 'SR' and resid 300 through 314 removed outlier: 3.539A pdb=" N ILESR 306 " --> pdb=" O ASPSR 302 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 3.526A pdb=" N GLUSR 345 " --> pdb=" O ALASR 341 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THRSR 346 " --> pdb=" O HISSR 342 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 361 removed outlier: 4.016A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HISSR 361 " --> pdb=" O LEUSR 357 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.342A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 417 removed outlier: 5.152A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.858A 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: 4.100A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 4.928A 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: 3.963A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.652A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SR' and resid 474 through 503 removed outlier: 4.762A pdb=" N LEUSR 478 " --> pdb=" O ASPSR 474 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLNSR 486 " --> pdb=" O GLNSR 482 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N THRSR 503 " --> pdb=" O LYSSR 499 " (cutoff:3.500A) Processing helix chain 'SR' and resid 509 through 514 removed outlier: 3.816A pdb=" N LYSSR 513 " --> pdb=" O PROSR 509 " (cutoff:3.500A) removed outlier: 5.075A 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: 3.694A pdb=" N LEUSR 520 " --> pdb=" O GLNSR 516 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLUSR 521 " --> pdb=" O ARGSR 517 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEUSR 527 " --> pdb=" O GLUSR 523 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLYSR 528 " --> pdb=" O METSR 524 " (cutoff:3.500A) Processing helix chain 'SR' and resid 537 through 551 removed outlier: 3.765A pdb=" N SERSR 548 " --> pdb=" O ARGSR 544 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILESR 549 " --> pdb=" O ARGSR 545 " (cutoff:3.500A) Processing helix chain 'SR' and resid 574 through 579 removed outlier: 4.141A pdb=" N GLYSR 579 " --> pdb=" O ARGSR 575 " (cutoff:3.500A) Processing helix chain 'SR' and resid 582 through 604 removed outlier: 3.570A pdb=" N LYSSR 598 " --> pdb=" O LYSSR 594 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYSSR 599 " --> pdb=" O ASNSR 595 " (cutoff:3.500A) removed outlier: 5.164A 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 removed outlier: 3.557A pdb=" N LYSSV 43 " --> pdb=" O ASNSV 39 " (cutoff:3.500A) Processing helix chain 'SV' and resid 45 through 50 removed outlier: 3.602A pdb=" N VALSV 49 " --> pdb=" O ASNSV 45 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 45 through 50' Processing helix chain 'SV' and resid 52 through 60 removed outlier: 3.538A pdb=" N ARGSV 56 " --> pdb=" O THRSV 52 " (cutoff:3.500A) Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.368A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.724A 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 130 removed outlier: 3.715A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEUSV 118 " --> pdb=" O LYSSV 114 " (cutoff:3.500A) Processing helix chain 'VB' and resid 41 through 73 removed outlier: 3.558A pdb=" N GLNVB 46 " --> pdb=" O ARGVB 42 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEUVB 49 " --> pdb=" O GLNVB 45 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYSVB 50 " --> pdb=" O GLNVB 46 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYSVB 59 " --> pdb=" O VALVB 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'L5' and resid 48 through 51 removed outlier: 3.745A pdb=" N ALAL5 69 " --> pdb=" O SERL5 51 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILEL5 68 " --> pdb=" O VALL5 26 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYSL5 19 " --> pdb=" O VALL5 133 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASNL5 23 " --> pdb=" O ASPL5 129 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASPL5 129 " --> pdb=" O ASNL5 23 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N CYSL5 25 " --> pdb=" O GLYL5 127 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLYL5 127 " --> pdb=" O CYSL5 25 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'L5' and resid 92 through 96 Processing sheet with id= 3, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 4, first strand: chain 'L8' and resid 11 through 16 