Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 13:22:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/04_2023/5tcu_8402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/04_2023/5tcu_8402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/04_2023/5tcu_8402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/04_2023/5tcu_8402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/04_2023/5tcu_8402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/04_2023/5tcu_8402_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4491 5.49 5 Mg 129 5.21 5 S 83 5.16 5 C 66377 2.51 5 N 24829 2.21 5 O 37967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "SB ARG 87": "NH1" <-> "NH2" Residue "SB ARG 113": "NH1" <-> "NH2" Residue "SB ARG 121": "NH1" <-> "NH2" Residue "SB ARG 126": "NH1" <-> "NH2" Residue "SB ARG 139": "NH1" <-> "NH2" Residue "SB ARG 163": "NH1" <-> "NH2" Residue "SC ARG 58": "NH1" <-> "NH2" Residue "SD ARG 29": "NH1" <-> "NH2" Residue "SD ARG 30": "NH1" <-> "NH2" Residue "SD ARG 32": "NH1" <-> "NH2" Residue "SE ARG 11": "NH1" <-> "NH2" Residue "SE ARG 46": "NH1" <-> "NH2" Residue "SE ARG 64": "NH1" <-> "NH2" Residue "SE ARG 78": "NH1" <-> "NH2" Residue "SE ARG 88": "NH1" <-> "NH2" Residue "SG ARG 3": "NH1" <-> "NH2" Residue "SG ARG 10": "NH1" <-> "NH2" Residue "SG ARG 36": "NH1" <-> "NH2" Residue "SG ARG 41": "NH1" <-> "NH2" Residue "SG ARG 92": "NH1" <-> "NH2" Residue "SG ARG 96": "NH1" <-> "NH2" Residue "SG ARG 111": "NH1" <-> "NH2" Residue "SF TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF ARG 61": "NH1" <-> "NH2" Residue "SF ARG 72": "NH1" <-> "NH2" Residue "SF ARG 119": "NH1" <-> "NH2" Residue "SH ARG 38": "NH1" <-> "NH2" Residue "SH ARG 82": "NH1" <-> "NH2" Residue "SH ARG 115": "NH1" <-> "NH2" Residue "SH ARG 125": "NH1" <-> "NH2" Residue "SH PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ARG 16": "NH1" <-> "NH2" Residue "S2 ARG 111": "NH1" <-> "NH2" Residue "S3 ARG 9": "NH1" <-> "NH2" Residue "S3 ARG 12": "NH1" <-> "NH2" Residue "S3 ARG 63": "NH1" <-> "NH2" Residue "S3 ARG 69": "NH1" <-> "NH2" Residue "S3 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S4 ARG 11": "NH1" <-> "NH2" Residue "S4 ARG 14": "NH1" <-> "NH2" Residue "S4 ARG 70": "NH1" <-> "NH2" Residue "S4 ARG 71": "NH1" <-> "NH2" Residue "S4 ARG 79": "NH1" <-> "NH2" Residue "S4 ARG 98": "NH1" <-> "NH2" Residue "S5 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S5 ARG 26": "NH1" <-> "NH2" Residue "S5 ARG 29": "NH1" <-> "NH2" Residue "S5 ARG 41": "NH1" <-> "NH2" Residue "S5 ARG 57": "NH1" <-> "NH2" Residue "S6 ARG 7": "NH1" <-> "NH2" Residue "S6 ARG 16": "NH1" <-> "NH2" Residue "S6 ARG 54": "NH1" <-> "NH2" Residue "S6 ARG 63": "NH1" <-> "NH2" Residue "S6 ARG 71": "NH1" <-> "NH2" Residue "S6 ARG 88": "NH1" <-> "NH2" Residue "S7 ARG 26": "NH1" <-> "NH2" Residue "S7 ARG 29": "NH1" <-> "NH2" Residue "S8 ARG 39": "NH1" <-> "NH2" Residue "S9 ARG 47": "NH1" <-> "NH2" Residue "SI ARG 37": "NH1" <-> "NH2" Residue "SI ARG 55": "NH1" <-> "NH2" Residue "SA ARG 10": "NH1" <-> "NH2" Residue "L2 ARG 43": "NH1" <-> "NH2" Residue "L2 ARG 243": "NH1" <-> "NH2" Residue "LC ARG 89": "NH1" <-> "NH2" Residue "LJ ARG 45": "NH1" <-> "NH2" Residue "LJ ARG 54": "NH1" <-> "NH2" Residue "LJ ARG 107": "NH1" <-> "NH2" Residue "LJ ARG 168": "NH1" <-> "NH2" Residue "LK ARG 112": "NH1" <-> "NH2" Residue "LL ARG 69": "NH1" <-> "NH2" Residue "LL ARG 163": "NH1" <-> "NH2" Residue "LM ARG 2": "NH1" <-> "NH2" Residue "LM ARG 100": "NH1" <-> "NH2" Residue "LN ARG 17": "NH1" <-> "NH2" Residue "LN ARG 88": "NH1" <-> "NH2" Residue "LO ARG 21": "NH1" <-> "NH2" Residue "LO ARG 64": "NH1" <-> "NH2" Residue "LP ARG 10": "NH1" <-> "NH2" Residue "LP ARG 20": "NH1" <-> "NH2" Residue "LP ARG 45": "NH1" <-> "NH2" Residue "LP ARG 51": "NH1" <-> "NH2" Residue "LP ARG 56": "NH1" <-> "NH2" Residue "LP ARG 115": "NH1" <-> "NH2" Residue "LQ ARG 110": "NH1" <-> "NH2" Residue "LR ARG 14": "NH1" <-> "NH2" Residue "LR ARG 35": "NH1" <-> "NH2" Residue "L1 ARG 16": "NH1" <-> "NH2" Residue "L1 ARG 23": "NH1" <-> "NH2" Residue "L1 ARG 33": "NH1" <-> "NH2" Residue "L1 ARG 90": "NH1" <-> "NH2" Residue "L3 ARG 48": "NH1" <-> "NH2" Residue "L4 ARG 67": "NH1" <-> "NH2" Residue "L4 ARG 84": "NH1" <-> "NH2" Residue "L5 ARG 8": "NH1" <-> "NH2" Residue "L5 ARG 11": "NH1" <-> "NH2" Residue "L5 ARG 88": "NH1" <-> "NH2" Residue "L6 ARG 64": "NH1" <-> "NH2" Residue "L6 ARG 76": "NH1" <-> "NH2" Residue "L7 ARG 32": "NH1" <-> "NH2" Residue "L8 ARG 22": "NH1" <-> "NH2" Residue "L8 ARG 57": "NH1" <-> "NH2" Residue "L9 ARG 22": "NH1" <-> "NH2" Residue "L9 ARG 28": "NH1" <-> "NH2" Residue "L9 ARG 49": "NH1" <-> "NH2" Residue "L9 ARG 79": "NH1" <-> "NH2" Residue "L9 ARG 82": "NH1" <-> "NH2" Residue "LA ARG 37": "NH1" <-> "NH2" Residue "LB ARG 7": "NH1" <-> "NH2" Residue "LB ARG 44": "NH1" <-> "NH2" Residue "LB ARG 47": "NH1" <-> "NH2" Residue "LB ARG 52": "NH1" <-> "NH2" Residue "LB ARG 58": "NH1" <-> "NH2" Residue "LB ARG 60": "NH1" <-> "NH2" Residue "LD ARG 10": "NH1" <-> "NH2" Residue "LE ARG 7": "NH1" <-> "NH2" Residue "LS ARG 46": "NH1" <-> "NH2" Residue "LG ARG 20": "NH1" <-> "NH2" Residue "LG ARG 22": "NH1" <-> "NH2" Residue "LG ARG 40": "NH1" <-> "NH2" Residue "LH ARG 48": "NH1" <-> "NH2" Residue "LI ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 133876 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 31369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1464, 31369 Inner-chain residues flagged as termini: ['pdbres=" U A 494 "', 'pdbres=" G A 855 "'] Classifications: {'RNA': 1464} Modifications used: {'5*END': 2, 'rna2p_pur': 150, 'rna2p_pyr': 100, 'rna3p_pur': 681, 'rna3p_pyr': 533} Link IDs: {'rna2p': 250, 'rna3p': 1213} Chain breaks: 7 Chain: "SB" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1551 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 198} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "SC" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1058 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 8, 'TRANS': 189} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 579 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 326 Chain: "SD" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1153 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 148} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "SE" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "SG" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1164 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 148} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 57 Chain: "SF" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1007 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "SH" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 975 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "S1" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 74} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "S2" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 826 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S3" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 976 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 127} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 57 Chain: "S4" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 828 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "S5" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 497 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S6" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 713 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S7" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 537 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 77} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "S8" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 520 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "S9" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 458 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "SI" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 541 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "SA" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 503 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 77} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "X" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 213 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 6} Chain: "E" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1600 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 64} Chain: "D" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain: "B" Number of atoms: 59059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2755, 59059 Classifications: {'RNA': 2755} Modifications used: {'rna2p_pur': 287, 'rna2p_pyr': 156, 'rna3p_pur': 1294, 'rna3p_pyr': 1017} Link IDs: {'rna2p': 443, 'rna3p': 2311} Chain breaks: 8 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2430 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 54, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 101} Chain: "L2" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2066 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 256} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "LC" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1570 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 45 Chain: "LJ" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1514 Classifications: {'peptide': 205} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 195} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 44 Chain: "LK" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1026 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 5, 'TRANS': 160} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 153 Chain: "LL" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1062 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 7, 'TRANS': 166} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 305 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 169 Chain: "LM" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1124 Classifications: {'peptide': 145} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 138} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "LN" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 918 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LO" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1020 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 139} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "LP" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1043 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "LQ" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 898 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "LR" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 765 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 1, 'TRANS': 111} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "L1" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "L3" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L4" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 749 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "L5" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 837 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "L6" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "L7" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 734 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "L8" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 648 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 36 Chain: "L9" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 615 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "LA" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 443 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "LB" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 493 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "LD" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LE" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 356 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "LS" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 380 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "LG" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 367 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "LH" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 446 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "LI" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 272 Classifications: {'peptide': 37} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "LF" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 447 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 69 Unusual residues: {' MG': 27, 'PAR': 1} Classifications: {'undetermined': 28} Link IDs: {None: 27} Chain: "SG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Unusual residues: {' MG': 99} Classifications: {'undetermined': 99} Link IDs: {None: 98} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 49.72, per 1000 atoms: 0.37 Number of scatterers: 133876 At special positions: 0 Unit cell: (284.16, 263.04, 226.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 83 16.00 P 4491 15.00 Mg 129 11.99 O 37967 8.00 N 24829 7.00 C 66377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYSS5 24 " - pdb=" SG CYSS5 40 " distance=2.04 Simple disulfide: pdb=" SG CYSS5 27 " - pdb=" SG CYSS5 43 " distance=2.03 Simple disulfide: pdb=" SG CYSLS 9 " - pdb=" SG CYSLS 12 " distance=2.02 Simple disulfide: pdb=" SG CYSLS 9 " - pdb=" SG CYSLS 36 " distance=2.04 Simple disulfide: pdb=" SG CYSLS 12 " - pdb=" SG CYSLS 36 " distance=2.03 Simple disulfide: pdb=" SG CYSLI 14 " - pdb=" SG CYSLI 27 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 55.62 Conformation dependent library (CDL) restraints added in 5.4 seconds 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9420 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 123 helices and 58 sheets defined 31.3% alpha, 15.1% beta 837 base pairs and 1902 stacking pairs defined. Time for finding SS restraints: 47.41 Creating SS restraints... Processing helix chain 'SB' and resid 6 through 12 removed outlier: 4.309A pdb=" N LEUSB 10 " --> pdb=" O ASNSB 6 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARGSB 11 " --> pdb=" O PROSB 7 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VALSB 12 " --> pdb=" O ILESB 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 6 through 12' Processing helix chain 'SB' and resid 27 through 45 removed outlier: 3.704A pdb=" N LEUSB 36 " --> pdb=" O LEUSB 32 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LYSSB 40 " --> pdb=" O LEUSB 36 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N PHESB 41 " --> pdb=" O LYSSB 37 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILESB 42 " --> pdb=" O ILESB 38 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASPSB 43 " --> pdb=" O ARGSB 39 " (cutoff:3.500A) Processing helix chain 'SB' and resid 71 through 77 removed outlier: 4.202A pdb=" N VALSB 75 " --> pdb=" O LYSSB 71 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILESB 76 " --> pdb=" O PROSB 72 " (cutoff:3.500A) Processing helix chain 'SB' and resid 80 through 95 removed outlier: 4.297A pdb=" N GLUSB 84 " --> pdb=" O GLYSB 80 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEUSB 93 " --> pdb=" O LYSSB 89 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N THRSB 94 " --> pdb=" O LEUSB 90 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASPSB 95 " --> pdb=" O ASNSB 91 " (cutoff:3.500A) Processing helix chain 'SB' and resid 111 through 126 removed outlier: 3.503A pdb=" N VALSB 115 " --> pdb=" O ASPSB 111 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARGSB 121 " --> pdb=" O GLUSB 117 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLNSB 122 " --> pdb=" O ASNSB 118 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEUSB 123 " --> pdb=" O ILESB 119 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASNSB 125 " --> pdb=" O ARGSB 121 " (cutoff:3.500A) Processing helix chain 'SB' and resid 128 through 144 removed outlier: 4.007A pdb=" N VALSB 132 " --> pdb=" O SERSB 128 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLNSB 135 " --> pdb=" O ARGSB 131 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALASB 136 " --> pdb=" O VALSB 132 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALASB 140 " --> pdb=" O ALASB 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N METSB 141 " --> pdb=" O ILESB 137 " (cutoff:3.500A) Processing helix chain 'SC' and resid 7 through 16 removed outlier: 5.245A pdb=" N ARGSC 13 " --> pdb=" O TRPSC 9 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARGSC 14 " --> pdb=" O LYSSC 10 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEUSC 15 " --> pdb=" O LYSSC 11 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLYSC 16 " --> pdb=" O SERSC 12 " (cutoff:3.500A) Processing helix chain 'SC' and resid 24 through 29 removed outlier: 5.634A pdb=" N LYSSC 28 " --> pdb=" O LYSSC 24 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARGSC 29 " --> pdb=" O GLUSC 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 24 through 29' Processing helix chain 'SC' and resid 45 through 62 removed outlier: 3.827A pdb=" N TYRSC 59 " --> pdb=" O GLNSC 55 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEUSC 60 " --> pdb=" O LYSSC 56 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLYSC 62 " --> pdb=" O ARGSC 58 " (cutoff:3.500A) Processing helix chain 'SC' and resid 64 through 78 removed outlier: 3.909A pdb=" N PHESC 68 " --> pdb=" O THRSC 64 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARGSC 69 " --> pdb=" O GLUSC 65 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASNSC 70 " --> pdb=" O ARGSC 66 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYSSC 78 " --> pdb=" O ILESC 74 " (cutoff:3.500A) Processing helix chain 'SC' and resid 81 through 91 removed outlier: 4.465A pdb=" N METSC 87 " --> pdb=" O GLYSC 83 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ALASC 91 " --> pdb=" O METSC 87 " (cutoff:3.500A) Processing helix chain 'SC' and resid 93 through 101 Processing helix chain 'SC' and resid 106 through 117 removed outlier: 3.887A pdb=" N GLNSC 112 " --> pdb=" O ARGSC 108 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEUSC 113 " --> pdb=" O GLNSC 109 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VALSC 114 " --> pdb=" O ALASC 110 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASNSC 115 " --> pdb=" O ARGSC 111 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HISSC 116 " --> pdb=" O GLNSC 112 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLYSC 117 " --> pdb=" O LEUSC 113 " (cutoff:3.500A) Processing helix chain 'SC' and resid 148 through 156 removed outlier: 4.910A pdb=" N VALSC 152 " --> pdb=" O LEUSC 148 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLUSC 156 " --> pdb=" O VALSC 152 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 199 removed outlier: 3.625A pdb=" N ILESC 194 " --> pdb=" O ASNSC 190 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLUSC 196 " --> pdb=" O GLNSC 192 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYRSC 197 " --> pdb=" O LEUSC 193 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYRSC 198 " --> pdb=" O ILESC 194 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N SERSC 199 " --> pdb=" O VALSC 195 " (cutoff:3.500A) Processing helix chain 'SD' and resid 56 through 71 removed outlier: 3.707A pdb=" N ILESD 60 " --> pdb=" O VALSD 56 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYSSD 61 " --> pdb=" O PROSD 57 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALASD 66 " --> pdb=" O LYSSD 62 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYSSD 68 " --> pdb=" O VALSD 64 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYSSD 69 " --> pdb=" O GLUSD 65 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASPSD 70 " --> pdb=" O ALASD 66 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEUSD 71 " --> pdb=" O ALASD 67 " (cutoff:3.500A) Processing helix chain 'SD' and resid 109 through 119 removed outlier: 4.052A pdb=" N ALASD 113 " --> pdb=" O GLYSD 109 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALSD 114 " --> pdb=" O PROSD 110 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEUSD 115 " --> pdb=" O VALSD 111 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEUSD 117 " --> pdb=" O ALASD 113 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALASD 118 " --> pdb=" O VALSD 114 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLYSD 119 " --> pdb=" O LEUSD 115 " (cutoff:3.500A) Processing helix chain 'SD' and resid 132 through 148 removed outlier: 3.541A pdb=" N METSD 136 " --> pdb=" O THRSD 132 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VALSD 137 " --> pdb=" O PROSD 133 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARGSD 138 " --> pdb=" O ILESD 134 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALASD 139 " --> pdb=" O ASNSD 135 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYSSD 148 " --> pdb=" O LEUSD 144 " (cutoff:3.500A) Processing helix chain 'SD' and resid 149 through 158 removed outlier: 4.163A pdb=" N VALSD 153 " --> pdb=" O ASNSD 149 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ALASD 154 " --> pdb=" O ALASD 150 " (cutoff:3.500A) Processing helix chain 'SD' and resid 160 through 165 removed outlier: 4.009A pdb=" N LEUSD 164 " --> pdb=" O THRSD 160 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYRSD 165 " --> pdb=" O VALSD 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'SD' and resid 160 through 165' Processing helix chain 'SE' and resid 15 through 32 removed outlier: 3.697A pdb=" N VALSE 23 " --> pdb=" O LYSSE 19 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUSE 24 " --> pdb=" O LYSSE 20 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASNSE 27 " --> pdb=" O VALSE 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLYSE 28 " --> pdb=" O GLUSE 24 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALASE 31 " --> pdb=" O ASNSE 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THRSE 32 " --> pdb=" O GLYSE 28 " (cutoff:3.500A) Processing helix chain 'SE' and resid 70 through 84 removed outlier: 5.223A pdb=" N ASPSE 74 " --> pdb=" O ASNSE 70 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLUSE 75 " --> pdb=" O LYSSE 71 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHESE 76 " --> pdb=" O ALASE 72 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYSSE 81 " --> pdb=" O GLNSE 77 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILESE 82 " --> pdb=" O ARGSE 78 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SERSE 83 " --> pdb=" O LEUSE 79 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASPSE 84 " --> pdb=" O ALASE 80 " (cutoff:3.500A) Processing helix chain 'SG' and resid 20 through 32 removed outlier: 4.131A pdb=" N THRSG 24 " --> pdb=" O SERSG 20 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYSSG 25 " --> pdb=" O LYSSG 21 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEUSG 26 " --> pdb=" O LEUSG 22 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILESG 27 " --> pdb=" O VALSG 23 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASNSG 28 " --> pdb=" O THRSG 24 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILESG 30 " --> pdb=" O LEUSG 26 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N METSG 31 " --> pdb=" O ILESG 27 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEUSG 32 " --> pdb=" O ASNSG 28 " (cutoff:3.500A) Processing helix chain 'SG' and resid 35 through 54 removed outlier: 4.083A pdb=" N ALASG 39 " --> pdb=" O LYSSG 35 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLNSG 40 " --> pdb=" O ARGSG 36 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARGSG 41 " --> pdb=" O GLYSG 37 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILESG 42 " --> pdb=" O THRSG 38 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SERSG 45 " --> pdb=" O ARGSG 41 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEUSG 49 " --> pdb=" O SERSG 45 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VALSG 50 " --> pdb=" O ALASG 46 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLUSG 51 " --> pdb=" O PHESG 47 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLNSG 52 " --> pdb=" O ASPSG 48 " (cutoff:3.500A) Processing helix chain 'SG' and resid 57 through 70 removed outlier: 3.563A pdb=" N VALSG 61 " --> pdb=" O ASPSG 57 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLUSG 63 " --> pdb=" O LEUSG 59 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLUSG 64 " --> pdb=" O GLUSG 60 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILESG 69 " --> pdb=" O ALASG 65 " (cutoff:3.500A) Processing helix chain 'SG' and resid 92 through 111 removed outlier: 4.543A pdb=" N THRSG 97 " --> pdb=" O PROSG 93 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THRSG 98 " --> pdb=" O GLUSG 94 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARGSG 102 " --> pdb=" O THRSG 98 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N TRPSG 103 " --> pdb=" O LEUSG 99 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEUSG 104 " --> pdb=" O GLYSG 100 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VALSG 105 " --> pdb=" O LEUSG 101 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYRSG 107 " --> pdb=" O TRPSG 103 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEUSG 110 " --> pdb=" O ASNSG 106 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARGSG 111 " --> pdb=" O TYRSG 107 " (cutoff:3.500A) Processing helix chain 'SG' and resid 115 through 130 removed outlier: 4.531A pdb=" N ALASG 121 " --> pdb=" O GLUSG 117 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASNSG 122 " --> pdb=" O ASPSG 118 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLUSG 123 " --> pdb=" O ARGSG 119 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILESG 124 " --> pdb=" O LEUSG 120 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASPSG 126 " --> pdb=" O ASNSG 122 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALASG 127 " --> pdb=" O GLUSG 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALASG 128 " --> pdb=" O ILESG 124 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASNSG 129 " --> pdb=" O