removed outlier: 4.541A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L8' and resid 28 through 31 removed outlier: 6.535A pdb=" N ARGL8 35 " --> pdb=" O ILEL8 31 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.314A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'LA' and resid 14 through 20 removed outlier: 6.777A pdb=" N ILELA 149 " --> pdb=" O GLULA 115 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'LA' and resid 57 through 60 removed outlier: 5.333A pdb=" N GLNLA 80 " --> pdb=" O PHELA 60 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LA' and resid 116 through 122 Processing sheet with id= 10, first strand: chain 'LA' and resid 124 through 131 removed outlier: 3.671A pdb=" N METLA 125 " --> pdb=" O SERLA 141 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARGLA 127 " --> pdb=" O TYRLA 139 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARGLA 135 " --> pdb=" O ARGLA 131 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LB' and resid 118 through 121 removed outlier: 4.999A pdb=" N LYSLB 99 " --> pdb=" O LYSLB 78 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.653A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.238A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.696A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LE' and resid 39 through 42 removed outlier: 4.160A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 17, first strand: chain 'LF' and resid 61 through 65 removed outlier: 5.962A pdb=" N GLULF 108 " --> pdb=" O LYSLF 20 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LG' and resid 36 through 39 removed outlier: 4.849A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASNLG 101 " --> pdb=" O VALLG 25 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILELG 105 " --> pdb=" O ALALG 29 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASPLG 59 " --> pdb=" O VALLG 81 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LG' and resid 87 through 90 removed outlier: 3.917A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LG' and resid 82 through 85 removed outlier: 4.405A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.769A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLULH 133 " --> pdb=" O ARGLH 129 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYSLH 123 " --> pdb=" O ARGLH 139 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.746A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.548A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LJ' and resid 10 through 14 removed outlier: 4.109A pdb=" N ARGLJ 21 " --> pdb=" O VALLJ 13 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LJ' and resid 27 through 30 removed outlier: 6.159A pdb=" N HISLJ 40 " --> pdb=" O ILELJ 29 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.508A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LN' and resid 53 through 59 removed outlier: 3.571A pdb=" N GLULN 74 " --> pdb=" O ILELN 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.782A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LN' and resid 202 through 205 removed outlier: 4.005A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N METLN 84 " --> pdb=" O VALLN 205 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILELN 160 " --> pdb=" O VALLN 185 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 10.760A pdb=" N LEULN 180 " --> pdb=" O GLYLN 48 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N GLYLN 48 " --> pdb=" O LEULN 180 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N GLULN 182 " --> pdb=" O PHELN 46 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHELN 46 " --> pdb=" O GLULN 182 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLNLN 184 " --> pdb=" O THRLN 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THRLN 44 " --> pdb=" O GLNLN 184 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THRLN 44 " --> pdb=" O LYSLN 349 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LN' and resid 88 through 93 removed outlier: 3.744A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LN' and resid 215 through 218 removed outlier: 4.307A pdb=" N GLULN 215 " --> pdb=" O ILELN 284 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LO' and resid 26 through 29 removed outlier: 6.411A pdb=" N LYSLO 26 " --> pdb=" O ILELO 97 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEULO 45 " --> pdb=" O ILELO 96 