LEUSG 125 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNSG 130 " --> pdb=" O ASPSG 126 " (cutoff:3.500A) Processing helix chain 'SG' and resid 132 through 149 removed outlier: 4.844A pdb=" N LYSSG 136 " --> pdb=" O GLYSG 132 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYSSG 137 " --> pdb=" O GLYSG 133 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARGSG 138 " --> pdb=" O ALASG 134 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYSSG 143 " --> pdb=" O GLUSG 139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N METSG 144 " --> pdb=" O ASPSG 140 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALASG 145 " --> pdb=" O THRSG 141 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUSG 146 " --> pdb=" O HISSG 142 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALASG 147 " --> pdb=" O LYSSG 143 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASNSG 148 " --> pdb=" O METSG 144 " (cutoff:3.500A) Processing helix chain 'SF' and resid 5 through 21 removed outlier: 3.898A pdb=" N ASPSF 9 " --> pdb=" O ASPSF 5 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N METSF 10 " --> pdb=" O PROSF 6 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARGSF 13 " --> pdb=" O ASPSF 9 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VALSF 14 " --> pdb=" O METSF 10 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARGSF 15 " --> pdb=" O LEUSF 11 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASNSF 16 " --> pdb=" O THRSF 12 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VALSF 20 " --> pdb=" O ASNSF 16 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARGSF 21 " --> pdb=" O ALASF 17 " (cutoff:3.500A) Processing helix chain 'SF' and resid 30 through 44 removed outlier: 4.377A pdb=" N LYSSF 34 " --> pdb=" O SERSF 30 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLUSF 35 " --> pdb=" O ASNSF 31 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLUSF 38 " --> pdb=" O LYSSF 34 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLUSF 43 " --> pdb=" O ILESF 39 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLYSF 44 " --> pdb=" O LEUSF 40 " (cutoff:3.500A) Processing helix chain 'SF' and resid 114 through 122 removed outlier: 4.740A pdb=" N ARGSF 119 " --> pdb=" O ASPSF 115 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYSSF 120 " --> pdb=" O LYSSF 116 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARGSF 121 " --> pdb=" O GLUSF 117 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASNSF 122 " --> pdb=" O ALASF 118 " (cutoff:3.500A) Processing helix chain 'SH' and resid 36 through 41 removed outlier: 4.448A pdb=" N TYRSH 40 " --> pdb=" O ASPSH 36 " (cutoff:3.500A) Processing helix chain 'SH' and resid 46 through 58 removed outlier: 4.107A pdb=" N LEUSH 50 " --> pdb=" O LEUSH 46 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASNSH 51 " --> pdb=" O ILESH 47 " (cutoff:3.500A) Proline residue: SH 53 - end of helix removed outlier: 4.233A pdb=" N GLUSH 58 " --> pdb=" O PHESH 54 " (cutoff:3.500A) Processing helix chain 'SH' and resid 73 through 94 removed outlier: 4.174A pdb=" N GLNSH 77 " --> pdb=" O GLYSH 73 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLNSH 79 " --> pdb=" O THRSH 75 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALASH 80 " --> pdb=" O GLYSH 76 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILESH 81 " --> pdb=" O GLNSH 77 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARGSH 82 " --> pdb=" O ALASH 78 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALASH 86 " --> pdb=" O ARGSH 82 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARGSH 87 " --> pdb=" O HISSH 83 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALASH 88 " --> pdb=" O GLYSH 84 " (cutoff:3.500A) Proline residue: SH 94 - end of helix Processing helix chain 'SH' and resid 95 through 103 removed outlier: 3.919A pdb=" N SERSH 99 " --> pdb=" O GLUSH 95 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ARGSH 102 " --> pdb=" O GLYSH 98 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALASH 103 " --> pdb=" O SERSH 99 " (cutoff:3.500A) Processing helix chain 'S1' and resid 14 through 33 removed outlier: 4.041A pdb=" N ILES1 18 " --> pdb=" O ASPS1 14 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASPS1 19 " --> pdb=" O HISS1 15 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SERS1 32 " --> pdb=" O THRS1 28 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLYS1 33 " --> pdb=" O ALAS1 29 " (cutoff:3.500A) Processing helix chain 'S2' and resid 46 through 51 removed outlier: 4.669A pdb=" N LEUS2 50 " --> pdb=" O SERS2 46 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLYS2 51 " --> pdb=" O ALAS2 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'S2' and resid 46 through 51' Processing helix chain 'S2' and resid 59 through 74 removed outlier: 4.530A pdb=" N GLUS2 68 " --> pdb=" O GLNS2 64 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THRS2 69 " --> pdb=" O METS2 65 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SERS2 73 " --> pdb=" O THRS2 69 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALAS2 74 " --> pdb=" O ALAS2 70 " (cutoff:3.500A) Processing helix chain 'S2' and resid 92 through 104 removed outlier: 4.204A pdb=" N ALAS2 96 " --> pdb=" O GLYS2 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILES2 97 " --> pdb=" O ARGS2 93 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAS2 99 " --> pdb=" O SERS2 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEUS2 100 " --> pdb=" O ALAS2 96 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLNS2 101 " --> pdb=" O ILES2 97 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SERS2 102 " --> pdb=" O ARGS2 98 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALAS2 103 " --> pdb=" O ALAS2 99 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLYS2 104 " --> pdb=" O LEUS2 100 " (cutoff:3.500A) Processing helix chain 'S3' and resid 3 through 11 removed outlier: 4.170A pdb=" N LYSS3 10 " --> pdb=" O GLNS3 6 " (cutoff:3.500A) Proline residue: S3 11 - end of helix Processing helix chain 'S4' and resid 14 through 23 removed outlier: 4.687A pdb=" N THRS4 20 " --> pdb=" O VALS4 16 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYRS4 21 " --> pdb=" O ILES4 17 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILES4 22 " --> pdb=" O SERS4 18 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYRS4 23 " --> pdb=" O LEUS4 19 " (cutoff:3.500A) Processing helix chain 'S4' and resid 27 through 35 removed outlier: 4.918A pdb=" N GLNS4 31 " --> pdb=" O THRS4 27 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYSS4 32 " --> pdb=" O SERS4 28 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLUS4 35 " --> pdb=" O GLNS4 31 " (cutoff:3.500A) Processing helix chain 'S4' and resid 50 through 64 removed outlier: 5.581A pdb=" N GLYS4 54 " --> pdb=" O ASPS4 50 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARGS4 55 " --> pdb=" O ASPS4 51 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILES4 56 " --> pdb=" O GLUS4 52 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARGS4 57 " --> pdb=" O LEUS4 53 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VALS4 60 " --> pdb=" O ILES4 56 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYSS4 64 " --> pdb=" O VALS4 60 " (cutoff:3.500A) Processing helix chain 'S4' and resid 70 through 83 removed outlier: 4.198A pdb=" N ASNS4 74 " --> pdb=" O ARGS4 70 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEUS4 75 " --> pdb=" O ARGS4 71 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILES4 83 " --> pdb=" O ARGS4 79 " (cutoff:3.500A) Processing helix chain 'S4' and resid 87 through 94 removed outlier: 6.897A pdb=" N HISS4 91 " --> pdb=" O ARGS4 87 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARGS4 92 " --> pdb=" O GLYS4 88 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLYS4 94 " --> pdb=" O ARGS4 90 " (cutoff:3.500A) Processing helix chain 'S5' and resid 2 through 13 removed outlier: 5.249A pdb=" N METS5 6 " --> pdb=" O ALAS5 2 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALAS5 8 " --> pdb=" O THRS5 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLNS5 11 " --> pdb=" O VALS5 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYSS5 12 " --> pdb=" O ALAS5 8 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYSS5 13 " --> pdb=" O LYSS5 9 " (cutoff:3.500A) Processing helix chain 'S5' and resid 41 through 50 removed outlier: 4.748A pdb=" N ARGS5 45 " --> pdb=" O ARGS5 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLUS5 46 " --> pdb=" O ILES5 42 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEUS5 47 " --> pdb=" O CYSS5 43 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LYSS5 50 " --> pdb=" O GLUS5 46 " (cutoff:3.500A) Processing helix chain 'S6' and resid 4 through 16 removed outlier: 4.104A pdb=" N LYSS6 13 " --> pdb=" O ASNS6 9 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLUS6 14 " --> pdb=" O GLUS6 10 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYRS6 15 " --> pdb=" O ILES6 11 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARGS6 16 " --> pdb=" O ILES6 12 " (cutoff:3.500A) Processing helix chain 'S6' and resid 24 through 47 removed outlier: 5.657A pdb=" N ILES6 29 " --> pdb=" O PROS6 25 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALAS6 30 " --> pdb=" O GLUS6 26 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLUS6 41 " --> pdb=" O ASNS6 37 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N HISS6 42 " --> pdb=" O ALAS6 38 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARGS6 44 " --> pdb=" O ASNS6 40 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THRS6 45 " --> pdb=" O GLUS6 41 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYSS6 47 " --> pdb=" O LEUS6 43 " (cutoff:3.500A) Processing helix chain 'S6' and resid 49 through 74 removed outlier: 5.582A pdb=" N ARGS6 53 " --> pdb=" O ASPS6 49 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARGS6 54 " --> pdb=" O HISS6 50 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLYS6 55 " --> pdb=" O HISS6 51 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N METS6 59 " --> pdb=" O GLYS6 55 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARGS6 71 " --> pdb=" O LEUS6 67 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SERS6 72 " --> pdb=" O ASNS6 68 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LYSS6 73 " --> pdb=" O TYRS6 69 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASPS6 74 " --> pdb=" O LEUS6 70 " (cutoff:3.500A) Processing helix chain 'S6' and resid 75 through 86 removed outlier: 4.028A pdb=" N GLUS6 80 " --> pdb=" O GLNS6 76 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLYS6 86 " --> pdb=" O ILES6 82 " (cutoff:3.500A) Processing helix chain 'S7' and resid 53 through 64 removed outlier: 4.254A pdb=" N ALAS7 57 " --> pdb=" O ASPS7 53 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYSS7 59 " --> pdb=" O ALAS7 55 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TRPS7 60 " --> pdb=" O LEUS7 56 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEUS7 61 " --> pdb=" O ALAS7 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASNS7 62 " --> pdb=" O LEUS7 58 " (cutoff:3.500A) Processing helix chain 'S7' and resid 71 through 79 removed outlier: 4.969A pdb=" N GLYS7 79 " --> pdb=" O LEUS7 75 " (cutoff:3.500A) Processing helix chain 'S9' and resid 32 through 39 removed outlier: 3.696A pdb=" N ARGS9 36 " --> pdb=" O GLUS9 32 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHES9 37 " --> pdb=" O LEUS9 33 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SERS9 39 " --> pdb=" O LYSS9 35 " (cutoff:3.500A) Processing helix chain 'S9' and resid 46 through 51 Processing helix chain 'S9' and resid 53 through 71 removed outlier: 4.363A pdb=" N GLNS9 57 " --> pdb=" O SERS9 53 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYSS9 65 " --> pdb=" O THRS9 61 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARGS9 66 " --> pdb=" O THRS9 62 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N METS9 70 " --> pdb=" O ARGS9 66 " (cutoff:3.500A) Processing helix chain 'SI' and resid 12 through 22 removed outlier: 4.253A pdb=" N ALASI 21 " --> pdb=" O LYSSI 17 " (cutoff:3.500A) Processing helix chain 'SA' and resid 8 through 42 removed outlier: 5.274A pdb=" N LYSSA 12 " --> pdb=" O ILESA 8 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THRSA 13 " --> pdb=" O LYSSA 9 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THRSA 14 " --> pdb=" O ARGSA 10 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLUSA 15 " --> pdb=" O VALSA 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYSSA 16 " --> pdb=" O LYSSA 12 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SERSA 23 " --> pdb=" O ALASA 19 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLNSA 24 " --> pdb=" O ARGSA 20 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASNSA 34 " --> pdb=" O THRSA 30 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALASA 35 " --> pdb=" O ALASA 31 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYSSA 36 " --> pdb=" O VALSA 32 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THRSA 37 " --> pdb=" O LYSSA 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SERSA 40 " --> pdb=" O LYSSA 36 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASNSA 42 " --> pdb=" O ALASA 38 " (cutoff:3.500A) Processing helix chain 'SA' and resid 47 through 64 removed outlier: 6.316A pdb=" N SERSA 51 " --> pdb=" O ASNSA 47 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEUSA 52 " --> pdb=" O GLUSA 48 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SERSA 63 " --> pdb=" O LYSSA 59 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASNSA 64 " --> pdb=" O ALASA 60 " (cutoff:3.500A) Processing helix chain 'SA' and resid 67 through 82 removed outlier: 4.506A pdb=" N THRSA 80 " --> pdb=" O SERSA 76 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALASA 81 " --> pdb=" O GLNSA 77 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASNSA 82 " --> pdb=" O LEUSA 78 " (cutoff:3.500A) Processing helix chain 'L2' and resid 207 through 215 removed outlier: 4.451A pdb=" N SERL2 211 " --> pdb=" O LYSL2 207 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARGL2 212 " --> pdb=" O ALAL2 208 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYSL2 214 " --> pdb=" O ARGL2 210 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLYL2 215 " --> pdb=" O SERL2 211 " (cutoff:3.500A) Processing helix chain 'L2' and resid 266 through 271 removed outlier: 5.489A pdb=" N VALL2 271 " --> pdb=" O ASPL2 267 " (cutoff:3.500A) Processing helix chain 'LC' and resid 70 through 81 removed outlier: 3.931A pdb=" N GLYLC 75 " --> pdb=" O LYSLC 71 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYSLC 79 " --> pdb=" O GLYLC 75 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALALC 80 " --> pdb=" O HISLC 76 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 29 through 45 removed outlier: 3.601A pdb=" N LEULJ 33 " --> pdb=" O ASNLJ 29 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLULJ 35 " --> pdb=" O SERLJ 31 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALALJ 36 " --> pdb=" O VALLJ 32 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEULJ 39 " --> pdb=" O GLULJ 35 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARGLJ 41 " --> pdb=" O ILELJ 37 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARGLJ 45 " --> pdb=" O ARGLJ 41 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 102 through 119 removed outlier: 3.757A pdb=" N ARGLJ 107 " --> pdb=" O LYSLJ 103 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEULJ 110 " --> pdb=" O ARGLJ 106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEULJ 114 " --> pdb=" O LEULJ 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SERLJ 115 " --> pdb=" O ARGLJ 111 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYSLJ 117 " --> pdb=" O ALALJ 113 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 135 through 147 removed outlier: 3.855A pdb=" N PHELJ 139 " --> pdb=" O LYSLJ 135 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VALLJ 142 " --> pdb=" O GLULJ 138 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SERLJ 144 " --> pdb=" O LYSLJ 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEULJ 146 " --> pdb=" O VALLJ 142 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLULJ 147 " --> pdb=" O LEULJ 143 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 160 through 168 removed outlier: 3.602A pdb=" N GLULJ 164 " --> pdb=" O ASPLJ 160 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEULJ 165 " --> pdb=" O VALLJ 161 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALALJ 167 " --> pdb=" O VALLJ 163 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARGLJ 168 " --> pdb=" O GLULJ 164 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 182 through 190 removed outlier: 4.644A pdb=" N ILELJ 186 " --> pdb=" O ASNLJ 182 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THRLJ 187 " --> pdb=" O VALLJ 183 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASPLJ 190 " --> pdb=" O ILELJ 186 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 195 through 206 removed outlier: 3.513A pdb=" N ALALJ 199 " --> pdb=" O THRLJ 195 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYSLJ 200 " --> pdb=" O GLULJ 196 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYSLJ 201 " --> pdb=" O ALALJ 197 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLULJ 203 " --> pdb=" O ALALJ 199 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLULJ 204 " --> pdb=" O LYSLJ 200 " (cutoff:3.500A) Processing helix chain 'LK' and resid 2 through 21 removed outlier: 4.701A pdb=" N VALLK 12 " --> pdb=" O PHELK 8 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N THRLK 13 " --> pdb=" O ASNLK 9 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLULK 14 " --> pdb=" O THRLK 10 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASNLK 15 " --> pdb=" O GLULK 11 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N METLK 17 " --> pdb=" O THRLK 13 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASNLK 21 " --> pdb=" O METLK 17 " (cutoff:3.500A) Processing helix chain 'LK' and resid 45 through 59 removed outlier: 4.319A pdb=" N VALLK 49 " --> pdb=" O GLNLK 45 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASPLK 51 " --> pdb=" O SERLK 47 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASNLK 52 " --> pdb=" O LYSLK 48 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALALK 53 " --> pdb=" O VALLK 49 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VALLK 54 " --> pdb=" O LEULK 50 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLULK 55 " --> pdb=" O ASPLK 51 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEULK 57 " --> pdb=" O ALALK 53 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEULK 59 " --> pdb=" O GLULK 55 " (cutoff:3.500A) Processing helix chain 'LK' and resid 89 through 99 removed outlier: 4.155A pdb=" N GLULK 94 " --> pdb=" O THRLK 90 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N METLK 96 " --> pdb=" O ARGLK 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYRLK 97 " --> pdb=" O GLYLK 93 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHELK 99 " --> pdb=" O ARGLK 95 " (cutoff:3.500A) Processing helix chain 'LK' and resid 154 through 163 removed outlier: 3.642A pdb=" N THRLK 162 " --> pdb=" O THRLK 158 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASPLK 163 " --> pdb=" O THRLK 159 " (cutoff:3.500A) Processing helix chain 'LK' and resid 100 through 105 removed outlier: 4.243A pdb=" N LEULK 103 " --> pdb=" O LEULK 100 " (cutoff:3.500A) Processing helix chain 'LL' and resid 58 through 82 removed outlier: 4.256A pdb=" N THRLL 63 " --> pdb=" O LYSLL 59 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASNLL 64 " --> pdb=" O GLULL 60 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLYLL 66 " --> pdb=" O ARGLL 62 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THRLL 67 " --> pdb=" O THRLL 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THRLL 68 " --> pdb=" O ASNLL 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALALL 70 " --> pdb=" O GLYLL 66 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEULL 71 " --> pdb=" O THRLL 67 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VALLL 76 " --> pdb=" O LEULL 72 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLNLL 77 " --> pdb=" O ASNLL 73 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLYLL 78 " --> pdb=" O ASNLL 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VALLL 79 " --> pdb=" O METLL 75 " (cutoff:3.500A) Processing helix chain 'LL' and resid 137 through 153 removed outlier: 3.810A pdb=" N ALALL 143 " --> pdb=" O GLULL 139 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEULL 144 " --> pdb=" O GLNLL 140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALALL 145 " --> pdb=" O VALLL 141 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARGLL 149 " --> pdb=" O ALALL 145 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VALLL 151 " --> pdb=" O ASNLL 147 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ARGLL 152 " --> pdb=" O ILELL 148 " (cutoff:3.500A) Proline residue: LL 153 - end of helix Processing helix chain 'LM' and resid 25 through 39 removed outlier: 5.642A pdb=" N LEULM 29 " --> pdb=" O THRLM 25 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLULM 32 " --> pdb=" O ARGLM 28 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALALM 34 " --> pdb=" O SERLM 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SERLM 35 " --> pdb=" O SERLM 31 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLYLM 39 " --> pdb=" O SERLM 35 " (cutoff:3.500A) Processing helix chain 'LM' and resid 68 through 73 removed outlier: 4.146A pdb=" N ASPLM 72 " --> pdb=" O ASNLM 68 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYSLM 73 " --> pdb=" O LYSLM 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 68 through 73' Processing helix chain 'LM' and resid 97 through 111 removed outlier: 4.105A pdb=" N LEULM 101 " --> pdb=" O ASNLM 97 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILELM 102 " --> pdb=" O PROLM 98 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SERLM 105 " --> pdb=" O LEULM 101 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYSLM 107 " --> pdb=" O GLULM 103 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N METLM 109 " --> pdb=" O SERLM 105 " (cutoff:3.500A) Proline residue: LM 111 - end of helix Processing helix chain 'LM' and resid 113 through 123 removed outlier: 4.458A pdb=" N LYSLM 118 " --> pdb=" O ARGLM 114 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYSLM 121 " --> pdb=" O GLULM 117 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYSLM 122 " --> pdb=" O LYSLM 118 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEULM 123 " --> pdb=" O GLNLM 119 " (cutoff:3.500A) Processing helix chain 'LN' and resid 111 through 118 removed outlier: 3.768A pdb=" N VALLN 115 " --> pdb=" O PHELN 111 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SERLN 116 " --> pdb=" O METLN 112 " (cutoff:3.500A) Processing helix chain 'LN' and resid 103 through 109 removed outlier: 3.965A pdb=" N LEULN 106 " --> pdb=" O ALALN 103 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARGLN 107 " --> pdb=" O ARGLN 104 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLULN 108 " --> pdb=" O GLULN 105 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLYLN 109 " --> pdb=" O LEULN 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 103 through 109' Processing helix chain 'LO' and resid 56 through 62 removed outlier: 4.104A pdb=" N ARGLO 60 " --> pdb=" O PROLO 56 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEULO 61 " --> pdb=" O LEULO 57 " (cutoff:3.500A) Proline residue: LO 62 - end of helix No H-bonds generated for 'chain 'LO' and resid 56 through 62' Processing helix chain 'LO' and resid 78 through 83 removed outlier: 4.981A pdb=" N LEULO 82 " --> pdb=" O ASNLO 78 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASNLO 83 " --> pdb=" O LEULO 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'LO' and resid 78 through 83' Processing helix chain 'LO' and resid 92 through 100 removed outlier: 4.438A pdb=" N VALLO 97 " --> pdb=" O PROLO 93 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLULO 98 " --> pdb=" O ALALO 94 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLYLO 100 " --> pdb=" O LEULO 96 " (cutoff:3.500A) Processing helix chain 'LO' and resid 129 through 140 removed outlier: 3.542A pdb=" N GLULO 134 " --> pdb=" O ALALO 130 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASPLO 137 " --> pdb=" O ALALO 133 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYSLO 139 " --> pdb=" O ALALO 135 " (cutoff:3.500A) Processing helix chain 'LP' and resid 43 through 59 removed outlier: 6.005A pdb=" N ILELP 47 " --> pdb=" O THRLP 43 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLULP 48 " --> pdb=" O SERLP 44 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARGLP 51 " --> pdb=" O ILELP 47 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALALP 53 " --> pdb=" O SERLP 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N METLP 54 " --> pdb=" O ALALP 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARGLP 56 " --> pdb=" O ILELP 52 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYRLP 57 " --> pdb=" O ALALP 53 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N METLP 58 " --> pdb=" O METLP 54 " (cutoff:3.500A) Processing helix chain 'LP' and resid 110 through 126 removed outlier: 3.598A pdb=" N ALALP 114 " --> pdb=" O SERLP 110 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLULP 116 " --> pdb=" O GLULP 112 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGLP 119 " --> pdb=" O ARGLP 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HISLP 123 " --> pdb=" O ARGLP 119 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYSLP 124 " --> pdb=" O LEULP 120 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEULP 125 " --> pdb=" O ALALP 121 " (cutoff:3.500A) Proline residue: LP 126 - end of helix Processing helix chain 'LQ' and resid 9 through 28 removed outlier: 3.965A pdb=" N LYSLQ 14 " --> pdb=" O SERLQ 10 