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLYLO 70 " --> pdb=" O LYSLO 44 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.686A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VALLP 122 " --> pdb=" O THRLP 22 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 35, first strand: chain 'LR' and resid 20 through 24 Processing sheet with id= 36, first strand: chain 'LT' and resid 8 through 12 removed outlier: 5.906A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYSLT 66 " --> pdb=" O ALALT 53 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LT' and resid 6 through 10 Processing sheet with id= 38, first strand: chain 'LV' and resid 7 through 10 removed outlier: 5.547A pdb=" N VALLV 67 " --> pdb=" O TYRLV 26 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LX' and resid 46 through 50 removed outlier: 8.542A pdb=" N LYSLX 46 " --> pdb=" O GLYLX 58 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLYLX 58 " --> pdb=" O LYSLX 46 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILELX 54 " --> pdb=" O ARGLX 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLYLX 53 " --> pdb=" O GLYLX 66 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYSLX 62 " --> pdb=" O CYSLX 57 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LY' and resid 2 through 5 removed outlier: 4.745A pdb=" N VALLY 46 " --> pdb=" O ILELY 5 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SERLY 22 " --> pdb=" O ARGLY 37 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYSLY 27 " --> pdb=" O LEULY 69 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'NP' and resid 61 through 64 removed outlier: 4.483A pdb=" N HISNP 61 " --> pdb=" O PHENP 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARGNP 68 " --> pdb=" O CYSNP 63 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'NR' and resid 128 through 132 Processing sheet with id= 43, first strand: chain 'SA' and resid 7 through 10 removed outlier: 5.046A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'SA' and resid 226 through 232 removed outlier: 3.516A pdb=" N THRSA 228 " --> pdb=" O PROSA 207 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'SB' and resid 60 through 66 removed outlier: 3.523A pdb=" N VALSB 53 " --> pdb=" O ASPSB 147 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SC' and resid 90 through 95 removed outlier: 9.131A pdb=" N ALASC 90 " --> pdb=" O LEUSC 109 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEUSC 109 " --> pdb=" O ALASC 90 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'SC' and resid 148 through 153 removed outlier: 4.225A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 49, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.739A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'SD' and resid 158 through 161 removed outlier: 7.031A pdb=" N GLYSD 158 " --> pdb=" O LEUSD 169 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 52, first strand: chain 'SF' and resid 47 through 50 removed outlier: 3.705A pdb=" N ASPSF 47 " --> pdb=" O LYSSF 60 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYSSF 60 " --> pdb=" O LYSSF 46 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLNSF 86 " --> pdb=" O VALSF 45 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SF' and resid 110 through 114 removed outlier: 4.241A pdb=" N THRSF 111 " --> pdb=" O VALSF 136 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VALSF 136 " --> pdb=" O THRSF 111 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARGSF 147 " --> pdb=" O ILESF 137 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYSSF 145 " --> pdb=" O ASNSF 140 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SERSF 138 " --> pdb=" O ARGSF 147 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SF' and resid 58 through 65 No H-bonds generated for sheet with id= 54 Processing sheet with id= 55, first strand: chain 'SF' and resid 145 through 150 removed outlier: 4.348A pdb=" N SERSF 154 " --> pdb=" O LEUSF 150 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.866A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 58, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.908A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.474A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYSSG 91 " --> pdb=" O SERSG 182 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'SG' and resid 87 through 91 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'SK' and