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEULQ 17 " --> pdb=" O ARGLQ 13 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASPLQ 19 " --> pdb=" O ALALQ 15 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALALQ 21 " --> pdb=" O LEULQ 17 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THRLQ 22 " --> pdb=" O ARGLQ 18 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SERLQ 23 " --> pdb=" O ASPLQ 19 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SERLQ 27 " --> pdb=" O SERLQ 23 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 34 through 54 removed outlier: 4.161A pdb=" N GLULQ 39 " --> pdb=" O ALALQ 35 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SERLQ 42 " --> pdb=" O LYSLQ 38 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VALLQ 43 " --> pdb=" O GLULQ 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VALLQ 44 " --> pdb=" O VALLQ 40 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLULQ 45 " --> pdb=" O ARGLQ 41 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYSLQ 46 " --> pdb=" O SERLQ 42 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THRLQ 49 " --> pdb=" O GLULQ 45 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEULQ 50 " --> pdb=" O LYSLQ 46 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLYLQ 51 " --> pdb=" O LEULQ 47 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYSLQ 52 " --> pdb=" O ILELQ 48 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 55 through 66 removed outlier: 3.957A pdb=" N ASNLQ 61 " --> pdb=" O ALALQ 57 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THRLQ 65 " --> pdb=" O ASNLQ 61 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 80 through 94 removed outlier: 5.901A pdb=" N LYSLQ 84 " --> pdb=" O THRLQ 80 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEULQ 85 " --> pdb=" O ALALQ 81 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHELQ 86 " --> pdb=" O LEULQ 82 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLYLQ 87 " --> pdb=" O GLNLQ 83 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILELQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ALALQ 90 " --> pdb=" O PHELQ 86 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLULQ 91 " --> pdb=" O GLYLQ 87 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARGLQ 92 " --> pdb=" O GLULQ 88 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THRLQ 94 " --> pdb=" O ALALQ 90 " (cutoff:3.500A) Processing helix chain 'LR' and resid 6 through 22 removed outlier: 4.123A pdb=" N VALLR 10 " --> pdb=" O ASPLR 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARGLR 14 " --> pdb=" O VALLR 10 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N HISLR 15 " --> pdb=" O ARGLR 11 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALALR 16 " --> pdb=" O LEULR 12 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARGLR 17 " --> pdb=" O LYSLR 13 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASNLR 21 " --> pdb=" O ARGLR 17 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEULR 22 " --> pdb=" O VALLR 18 " (cutoff:3.500A) Processing helix chain 'LR' and resid 70 through 80 removed outlier: 4.132A pdb=" N THRLR 74 " --> pdb=" O VALLR 70 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VALLR 76 " --> pdb=" O LEULR 72 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLYLR 77 " --> pdb=" O ALALR 73 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILELR 80 " --> pdb=" O VALLR 76 " (cutoff:3.500A) Processing helix chain 'LR' and resid 101 through 112 removed outlier: 3.822A pdb=" N VALLR 105 " --> pdb=" O TYRLR 101 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALALR 107 " --> pdb=" O GLYLR 103 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEULR 108 " --> pdb=" O ARGLR 104 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALALR 109 " --> pdb=" O VALLR 105 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLULR 110 " --> pdb=" O LYSLR 106 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALALR 111 " --> pdb=" O ALALR 107 " (cutoff:3.500A) Processing helix chain 'L1' and resid 4 through 16 removed outlier: 5.559A pdb=" N GLUL1 8 " --> pdb=" O HISL1 4 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALAL1 9 " --> pdb=" O LYSL1 5 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VALL1 10 " --> pdb=" O LEUL1 6 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SERL1 13 " --> pdb=" O ALAL1 9 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLNL1 14 " --> pdb=" O VALL1 10 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARGL1 16 " --> pdb=" O LYSL1 12 " (cutoff:3.500A) Processing helix chain 'L3' and resid 8 through 22 removed outlier: 4.461A pdb=" N ALAL3 12 " --> pdb=" O THRL3 8 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARGL3 13 " --> pdb=" O VALL3 9 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYSL3 15 " --> pdb=" O ARGL3 11 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYSL3 16 " --> pdb=" O ALAL3 12 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THRL3 17 " --> pdb=" O ARGL3 13 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYSL3 19 " --> pdb=" O LYSL3 15 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEUL3 20 " --> pdb=" O LYSL3 16 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYSL3 22 " --> pdb=" O ILEL3 18 " (cutoff:3.500A) Processing helix chain 'L3' and resid 32 through 37 removed outlier: 4.719A pdb=" N GLNL3 37 " --> pdb=" O LYSL3 33 " (cutoff:3.500A) Processing helix chain 'L3' and resid 43 through 56 removed outlier: 3.578A pdb=" N ARGL3 48 " --> pdb=" O GLNL3 44 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARGL3 50 " --> pdb=" O ALAL3 46 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARGL3 51 " --> pdb=" O PHEL3 47 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLNL3 52 " --> pdb=" O ARGL3 48 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYSL3 54 " --> pdb=" O ARGL3 50 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARGL3 55 " --> pdb=" O ARGL3 51 " (cutoff:3.500A) Processing helix chain 'L3' and resid 59 through 73 removed outlier: 3.908A pdb=" N THRL3 63 " --> pdb=" O LYSL3 59 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALAL3 68 " --> pdb=" O ARGL3 64 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARGL3 70 " --> pdb=" O ASNL3 66 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLNL3 71 " --> pdb=" O ALAL3 67 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HISL3 72 " --> pdb=" O ALAL3 68 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLUL3 73 " --> pdb=" O ALAL3 69 " (cutoff:3.500A) Processing helix chain 'L3' and resid 75 through 87 removed outlier: 3.717A pdb=" N ASNL3 81 " --> pdb=" O SERL3 77 " (cutoff:3.500A) Processing helix chain 'L3' and resid 91 through 102 removed outlier: 4.044A pdb=" N LEUL3 95 " --> pdb=" O ASNL3 91 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SERL3 101 " --> pdb=" O GLUL3 97 " (cutoff:3.500A) Processing helix chain 'L3' and resid 103 through 116 removed outlier: 3.968A pdb=" N GLNL3 108 " --> pdb=" O LYSL3 104 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THRL3 111 " --> pdb=" O ALAL3 107 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALAL3 113 " --> pdb=" O LEUL3 109 " (cutoff:3.500A) Processing helix chain 'L5' and resid 15 through 25 removed outlier: 4.227A pdb=" N LEUL5 19 " --> pdb=" O ARGL5 15 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VALL5 20 " --> pdb=" O LYSL5 16 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEUL5 23 " --> pdb=" O LEUL5 19 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILEL5 24 " --> pdb=" O VALL5 20 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARGL5 25 " --> pdb=" O LEUL5 21 " (cutoff:3.500A) Processing helix chain 'L5' and resid 29 through 40 removed outlier: 4.152A pdb=" N ILEL5 33 " --> pdb=" O ALAL5 29 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALAL5 34 " --> pdb=" O ALAL5 30 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEUL5 36 " --> pdb=" O ALAL5 32 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THRL5 39 " --> pdb=" O ILEL5 35 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASNL5 40 " --> pdb=" O LEUL5 36 " (cutoff:3.500A) Processing helix chain 'L5' and resid 43 through 61 removed outlier: 3.800A pdb=" N GLUL5 48 " --> pdb=" O SERL5 44 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASNL5 57 " --> pdb=" O SERL5 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLUL5 59 " --> pdb=" O LEUL5 55 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HISL5 60 " --> pdb=" O ALAL5 56 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASNL5 61 " --> pdb=" O ASNL5 57 " (cutoff:3.500A) Processing helix chain 'L6' and resid 2 through 7 removed outlier: 5.863A pdb=" N ILEL6 6 " --> pdb=" O GLUL6 2 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEUL6 7 " --> pdb=" O ALAL6 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L6' and resid 2 through 7' Processing helix chain 'L6' and resid 13 through 23 removed outlier: 3.557A pdb=" N GLUL6 18 " --> pdb=" O GLUL6 14 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALAL6 19 " --> pdb=" O LYSL6 15 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALAL6 21 " --> pdb=" O SERL6 17 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLUL6 22 " --> pdb=" O GLUL6 18 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASPL6 23 " --> pdb=" O ALAL6 19 " (cutoff:3.500A) Processing helix chain 'L6' and resid 34 through 46 removed outlier: 3.619A pdb=" N VALL6 38 " --> pdb=" O ASNL6 34 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYSL6 39 " --> pdb=" O LYSL6 35 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALAL6 41 " --> pdb=" O GLNL6 37 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLUL6 44 " --> pdb=" O METL6 40 " (cutoff:3.500A) Processing helix chain 'L7' and resid 64 through 69 removed outlier: 4.679A pdb=" N VALL7 68 " --> pdb=" O HISL7 64 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLNL7 69 " --> pdb=" O VALL7 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'L7' and resid 64 through 69' Processing helix chain 'L8' and resid 17 through 25 removed outlier: 4.015A pdb=" N LEUL8 21 " --> pdb=" O ASPL8 17 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SERL8 24 " --> pdb=" O GLNL8 20 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLYL8 25 " --> pdb=" O LEUL8 21 " (cutoff:3.500A) Processing helix chain 'L8' and resid 44 through 55 removed outlier: 4.445A pdb=" N PHEL8 48 " --> pdb=" O ASPL8 44 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILEL8 49 " --> pdb=" O GLUL8 45 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYSL8 50 " --> pdb=" O VALL8 46 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VALL8 51 " --> pdb=" O GLUL8 47 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILEL8 52 " --> pdb=" O PHEL8 48 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARGL8 53 " --> pdb=" O ILEL8 49 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLUL8 54 " --> pdb=" O LYSL8 50 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VALL8 55 " --> pdb=" O VALL8 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'L8' and resid 44 through 55' Processing helix chain 'LB' and resid 13 through 33 removed outlier: 5.064A pdb=" N GLNLB 17 " --> pdb=" O GLULB 13 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYSLB 19 " --> pdb=" O GLULB 15 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SERLB 20 " --> pdb=" O GLULB 16 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEULB 28 " --> pdb=" O GLULB 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHELB 30 " --> pdb=" O PHELB 26 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLNLB 31 " --> pdb=" O ASNLB 27 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALALB 33 " --> pdb=" O ARGLB 29 " (cutoff:3.500A) Processing helix chain 'LB' and resid 38 through 65 removed outlier: 3.692A pdb=" N ARGLB 42 " --> pdb=" O GLULB 38 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILELB 43 " --> pdb=" O GLULB 39 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARGLB 44 " --> pdb=" O THRLB 40 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N THRLB 45 " --> pdb=" O ALALB 41 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VALLB 46 " --> pdb=" O ARGLB 42 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARGLB 47 " --> pdb=" O ILELB 43 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THRLB 49 " --> pdb=" O THRLB 45 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALALB 51 " --> pdb=" O ARGLB 47 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYSLB 54 " --> pdb=" O ILELB 50 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLULB 59 " --> pdb=" O THRLB 55 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARGLB 60 " --> pdb=" O VALLB 56 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLULB 61 " --> pdb=" O ALALB 57 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILELB 62 " --> pdb=" O ARGLB 58 " (cutoff:3.500A) Processing helix chain 'LD' and resid 16 through 27 removed outlier: 4.411A pdb=" N GLULD 24 " --> pdb=" O ARGLD 20 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALALD 25 " --> pdb=" O LYSLD 21 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEULD 26 " --> pdb=" O THRLD 22 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLYLD 27 " --> pdb=" O VALLD 23 " (cutoff:3.500A) Processing helix chain 'LD' and resid 40 through 51 removed outlier: 3.752A pdb=" N GLYLD 45 " --> pdb=" O PROLD 41 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLNLD 46 " --> pdb=" O ALALD 42 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASNLD 48 " --> pdb=" O ARGLD 44 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYSLD 49 " --> pdb=" O GLYLD 45 " (cutoff:3.500A) Processing helix chain 'LE' and resid 9 through 19 removed outlier: 4.519A pdb=" N ASNLE 14 " --> pdb=" O LYSLE 10 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARGLE 16 " --> pdb=" O ARGLE 12 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THRLE 18 " --> pdb=" O ASNLE 14 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N HISLE 19 " --> pdb=" O LYSLE 15 " (cutoff:3.500A) Processing helix chain 'LG' and resid 9 through 17 removed outlier: 3.586A pdb=" N SERLG 14 " --> pdb=" O LYSLG 10 " (cutoff:3.500A) Processing helix chain 'LG' and resid 18 through 25 removed outlier: 3.786A pdb=" N METLG 23 " --> pdb=" O PHELG 19 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SERLG 24 " --> pdb=" O ARGLG 20 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THRLG 25 " --> pdb=" O LYSLG 21 " (cutoff:3.500A) Processing helix chain 'LG' and resid 26 through 39 removed outlier: 3.765A pdb=" N LEULG 32 " --> pdb=" O GLYLG 28 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARGLG 34 " --> pdb=" O LYSLG 30 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARGLG 35 " --> pdb=" O VALLG 31 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYSLG 38 " --> pdb=" O ARGLG 34 " (cutoff:3.500A) Processing helix chain 'LH' and resid 9 through 14 removed outlier: 5.047A pdb=" N ARGLH 13 " --> pdb=" O GLYLH 9 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VALLH 14 " --> pdb=" O ALALH 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'LH' and resid 9 through 14' Processing helix chain 'LH' and resid 34 through 41 removed outlier: 4.071A pdb=" N GLNLH 40 " --> pdb=" O LYSLH 36 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYSLH 41 " --> pdb=" O SERLH 37 " (cutoff:3.500A) Processing helix chain 'LH' and resid 49 through 58 removed outlier: 3.720A pdb=" N SERLH 53 " --> pdb=" O LEULH 49 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N METLH 55 " --> pdb=" O SERLH 51 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYSLH 56 " --> pdb=" O LYSLH 52 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ARGLH 57 " --> pdb=" O SERLH 53 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VALLH 58 " --> pdb=" O ASPLH 54 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'SB' and resid 52 through 58 removed outlier: 7.402A pdb=" N HISSB 53 " --> pdb=" O HISSB 68 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HISSB 68 " --> pdb=" O HISSB 53 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N HISSB 99 " --> pdb=" O ILESB 63 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILESB 65 " --> pdb=" O HISSB 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASNSB 101 " --> pdb=" O ILESB 65 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THRSB 69 " --> pdb=" O ILESB 103 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'SB' and resid 164 through 170 removed outlier: 4.167A pdb=" N VALSB 152 " --> pdb=" O GLUSB 165 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THRSB 150 " --> pdb=" O TYRSB 167 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILESB 148 " --> pdb=" O GLUSB 169 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLYSB 147 " --> pdb=" O TYRSB 202 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLYSB 196 " --> pdb=" O SERSB 153 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEUSB 195 " --> pdb=" O ALASB 188 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VALSB 199 " --> pdb=" O ALASB 184 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'SD' and resid 11 through 15 Processing sheet with id= 4, first strand: chain 'SD' and resid 84 through 88 removed outlier: 3.557A pdb=" N ILESD 85 " --> pdb=" O METSD 96 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLYSD 87 " --> pdb=" O VALSD 94 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALASD 99 " --> pdb=" O ASPSD 122 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASPSD 122 " --> pdb=" O ALASD 99 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'SD' and resid 33 through 41 removed outlier: 5.760A pdb=" N ARGSD 45 " --> pdb=" O ASPSD 41 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'SE' and resid 58 through 67 removed outlier: 3.843A pdb=" N SERSE 67 " --> pdb=" O ARGSE 2 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ARGSE 88 " --> pdb=" O ILESE 9 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'SG' and resid 73 through 79 removed outlier: 3.594A pdb=" N LYSSG 76 " --> pdb=" O VALSG 87 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VALSG 87 " --> pdb=" O LYSSG 76 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARGSG 78 " --> pdb=" O TYRSG 85 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYRSG 85 " --> pdb=" O ARGSG 78 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'SF' and resid 23 through 27 removed outlier: 6.666A pdb=" N GLUSF 23 " --> pdb=" O LEUSF 64 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEUSF 64 " --> pdb=" O GLUSF 23 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEUSF 25 " --> pdb=" O LEUSF 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEUSF 62 " --> pdb=" O LEUSF 25 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEUSF 60 " --> pdb=" O LEUSF 27 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'SF' and resid 77 through 80 removed outlier: 7.331A pdb=" N ILESF 128 " --> pdb=" O ILESF 80 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEUSF 105 " --> pdb=" O ILESF 128 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TYRSF 130 " --> pdb=" O ILESF 103 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILESF 103 " --> pdb=" O TYRSF 130 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'SH' and resid 8 through 13 removed outlier: 5.173A pdb=" N TYRSH 8 " --> pdb=" O LEUSH 23 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEUSH 23 " --> pdb=" O TYRSH 8 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLYSH 10 " --> pdb=" O VALSH 21 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARGSH 22 " --> pdb=" O LEUSH 66 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEUSH 66 " --> pdb=" O ARGSH 22 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'S1' and resid 6 through 13 removed outlier: 6.333A pdb=" N ILES1 76 " --> pdb=" O ILES1 6 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEUS1 10 " --> pdb=" O ARGS1 72 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYSS1 71 " --> pdb=" O LEUS1 42 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'S1' and resid 44 through 52 Processing sheet with id= 13, first strand: chain 'S2' and resid 30 through 35 removed outlier: 4.663A pdb=" N GLUS2 83 " --> pdb=" O GLYS2 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SERS2 25 " --> pdb=" O LYSS2 87 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALAS2 109 " --> pdb=" O VALS2 82 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VALS2 84 " --> pdb=" O ALAS2 109 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'S3' and resid 26 through 29 removed outlier: 4.334A pdb=" N GLYS3 27 " --> pdb=" O THRS3 36 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THRS3 36 " --> pdb=" O GLYS3 27 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYSS3 34 " --> pdb=" O ASNS3 29 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'S3' and resid 43 through 46 removed outlier: 4.602A pdb=" N LEUS3 94 " --> pdb=" O VALS3 111 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'S3' and resid 65 through 69 removed outlier: 3.756A pdb=" N ALAS3 78 " --> pdb=" O ALAS3 66 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VALS3 68 " --> pdb=" O ILES3 76 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'S7' and resid 38 through 41 No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'S8' and resid 9 through 12 removed outlier: 3.536A pdb=" N TYRS8 10 " --> pdb=" O ILES8 63 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLYS8 12 " --> pdb=" O VALS8 61 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'S8' and resid 22 through 32 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'L2' and resid 33 through 36 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'L2' and resid 76 through 79 removed outlier: 7.001A pdb=" N LEUL2 93 " --> pdb=" O ASPL2 79 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SERL2 80 " --> pdb=" O LEUL2 93 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'L2' and resid 162 through 165 removed outlier: 6.813A pdb=" N LEUL2 173 " --> pdb=" O LEUL2 165 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYSL2 170 " --> pdb=" O SERL2 186 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILEL2 184 " --> pdb=" O VALL2 172 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLUL2 180 " --> pdb=" O LEUL2 176 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L2' and resid 91 through 96 removed outlier: 4.127A pdb=" N GLUL2 100 " --> pdb=" O TYRL2 96 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LC' and resid 4 through 8 Processing sheet with id= 25, first strand: chain 'LC' and resid 11 through 18 removed outlier: 4.076A pdb=" N GLYLC 11 " --> pdb=" O VALLC 27 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLULC 21 " --> pdb=" O GLYLC 17 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VALLC 194 " --> pdb=" O ASPLC 189 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLNLC 187 " --> pdb=" O LEULC 196 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LC' and resid 48 through 53 removed outlier: 5.556A pdb=" N PHELC 87 " --> pdb=" O PHELC 53 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LJ' and resid 122 through 125 removed outlier: 5.122A pdb=" N LEULJ 192 " --> pdb=" O GLYLJ 122 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SERLJ 191 " --> pdb=" O LYSLJ 151 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THRLJ 156 " --> pdb=" O THRLJ 176 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LK' and resid 81 through 88 removed outlier: 6.189A pdb=" N GLULK 81 " --> pdb=" O VALLK 40 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VALLK 40 " --> pdb=" O GLULK 81 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N METLK 83 " --> pdb=" O METLK 38 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N METLK 38 " --> pdb=" O METLK 83 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYSLK 33 " --> pdb=" O VALLK 149 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VALLK 149 " --> pdb=" O LYSLK 33 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VALLK 35 " --> pdb=" O SERLK 147 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLYLK 39 " --> pdb=" O TYRLK 143 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYRLK 143 " --> pdb=" O GLYLK 39 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LL' and resid 15 through 19 No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain 'LL' and resid 42 through 45 removed outlier: 4.185A pdb=" N THRLL 42 " --> pdb=" O VALLL 53 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LL' and resid 84 through 88 removed outlier: 4.607A pdb=" N LYSLL 85 " --> pdb=" O VALLL 133 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SERLL 124 " --> pdb=" O LYSLL 132 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LL' and resid 94 through 98 removed outlier: 3.929A pdb=" N ARGLL 95 " --> pdb=" O ASNLL 106 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASNLL 106 " --> pdb=" O ARGLL 95 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILELL 104 " --> pdb=" O GLNLL 97 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEULL 103 " --> pdb=" O ILELL 115 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILELL 115 " --> pdb=" O LEULL 103 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LM' and resid 15 through 20 removed outlier: 3.548A pdb=" N TYRLM 17 " --> pdb=" O TYRLM 54 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LM' and resid 76 through 79 removed outlier: 4.221A pdb=" N ARGLM 77 " --> pdb=" O LYSLM 86 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLYLM 84 " --> pdb=" O SERLM 79 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LN' and resid 17 through 22 removed outlier: 5.903A pdb=" N ARGLN 17 " --> pdb=" O VALLN 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THRLN 21 " --> pdb=" O THRLN 6 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THRLN 6 " --> pdb=" O THRLN 21 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LN' and resid 38 through 42 Processing sheet with id= 37, first strand: chain 'LN' and resid 66 through 71 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'LP' and resid 63 through 67 removed outlier: 4.142A pdb=" N GLULP 105 " --> pdb=" O