resid 1 through 5 Processing sheet with id= 62, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 63, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 64, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 65, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 6.860A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.591A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.335A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SR' and resid 204 through 211 removed outlier: 7.465A pdb=" N SERSR 204 " --> pdb=" O PROSR 223 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'SV' and resid 3 through 6 removed outlier: 4.280A pdb=" N GLYSV 11 " --> pdb=" O CYSSV 6 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SV' and resid 18 through 22 2473 hydrogen bonds defined for protein. 7364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2978 hydrogen bonds 5072 hydrogen bond angles 0 basepair planarities 1128 basepair parallelities 1707 stacking parallelities Total time for adding SS restraints: 269.58 Time building geometry restraints manager: 55.05 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: 14917 1.31 - 1.44: 61573 1.44 - 1.56: 65621 1.56 - 1.69: 7286 1.69 - 1.82: 434 Bond restraints: 149831 Sorted by residual: bond pdb=" C2' A2ML32815 " pdb=" C1' A2ML32815 " ideal model delta sigma weight residual 1.305 1.554 -0.249 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C2' A2ML33867 " pdb=" C1' A2ML33867 " ideal model delta sigma weight residual 1.305 1.554 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C2' A2ML31326 " pdb=" C1' A2ML31326 " ideal model delta sigma weight residual 1.305 1.553 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C2' A2ML31524 " pdb=" C1' A2ML31524 " ideal model delta sigma weight residual 1.305 1.553 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C2' A2ML33718 " pdb=" C1' A2ML33718 " ideal model delta sigma weight residual 1.305 1.552 -0.247 2.00e-02 2.50e+03 1.52e+02 ... (remaining 149826 not shown) Histogram of bond angle deviations from ideal: 90.78 - 100.46: 40 100.46 - 110.15: 63728 110.15 - 119.83: 92569 119.83 - 129.51: 61007 129.51 - 139.19: 2462 Bond angle restraints: 219806 Sorted by residual: angle pdb=" C1' A2ML34590 " pdb=" N9 A2ML34590 " pdb=" C8 A2ML34590 " ideal model delta sigma weight residual 88.50 127.93 -39.43 3.00e+00 1.11e-01 1.73e+02 angle pdb=" C1' A2ML31871 " pdb=" N9 A2ML31871 " pdb=" C8 A2ML31871 " ideal model delta sigma weight residual 88.50 126.80 -38.30 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C1' A2ML32787 " pdb=" N9 A2ML32787 " pdb=" C8 A2ML32787 " ideal model delta sigma weight residual 88.50 126.66 -38.16 3.00e+00 1.11e-01 1.62e+02 angle pdb=" C1' A2ML33830 " pdb=" N9 A2ML33830 " pdb=" C8 A2ML33830 " ideal model delta sigma weight residual 88.50 126.61 -38.11 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 88.50 126.60 -38.10 3.00e+00 1.11e-01 1.61e+02 ... (remaining 219801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 85368 35.33 - 70.67: 7673 70.67 - 106.00: 1328 106.00 - 141.34: 19 141.34 - 176.67: 12 Dihedral angle restraints: 94400 sinusoidal: 72292 harmonic: 22108 Sorted by residual: 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 34.50 -69.50 1 8.00e+00 1.56e-02 9.75e+01 dihedral pdb=" C5' CL3 502 " pdb=" C4' CL3 502 " pdb=" C3' CL3 502 " pdb=" O3' CL3 502 " ideal model delta sinusoidal sigma weight residual 147.00 81.54 65.46 1 8.00e+00 1.56e-02 8.77e+01 dihedral pdb=" O4' CL34303 " pdb=" C1' CL34303 " pdb=" N1 CL34303 " pdb=" C2 CL34303 " ideal model delta sinusoidal sigma weight residual 200.00 34.09 165.91 1 1.50e+01 4.44e-03 8.41e+01 ... (remaining 94397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 25993 0.081 - 0.161: 955 0.161 - 0.242: 49 0.242 - 0.322: 4 0.322 - 0.403: 18 Chirality restraints: 27019 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 -2.79 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C2' A2ML33825 " pdb=" C3' A2ML33825 " pdb=" O2' A2ML33825 " pdb=" C1' A2ML33825 " both_signs ideal model delta sigma weight residual False -2.39 -2.79 0.40 2.00e-01 2.50e+01 4.05e+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 4.05e+00 ... (remaining 27016 not shown) Planarity restraints: 14291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34494 " -0.053 2.00e-02 2.50e+03 6.13e-01 8.45e+03 pdb=" C4' OMGL34494 " -0.458 2.00e-02 2.50e+03 pdb=" O4' OMGL34494 " -0.732 2.00e-02 2.50e+03 pdb=" C3' OMGL34494 " 0.593 2.00e-02 2.50e+03 pdb=" O3' OMGL34494 " 0.623 2.00e-02 2.50e+03 pdb=" C2' OMGL34494 " 0.206 2.00e-02 2.50e+03 pdb=" O2' OMGL34494 " -0.943 2.00e-02 2.50e+03 pdb=" C1' OMGL34494 " -0.197 2.00e-02 2.50e+03 pdb=" N9 OMGL34494 " 0.961 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCL33887 " 0.023 2.00e-02 2.50e+03 6.05e-01 8.24e+03 pdb=" C4' OMCL33887 " 0.469 2.00e-02 2.50e+03 pdb=" O4' OMCL33887 " 0.812 2.00e-02 2.50e+03 pdb=" C3' OMCL33887 " -0.579 2.00e-02 2.50e+03 pdb=" O3' OMCL33887 " -0.564 2.00e-02 2.50e+03 pdb=" C2' OMCL33887 " -0.249 2.00e-02 2.50e+03 pdb=" O2' OMCL33887 " 0.862 2.00e-02 2.50e+03 pdb=" C1' OMCL33887 " 0.187 2.00e-02 2.50e+03 pdb=" N1 OMCL33887 " -0.961 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34228 " 0.887 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' OMGL34228 " -0.212 2.00e-02 2.50e+03 pdb=" O4' OMGL34228 " -0.702 2.00e-02 2.50e+03 pdb=" C3' OMGL34228 " 0.205 2.00e-02 2.50e+03 pdb=" O3' OMGL34228 " -0.936 2.00e-02 2.50e+03 pdb=" C2' OMGL34228 " 0.616 2.00e-02 2.50e+03 pdb=" O2' OMGL34228 " 0.620 2.00e-02 2.50e+03 pdb=" C1' OMGL34228 " -0.445 2.00e-02 2.50e+03 pdb=" N9 OMGL34228 " -0.032 2.00e-02 2.50e+03 ... (remaining 14288 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.61: 2505 2.61 - 3.24: 128296 3.24 - 3.87: 313127 3.87 - 4.51: 432240 4.51 - 5.14: 585044 Nonbonded interactions: 1461212 Sorted by model distance: nonbonded pdb=" OP2 AL31917 " pdb="MG MGL36023 " model vdw 1.975 2.170 nonbonded pdb=" OD2 ASPLJ 92 " pdb=" OG1 THRLJ 94 " model vdw 1.984 2.440 nonbonded pdb=" O2' CL31480 " pdb=" OP2 GL31482 " model vdw 1.985 2.440 nonbonded pdb=" O2' CL34688 " pdb=" OG SERSG 155 " model vdw 1.985 2.440 nonbonded pdb=" OP1 CL31676 " pdb="MG MGL36054 " model vdw 1.985 2.170 ... (remaining 1461207 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: 7.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 26.240 Check model and map are aligned: 1.490 Set scattering table: 0.940 Process input model: 570.840 Find NCS groups from input model: 3.060 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 621.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.007 0.249 149831 Z= 0.396 Angle : 0.756 39.430 219806 Z= 0.323 Chirality : 0.035 0.403 27019 Planarity : 0.027 0.613 14291 Dihedral : 21.628 176.672 80114 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.45 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.65 (0.09), residues: 7504 helix: 1.02 (0.10), residues: 2767 sheet: 0.35 (0.16), residues: 1019 loop : 0.12 (0.10), residues: 3718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPLF 99 HIS 0.015 0.001 HISNP 85 PHE 0.015 0.001 PHESR 18 TYR 0.023 0.001 TYRLK 48 ARG 0.012 0.001 ARGLA 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1661 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1661 time to evaluate : 7.259 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: 2 residues processed: 1661 average time/residue: 2.2033 time to fit residues: 5182.7787 Evaluate side-chains 1079 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1077 time to evaluate : 7.387 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.4280 time to fit residues: 11.5683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 933 optimal weight: 10.0000 chunk 837 optimal weight: 6.9990 chunk 464 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 564 optimal weight: 8.9990 chunk 447 optimal weight: 5.9990 chunk 866 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 526 optimal weight: 7.9990 chunk 644 optimal weight: 7.9990 chunk 1003 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 112 HIS L5 167 GLN L6 40 GLN L8 69 HIS L9 8 GLN L9 86 HIS L9 87 HIS L9 178 HIS LA 34 GLN LA 75 GLN LA 97 ASN LB 160 HIS LC 122 HIS LD 34 ASN LD 40 GLN LD 58 HIS LE 58 HIS LF 94 ASN LF 119 GLN LH 69 ASN LI 20 ASN LI 65 GLN LI 86 GLN LK 17 HIS LK 66 ASN LK 85 GLN LK 120 GLN LM 49 HIS LM 60 ASN LN 42 HIS LN 204 GLN LO 51 ASN LP 30 HIS LP 118 GLN LQ 34 ASN LQ 52 GLN LQ 124 ASN LQ 126 ASN LU 20 ASN LV 45 GLN LV 102 GLN LX 72 ASN LZ 20 ASN NR 65 GLN NR 115 GLN NR 123 GLN SB 275 GLN ** SC 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 206 ASN ** SE 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 149 ASN SE 206 GLN SF 38 HIS SG 8 GLN SG 39 ASN SG 40 HIS SG 156 ASN SK 74 ASN SK 83 