TRPLP 65 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEULP 103 " --> pdb=" O LYSLP 67 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYSLP 128 " --> pdb=" O THRLP 37 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LQ' and resid 29 through 33 removed outlier: 3.625A pdb=" N ILELQ 30 " --> pdb=" O ILELQ 119 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SERLQ 116 " --> pdb=" O GLNLQ 106 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LR' and resid 54 through 58 removed outlier: 4.168A pdb=" N ALALR 54 " --> pdb=" O ILELR 44 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILELR 44 " --> pdb=" O ALALR 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALALR 42 " --> pdb=" O ALALR 56 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILELR 40 " --> pdb=" O SERLR 58 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLNLR 43 " --> pdb=" O ASNLR 32 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARGLR 30 " --> pdb=" O ILELR 45 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VALLR 33 " --> pdb=" O GLULR 91 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'L1' and resid 42 through 47 Processing sheet with id= 42, first strand: chain 'L1' and resid 51 through 54 removed outlier: 4.000A pdb=" N LYSL1 51 " --> pdb=" O THRL1 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHEL1 61 " --> pdb=" O PHEL1 76 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'L4' and resid 3 through 6 removed outlier: 4.214A pdb=" N ALAL4 3 " --> pdb=" O VALL4 14 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'L4' and resid 18 through 21 removed outlier: 3.990A pdb=" N GLNL4 18 " --> pdb=" O ILEL4 97 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'L4' and resid 31 through 34 removed outlier: 4.447A pdb=" N ASPL4 31 " --> pdb=" O VALL4 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VALL4 62 " --> pdb=" O ASPL4 31 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'L5' and resid 73 through 78 removed outlier: 4.192A pdb=" N GLUL5 73 " --> pdb=" O VALL5 106 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASNL5 77 " --> pdb=" O HISL5 102 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'L6' and resid 24 through 29 removed outlier: 3.941A pdb=" N ALAL6 78 " --> pdb=" O PHEL6 27 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARGL6 76 " --> pdb=" O VALL6 29 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARGL6 75 " --> pdb=" O TYRL6 58 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSL6 77 " --> pdb=" O METL6 56 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'L7' and resid 7 through 10 removed outlier: 4.921A pdb=" N ASPL7 7 " --> pdb=" O VALL7 23 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'L7' and resid 25 through 28 removed outlier: 4.238A pdb=" N ALAL7 25 " --> pdb=" O VALL7 34 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEUL7 27 " --> pdb=" O ARGL7 32 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARGL7 32 " --> pdb=" O LEUL7 27 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'L7' and resid 40 through 46 removed outlier: 4.095A pdb=" N THRL7 59 " --> pdb=" O METL7 41 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYSL7 43 " --> pdb=" O LEUL7 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEUL7 57 " --> pdb=" O LYSL7 43 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLNL7 45 " --> pdb=" O GLYL7 55 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'L8' and resid 38 through 43 removed outlier: 3.962A pdb=" N VALL8 39 " --> pdb=" O VALL8 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILEL8 89 " --> pdb=" O PROL8 28 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VALL8 30 " --> pdb=" O ILEL8 89 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYRL8 32 " --> pdb=" O PHEL8 91 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALAL8 93 " --> pdb=" O TYRL8 32 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASPL8 90 " --> pdb=" O ALAL8 75 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'L9' and resid 45 through 48 removed outlier: 6.196A pdb=" N GLNL9 48 " --> pdb=" O ASPL9 65 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASPL9 65 " --> pdb=" O GLNL9 48 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THRL9 66 " --> pdb=" O GLYL9 62 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLYL9 62 " --> pdb=" O THRL9 66 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ASNL9 58 " --> pdb=" O LYSL9 70 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'L9' and resid 53 through 56 removed outlier: 3.542A pdb=" N VALL9 87 " --> pdb=" O TYRL9 54 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VALL9 89 " --> pdb=" O GLYL9 56 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'LD' and resid 32 through 38 removed outlier: 4.292A pdb=" N SERLD 33 " --> pdb=" O LEULD 8 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEULD 8 " --> pdb=" O SERLD 33 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LEULD 53 " --> pdb=" O THRLD 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LS' and resid 2 through 7 removed outlier: 3.602A pdb=" N VALLS 5 " --> pdb=" O THRLS 19 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEULS 7 " --> pdb=" O TYRLS 17 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYRLS 17 " --> pdb=" O LEULS 7 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'LS' and resid 30 through 33 removed outlier: 5.310A pdb=" N ILELS 30 " --> pdb=" O GLULS 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LH' and resid 20 through 23 removed outlier: 5.644A pdb=" N GLYLH 20 " --> pdb=" O LYSLH 46 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYSLH 46 " --> pdb=" O GLYLH 20 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEULH 44 " --> pdb=" O LEULH 22 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'LI' and resid 1 through 4 removed outlier: 3.563A pdb=" N ARGLI 4 " --> pdb=" O ARGLI 35 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLNLI 34 " --> pdb=" O VALLI 25 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLNLI 36 " --> pdb=" O VALLI 23 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VALLI 23 " --> pdb=" O GLNLI 36 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYSLI 22 " --> pdb=" O ARGLI 19 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N METLI 24 " --> pdb=" O ILELI 17 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2122 hydrogen bonds 3626 hydrogen bond angles 0 basepair planarities 837 basepair parallelities 1902 stacking parallelities Total time for adding SS restraints: 170.73 Time building geometry restraints manager: 60.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 15577 1.32 - 1.45: 65257 1.45 - 1.57: 55805 1.57 - 1.70: 8943 1.70 - 1.83: 150 Bond restraints: 145732 Sorted by residual: bond pdb=" C GLYSC 37 " pdb=" N PROSC 38 " ideal model delta sigma weight residual 1.334 1.231 0.103 2.34e-02 1.83e+03 1.93e+01 bond pdb=" CA ILES1 40 " pdb=" C ILES1 40 " ideal model delta sigma weight residual 1.525 1.497 0.028 8.40e-03 1.42e+04 1.08e+01 bond pdb=" C LEULP 125 " pdb=" N PROLP 126 " ideal model delta sigma weight residual 1.334 1.263 0.071 2.34e-02 1.83e+03 9.23e+00 bond pdb=" N9 A B2025 " pdb=" C4 A B2025 " ideal model delta sigma weight residual 1.374 1.314 0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" CA TYRLJ 97 " pdb=" CB TYRLJ 97 " ideal model delta sigma weight residual 1.536 1.415 0.121 4.10e-02 5.95e+02 8.69e+00 ... (remaining 145727 not shown) Histogram of bond angle deviations from ideal: 79.22 - 90.95: 2 90.95 - 102.67: 7173 102.67 - 114.40: 112152 114.40 - 126.13: 85428 126.13 - 137.86: 14438 Bond angle restraints: 219193 Sorted by residual: angle pdb=" O3' G B 317 " pdb=" P A B 318 " pdb=" OP1 A B 318 " ideal model delta sigma weight residual 108.00 79.22 28.78 3.00e+00 1.11e-01 9.20e+01 angle pdb=" C ASPS4 8 " pdb=" N ILES4 9 " pdb=" CA ILES4 9 " ideal model delta sigma weight residual 120.43 126.58 -6.15 9.60e-01 1.09e+00 4.10e+01 angle pdb=" O3' G B 317 " pdb=" P A B 318 " pdb=" OP2 A B 318 " ideal model delta sigma weight residual 108.00 90.33 17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C GLYS4 94 " pdb=" N LEUS4 95 " pdb=" CA LEUS4 95 " ideal model delta sigma weight residual 122.83 129.03 -6.20 1.08e+00 8.57e-01 3.30e+01 angle pdb=" N LEUSH 100 " pdb=" CA LEUSH 100 " pdb=" C LEUSH 100 " ideal model delta sigma weight residual 114.56 107.49 7.07 1.27e+00 6.20e-01 3.10e+01 ... (remaining 219188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 72539 35.99 - 71.99: 4150 71.99 - 107.98: 378 107.98 - 143.98: 46 143.98 - 179.97: 65 Dihedral angle restraints: 77178 sinusoidal: 62559 harmonic: 14619 Sorted by residual: dihedral pdb=" O4' U A 971 " pdb=" C1' U A 971 " pdb=" N1 U A 971 " pdb=" C2 U A 971 " ideal model delta sinusoidal sigma weight residual 200.00 22.31 177.69 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 524 " pdb=" C1' U A 524 " pdb=" N1 U A 524 " pdb=" C2 U A 524 " ideal model delta sinusoidal sigma weight residual -160.00 15.04 -175.04 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A 903 " pdb=" C1' C A 903 " pdb=" N1 C A 903 " pdb=" C2 C A 903 " ideal model delta sinusoidal sigma weight residual 200.00 25.78 174.22 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 77175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.439: 28393 0.439 - 0.879: 1 0.879 - 1.318: 0 1.318 - 1.757: 0 1.757 - 2.197: 1 Chirality restraints: 28395 Sorted by residual: chirality pdb=" P A B 318 " pdb=" OP1 A B 318 " pdb=" OP2 A B 318 " pdb=" O5' A B 318 " both_signs ideal model delta sigma weight residual True 2.41 0.21 2.20 2.00e-01 2.50e+01 1.21e+02 chirality pdb=" C3' C B 716 " pdb=" C4' C B 716 " pdb=" O3' C B 716 " pdb=" C2' C B 716 " both_signs ideal model delta sigma weight residual False -2.48 -1.95 -0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" C3' A B2338 " pdb=" C4' A B2338 " pdb=" O3' A B2338 " pdb=" C2' A B2338 " both_signs ideal model delta sigma weight residual False -2.50 -2.10 -0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 28392 not shown) Planarity restraints: 11121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B2416 " 0.026 2.00e-02 2.50e+03 4.16e-02 5.18e+01 pdb=" N9 G B2416 " -0.017 2.00e-02 2.50e+03 pdb=" C8 G B2416 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B2416 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G B2416 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G B2416 " -0.086 2.00e-02 2.50e+03 pdb=" O6 G B2416 " 0.059 2.00e-02 2.50e+03 pdb=" N1 G B2416 " 0.031 2.00e-02 2.50e+03 pdb=" C2 G B2416 " -0.078 2.00e-02 2.50e+03 pdb=" N2 G B2416 " 0.042 2.00e-02 2.50e+03 pdb=" N3 G B2416 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G B2416 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B2442 " 0.011 2.00e-02 2.50e+03 3.32e-02 3.30e+01 pdb=" N9 G B2442 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G B2442 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G B2442 " 0.013 2.00e-02 2.50e+03 pdb=" C5 G B2442 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G B2442 " -0.028 2.00e-02 2.50e+03 pdb=" O6 G B2442 " 0.021 2.00e-02 2.50e+03 pdb=" N1 G B2442 " 0.013 2.00e-02 2.50e+03 pdb=" C2 G B2442 " -0.091 2.00e-02 2.50e+03 pdb=" N2 G B2442 " 0.051 2.00e-02 2.50e+03 pdb=" N3 G B2442 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G B2442 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B2310 " 0.014 2.00e-02 2.50e+03 3.71e-02 3.10e+01 pdb=" N1 C B2310 " -0.000 2.00e-02 2.50e+03 pdb=" C2 C B2310 " -0.089 2.00e-02 2.50e+03 pdb=" O2 C B2310 " 0.044 2.00e-02 2.50e+03 pdb=" N3 C B2310 " 0.021 2.00e-02 2.50e+03 pdb=" C4 C B2310 " -0.034 2.00e-02 2.50e+03 pdb=" N4 C B2310 " 0.024 2.00e-02 2.50e+03 pdb=" C5 C B2310 " 0.012 2.00e-02 2.50e+03 pdb=" C6 C B2310 " 0.008 2.00e-02 2.50e+03 ... (remaining 11118 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 2429 2.58 - 3.16: 97913 3.16 - 3.74: 261155 3.74 - 4.32: 322060 4.32 - 4.90: 452137 Nonbonded interactions: 1135694 Sorted by model distance: nonbonded pdb=" OP1 C B1801 " pdb="MG MG B3089 " model vdw 2.000 2.170 nonbonded pdb=" OP2 G B1803 " pdb="MG MG B3088 " model vdw 2.005 2.170 nonbonded pdb=" N7 A B1037 " pdb=" N1 G B1206 " model vdw 2.016 2.600 nonbonded pdb=" OP1 U B2101 " pdb="MG MG B3091 " model vdw 2.018 2.170 nonbonded pdb=" OP1 A B1997 " pdb="MG MG B3084 " model vdw 2.023 2.170 ... (remaining 1135689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and resid 1 through 75) selection = (chain 'E' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name O2' or name C1' or name N9 or name C8 or \ name N7 or name C5 or name C6 or name O6 or name N1 or name C2 or name N2 or nam \ e N3 or name C4 )) or resid 2 through 75)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 22.600 Check model and map are aligned: 1.410 Set scattering table: 0.850 Process input model: 414.770 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 448.