HIS SR 27 GLN SR 41 HIS SR 157 HIS SR 209 HIS SR 246 HIS SR 274 ASN SR 304 GLN ** SR 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 486 GLN SR 538 HIS SV 39 ASN ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** VB 11 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 149831 Z= 0.481 Angle : 0.879 22.841 219806 Z= 0.453 Chirality : 0.044 0.385 27019 Planarity : 0.009 0.147 14291 Dihedral : 22.767 179.844 64136 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.13 % Allowed : 13.37 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.45 (0.09), residues: 7504 helix: 1.09 (0.09), residues: 2849 sheet: 0.25 (0.16), residues: 996 loop : -0.24 (0.10), residues: 3659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRPLW 49 HIS 0.013 0.002 HISL5 155 PHE 0.036 0.003 PHESR 18 TYR 0.029 0.003 TYRSB 119 ARG 0.011 0.001 ARGLV 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1090 time to evaluate : 7.106 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 outliers start: 265 outliers final: 132 residues processed: 1219 average time/residue: 2.0518 time to fit residues: 3635.7601 Evaluate side-chains 1099 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 967 time to evaluate : 7.084 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 64 residues processed: 71 average time/residue: 1.1643 time to fit residues: 155.2291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 557 optimal weight: 0.6980 chunk 311 optimal weight: 5.9990 chunk 835 optimal weight: 5.9990 chunk 683 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 1005 optimal weight: 10.0000 chunk 1085 optimal weight: 3.9990 chunk 895 optimal weight: 2.9990 chunk 996 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 806 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 184 ASN L8 125 ASN LD 34 ASN LE 127 GLN LH 69 ASN LI 65 GLN LI 86 GLN LK 120 GLN LM 60 ASN LN 204 GLN LO 51 ASN LQ 126 ASN LU 20 ASN LW 57 ASN LX 72 ASN NK 99 GLN NP 13 HIS NR 65 GLN NR 83 ASN NR 115 GLN SA 43 ASN SA 310 HIS ** SC 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SC 250 GLN SD 206 ASN SE 149 ASN SF 38 HIS SF 194 ASN SG 8 GLN SK 74 ASN SK 93 GLN SR 486 GLN SR 516 GLN SV 39 ASN SV 104 GLN VB 11 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 149831 Z= 0.356 Angle : 0.774 20.362 219806 Z= 0.411 Chirality : 0.039 0.355 27019 Planarity : 0.008 0.142 14291 Dihedral : 22.752 178.812 64136 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.46 % Allowed : 15.70 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 7504 helix: 1.28 (0.10), residues: 2867 sheet: 0.22 (0.16), residues: 1000 loop : -0.33 (0.10), residues: 3637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPLW 49 HIS 0.009 0.001 HISL5 155 PHE 0.029 0.002 PHELU 39 TYR 0.027 0.002 TYRSB 119 ARG 0.018 0.001 ARGLG 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1022 time to evaluate : 7.262 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: 286 outliers final: 156 residues processed: 1176 average time/residue: 2.0093 time to fit residues: 3468.0457 Evaluate side-chains 1119 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 963 time to evaluate : 7.095 Switching outliers to nearest non-outliers outliers start: 156 outliers final: 86 residues processed: 71 average time/residue: 1.1819 time to fit residues: 158.0515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 993 optimal weight: 5.9990 chunk 755 optimal weight: 4.9990 chunk 521 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 479 optimal weight: 4.9990 chunk 675 optimal weight: 8.9990 chunk 1008 optimal weight: 10.0000 chunk 1068 optimal weight: 9.9990 chunk 527 optimal weight: 9.9990 chunk 956 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 168 GLN L7 90 HIS L7 184 ASN LA 97 ASN LB 44 ASN LD 34 ASN LH 69 ASN LI 65 GLN LI 86 GLN LK 120 GLN LM 60 ASN LN 204 GLN LQ 126 ASN LU 20 ASN LX 72 ASN ** NP 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NR 65 GLN NR 83 ASN SA 310 HIS ** SC 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 206 ASN SE 149 ASN SF 38 HIS SF 194 ASN SK 74 ASN SK 93 GLN SR 144 GLN SR 486 GLN SV 17 HIS VB 11 HIS VB 45 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 149831 Z= 0.291 Angle : 0.741 19.749 219806 Z= 0.398 Chirality : 0.037 0.350 27019 Planarity : 0.008 0.138 14291 Dihedral : 22.699 178.595 64136 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.38 % Allowed : 16.98 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.60 (0.09), residues: 7504 helix: 1.43 (0.10), residues: 2859 sheet: 0.24 (0.16), residues: 1002 loop : -0.33 (0.10), residues: 3643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPNR 146 HIS 0.007 0.001 HISL5 155 PHE 0.024 0.002 PHELU 39 TYR 0.045 0.002 TYRL9 30 ARG 0.012 0.001 ARGSR 572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1034 time to evaluate : 7.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 281 outliers final: 147 residues processed: 1201 average time/residue: 2.0233 time to fit residues: 3591.0657 Evaluate side-chains 1130 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 983 time to evaluate : 7.181 Switching outliers to nearest non-outliers outliers start: 147 outliers final: 92 residues processed: 57 average time/residue: 1.1907 time to fit residues: 130.3737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 889 optimal weight: 5.9990 chunk 606 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 795 optimal weight: 9.9990 chunk 440 optimal weight: 8.9990 chunk 911 optimal weight: 4.9990 chunk 738 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 545 optimal weight: 0.7980 chunk 958 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LD 34 ASN LF 119 GLN LH 69 ASN LI 65 GLN LI 72 GLN LI 86 GLN LK 25 HIS LK 120 GLN LM 60 ASN LN 204 GLN LQ 126 ASN LW 57 ASN LX 72 ASN LZ 20 ASN ** NP 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NR 65 GLN NR 83 ASN SA 310 HIS SB 275 GLN ** SC 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 206 ASN SE 64 GLN ** SE 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 149 ASN SF 38 HIS SF 194 ASN SK 74 ASN SR 486 GLN VB 11 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 149831 Z= 0.427 Angle : 0.815 21.128 219806 Z= 0.428 Chirality : 0.042 0.350 27019 Planarity : 0.008 0.146 14291 Dihedral : 22.749 177.955 64136 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.88 % Allowed : 18.40 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.34 (0.09), residues: 7504 helix: 1.22 (0.10), residues: 2860 sheet: 0.15 (0.16), residues: 1008 loop : -0.51 (0.10), residues: 3636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPLW 49 HIS 0.011 0.002 HISL5 155 PHE 0.028 0.002 PHEL7 47 TYR 0.048 0.002 TYRL9 30 ARG 0.012 0.001 ARGSR 572 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1019 time to evaluate : 7.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 313 outliers final: 182 residues processed: 1208 average time/residue: 2.0019 time to fit residues: 3579.2824 Evaluate side-chains 1153 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 971 time to evaluate : 7.209 Switching outliers to nearest non-outliers outliers start: 182 outliers final: 125 residues processed: 60 average time/residue: 1.2291 time to fit residues: 140.7563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 359 optimal weight: 10.0000 chunk 961 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 627 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 1069 optimal weight: 0.9990 chunk 887 optimal weight: 4.9990 chunk 495 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 chunk 561 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L8 125 ASN LA 64 ASN LD 34 ASN LF 119 GLN LI 65 GLN LI 86 GLN LM 60 ASN LN 204 GLN ** LO 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 126 ASN LW 57 ASN LX 72 ASN ** NP 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NR 65 GLN NR 83 ASN NR 136 ASN SA 310 HIS SB 275 GLN SC 211 HIS SC 250 GLN SD 206 ASN SE 149 ASN SF 38 HIS SK 74 ASN SR 304 GLN SR 486 GLN VB 11 HIS VB 45 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 149831 Z= 0.296 Angle : 0.744 19.747 219806 Z= 0.400 Chirality : 0.037 0.343 27019 Planarity : 0.007 0.138 14291 Dihedral : 22.702 178.241 64136 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.27 % Allowed : 20.13 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 7504 helix: 1.40 (0.10), residues: 2866 sheet: 0.19 (0.16), residues: 1004 loop : -0.44 (0.10), residues: 3634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPLJ 129 HIS 0.006 0.001 HISL5 155 PHE 0.020 0.002 PHESB 160 TYR 0.061 0.002 TYRL9 30 ARG 0.014 0.001 ARGSA 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1008 time to evaluate : 7.281 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: 274 outliers final: 180 residues processed: 1189 average time/residue: 1.9637 time to fit residues: 3453.6499 Evaluate side-chains 1142 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 962 time to evaluate : 7.188 Switching outliers to nearest non-outliers outliers start: 180 outliers final: 132 residues processed: 50 average time/residue: 1.2283 time to fit residues: 116.6021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1105 random chunks: chunk 1030 optimal weight: 0.1980 chunk 120 optimal weight: 10.0000 chunk 609 optimal weight: 0.5980 chunk 780 optimal weight: 9.9990 chunk 604 optimal weight: 9.9990 chunk 899 optimal weight: 5.9990 chunk 597 optimal weight: 0.9990 chunk 1065 optimal weight: 8.9990 chunk 666 optimal weight: 0.9990 chunk 649 optimal weight: 7.9990 chunk 491 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 168 GLN L6 175 ASN L6 205 GLN LB 44 ASN LD 34 ASN ** LF 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 119 GLN LH 93 ASN LI 65 GLN LI 86 GLN LM 60 ASN LN 204 GLN ** LO 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 18 ASN LQ 126 ASN LX 72 ASN LZ 20 ASN ** NP 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NR 65 GLN NR 136 ASN SA 310 HIS SD 63 GLN SD 206 ASN SE 149 ASN SF 38 HIS SG 138 GLN ** SK 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 421 ASN SR 486 GLN VB 11 HIS VB 45 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 149831 Z= 0.159 Angle : 0.688 19.653 219806 Z= 0.377 Chirality : 0.033 0.320 27019 Planarity : 0.007 0.128 14291 Dihedral : 22.621 178.507 64136 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.38 % Allowed : 21.25 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.80 (0.10), residues: 7504 helix: 1.71 (0.10), residues: 2867 sheet: 0.22 (0.16), residues: 1010 loop : -0.29 (0.10), residues: 3627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPLJ 129 HIS 0.005 0.001 HISSB 81 PHE 0.016 0.001 PHELU 39 TYR 0.066 0.001 TYRL9 30 ARG 0.010 0.000 ARGL7 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15008 Ramachandran restraints generated. 7504 Oldfield, 0 Emsley, 7504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1024 time to evaluate : 7.285 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: 217 outliers final: 146 residues processed: 1180 average time/residue: 1.9813 time to fit residues: 3487.0204 Evaluate side-chains 1107 residues out of total 6605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 961 time to evaluate : 6.946 Switching outliers to nearest non-outliers outliers start: 146 outliers final: 121 residues processed: 28 average time/residue: 1.1521 time to fit residues: 67.2523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.8688 > 50: distance: 25 - 42: 6.736 distance: 37 - 42: 5.812 distance: 42 - 43: 8.599 distance: 43 - 44: 10.818 distance: 43 - 46: 7.674 distance: 44 - 45: 29.885 distance: 44 - 53: 19.647 distance: 46 - 47: 6.739 distance: 47 - 48: 3.459 distance: 47 - 49: 5.830 distance: 48 - 50: 10.202 distance: 49 - 51: 3.528 distance: 50 - 52: 4.993 distance: 51 - 52: 8.681 distance: 53 - 54: 25.753 distance: 54 - 55: 21.257 distance: 55 - 56: 16.672 distance: 55 - 57: 11.633 distance: 57 - 58: 5.418 distance: 58 - 59: 4.925 distance: 58 - 61: 4.584 distance: 61 - 62: 4.707 distance: 62 - 63: 4.730 distance: 63 - 64: 4.751 distance: 63 - 65: 9.814 distance: 67 - 68: 3.007 distance: 67 - 70: 4.117 distance: 70 - 71: 6.086 distance: 71 - 72: 5.078 distance: 71 - 73: 7.505 distance: 74 - 75: 3.007 distance: 75 - 76: 4.038 distance: 76 - 77: 5.851 distance: 77 - 176: 7.633 distance: 78 - 79: 3.324 distance: 80 - 81: 4.296 distance: 80 - 82: 4.985 distance: 84 - 85: 3.262 distance: 84 - 87: 3.061 distance: 87 - 88: 5.874 distance: 88 - 89: 6.407 distance: 89 - 90: 6.643 distance: 91 - 163: 4.371 distance: 92 - 93: 4.303 distance: 93 - 99: 3.707 distance: 94 - 160: 7.132 distance: 95 - 97: 4.518 distance: 96 - 98: 5.417 distance: 99 - 100: 3.517 distance: 100 - 103: 4.651 distance: 101 - 102: 4.648 distance: 102 - 223: 4.294 distance: 104 - 105: 5.232 distance: 107 - 143: 4.618 distance: 108 - 111: 4.941 distance: 109 - 110: 4.475 distance: 109 - 114: 3.805 distance: 110 - 140: 3.446 distance: 111 - 112: 4.561 distance: 111 - 113: 4.570 distance: 114 - 115: 5.561 distance: 114 - 211: 6.758 distance: 115 - 118: 3.730 distance: 116 - 117: 4.039 distance: 118 - 120: 3.573 distance: 119 - 121: 4.330