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.010 0.121 145732 Z= 0.627 Angle : 1.213 28.782 219193 Z= 0.585 Chirality : 0.060 2.197 28395 Planarity : 0.007 0.090 11121 Dihedral : 18.302 179.972 67740 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 17.39 % Favored : 82.37 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.50 (0.09), residues: 5042 helix: -4.48 (0.07), residues: 1070 sheet: -3.13 (0.16), residues: 729 loop : -3.70 (0.09), residues: 3243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1307 time to evaluate : 5.389 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASPSE 95 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRPSF 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSS4 114 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLQ 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 31 outliers final: 14 residues processed: 1327 average time/residue: 1.2716 time to fit residues: 2874.6580 Evaluate side-chains 1012 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 998 time to evaluate : 4.875 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 14 outliers final: 8 residues processed: 14 average time/residue: 0.9234 time to fit residues: 28.9472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 792 optimal weight: 5.9990 chunk 711 optimal weight: 10.0000 chunk 394 optimal weight: 20.0000 chunk 243 optimal weight: 6.9990 chunk 480 optimal weight: 8.9990 chunk 380 optimal weight: 0.9990 chunk 735 optimal weight: 50.0000 chunk 284 optimal weight: 5.9990 chunk 447 optimal weight: 20.0000 chunk 547 optimal weight: 0.8980 chunk 852 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 3 GLN SB 64 ASN SC 70 ASN SD 43 ASN SD 54 GLN SE 27 ASN SG 28 ASN SG 40 GLN ** SF 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 62 ASN S2 40 ASN S2 101 GLN S3 6 GLN S3 73 ASN ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S9 25 HIS ** SI 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SA 69 ASN L2 11 ASN L2 15 ASN L2 163 GLN ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 47 ASN LC 70 ASN LC 143 HIS LC 148 HIS LJ 29 ASN LJ 40 GLN ** LJ 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 130 ASN ** LJ 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 9 ASN ** LK 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LM 8 ASN LM 11 ASN ** LM 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 136 GLN LN 3 GLN LN 4 GLN ** LN 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 54 GLN LO 126 HIS L1 31 HIS ** L3 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 52 GLN ** L3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L4 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L5 77 ASN ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L7 67 ASN L8 84 ASN L9 37 GLN LA 16 ASN LA 20 HIS LA 32 ASN ** LB 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 40 HIS LS 25 ASN LS 40 ASN LG 7 GLN LG 17 HIS LG 27 ASN LI 36 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 145732 Z= 0.209 Angle : 0.716 27.382 219193 Z= 0.364 Chirality : 0.040 2.057 28395 Planarity : 0.005 0.067 11121 Dihedral : 18.571 179.923 59425 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.87 % Favored : 87.09 % Rotamer Outliers : 4.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.09), residues: 5042 helix: -3.40 (0.11), residues: 1176 sheet: -2.73 (0.17), residues: 747 loop : -3.47 (0.09), residues: 3119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1133 time to evaluate : 5.553 Fit side-chains TARDY: cannot create tardy model for: "ASPSE 95 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TRPSF 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSS4 114 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLQ 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 147 outliers final: 90 residues processed: 1215 average time/residue: 1.2104 time to fit residues: 2565.1493 Evaluate side-chains 1118 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1028 time to evaluate : 5.352 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 90 outliers final: 8 residues processed: 90 average time/residue: 0.9841 time to fit residues: 178.4147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 473 optimal weight: 10.0000 chunk 264 optimal weight: 4.9990 chunk 709 optimal weight: 8.9990 chunk 580 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 854 optimal weight: 9.9990 chunk 922 optimal weight: 10.0000 chunk 760 optimal weight: 0.7980 chunk 847 optimal weight: 9.9990 chunk 291 optimal weight: 8.9990 chunk 685 optimal weight: 9.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 145 GLN SG 28 ASN ** SG 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 148 ASN ** SH 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 6 GLN S4 31 GLN ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S9 57 GLN ** SI 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2 143 ASN L2 163 GLN ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 143 HIS LJ 75 GLN ** LJ 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LM 11 ASN LR 37 ASN LR 48 ASN L3 52 GLN ** L3 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 88 HIS ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 31 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 145732 Z= 0.308 Angle : 0.761 27.296 219193 Z= 0.381 Chirality : 0.042 2.053 28395 Planarity : 0.005 0.071 11121 Dihedral : 18.562 179.820 59425 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.87 % Favored : 84.07 % Rotamer Outliers : 4.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.10), residues: 5042 helix: -2.84 (0.12), residues: 1176 sheet: -2.53 (0.17), residues: 786 loop : -3.36 (0.10), residues: 3080 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1070 time to evaluate : 5.505 Fit side-chains TARDY: cannot create tardy model for: "ASPSE 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRPSF 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSS4 114 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLQ 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 146 outliers final: 92 residues processed: 1156 average time/residue: 1.1715 time to fit residues: 2367.7648 Evaluate side-chains 1102 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1010 time to evaluate : 5.470 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 92 outliers final: 8 residues processed: 92 average time/residue: 0.9483 time to fit residues: 172.6834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 844 optimal weight: 30.0000 chunk 642 optimal weight: 10.0000 chunk 443 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 407 optimal weight: 10.0000 chunk 573 optimal weight: 20.0000 chunk 857 optimal weight: 6.9990 chunk 907 optimal weight: 8.9990 chunk 447 optimal weight: 20.0000 chunk 812 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SG 28 ASN SG 67 ASN ** SG 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 148 ASN ** SH 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 77 ASN ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 143 ASN ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 143 HIS ** LJ 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 11 ASN LM 136 GLN LO 27 ASN LP 123 HIS L3 52 GLN ** L3 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 88 HIS ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L7 45 GLN LB 31 GLN LG 7 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 145732 Z= 0.376 Angle : 0.808 27.299 219193 Z= 0.402 Chirality : 0.044 2.049 28395 Planarity : 0.006 0.091 11121 Dihedral : 18.640 179.812 59425 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.91 % Favored : 84.01 % Rotamer Outliers : 4.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.10), residues: 5042 helix: -2.63 (0.12), residues: 1163 sheet: -2.48 (0.17), residues: 794 loop : -3.32 (0.10), residues: 3085 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1040 time to evaluate : 5.570 Fit side-chains TARDY: cannot create tardy model for: "ASPSE 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRPSF 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSS4 114 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLQ 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 162 outliers final: 99 residues processed: 1135 average time/residue: 1.2010 time to fit residues: 2384.3433 Evaluate side-chains 1094 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 995 time to evaluate : 5.403 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 99 outliers final: 8 residues processed: 99 average time/residue: 0.9705 time to fit residues: 189.4147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 755 optimal weight: 5.9990 chunk 515 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 675 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 774 optimal weight: 4.9990 chunk 627 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 463 optimal weight: 40.0000 chunk 814 optimal weight: 0.0770 chunk 229 optimal weight: 10.0000 overall best weight: 5.8148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 125 ASN SG 28 ASN SG 67 ASN ** SG 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 148 ASN ** SH 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 6 GLN ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 76 GLN ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 61 GLN ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 143 HIS ** LJ 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 15 ASN LM 11 ASN L1 79 HIS L3 66 ASN ** L3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 40 ASN LH 7 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 145732 Z= 0.261 Angle : 0.712 27.188 219193 Z= 0.358 Chirality : 0.040 2.061 28395 Planarity : 0.005 0.070 11121 Dihedral : 18.453 179.991 59425 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 15.25 % Favored : 84.71 % Rotamer Outliers : 3.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.10), residues: 5042 helix: -2.33 (0.13), residues: 1169 sheet: -2.34 (0.17), residues: 803 loop : -3.25 (0.10), residues: 3070 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1076 time to evaluate : 5.439 Fit side-chains TARDY: cannot create tardy model for: "ASPSE 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRPSF 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSS4 114 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLQ 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 127 outliers final: 77 residues processed: 1145 average time/residue: 1.2000 time to fit residues: 2397.7861 Evaluate side-chains 1087 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1010 time to evaluate : 5.427 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 77 outliers final: 8 residues processed: 77 average time/residue: 0.9726 time to fit residues: 147.7388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 305 optimal weight: 3.9990 chunk 817 optimal weight: 0.6980 chunk 179 optimal weight: 40.0000 chunk 532 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 908 optimal weight: 6.9990 chunk 754 optimal weight: 10.0000 chunk 420 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 300 optimal weight: 5.9990 chunk 476 optimal weight: 10.0000 overall best weight: 5.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SG 28 ASN ** SG 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 142 HIS ** SH 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 15 ASN S2 101 GLN S3 6 GLN ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S9 57 GLN L2 11 ASN ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 143 HIS ** LJ 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 133 HIS LQ 83 GLN ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 32 ASN LS 40 ASN LG 7 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 145732 Z= 0.257 Angle : 0.705 27.191 219193 Z= 0.354 Chirality : 0.040 2.061 28395 Planarity : 0.005 0.065 11121 Dihedral : 18.372 180.000 59425 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.66 % Favored : 85.30 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.10), residues: 5042 helix: -2.10 (0.13), residues: 1161 sheet: -2.28 (0.18), residues: 790 loop : -3.18 (0.10), residues: 3091 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1057 time to evaluate : 5.576 Fit side-chains TARDY: cannot create tardy model for: "ASPSE 95 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TRPSF 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSS4 114 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLQ 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 129 outliers final: 82 residues processed: 1115 average time/residue: 1.2416 time to fit residues: 2410.0630 Evaluate side-chains 1081 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 999 time to evaluate : 5.423 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 82 outliers final: 8 residues processed: 82 average time/residue: 1.0384 time to fit residues: 165.9101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 875 optimal weight: 0.6980 chunk 102 optimal weight: 20.0000 chunk 517 optimal weight: 10.0000 chunk 663 optimal weight: 1.9990 chunk 514 optimal weight: 10.0000 chunk 764 optimal weight: 4.9990 chunk 507 optimal weight: 20.0000 chunk 905 optimal weight: 9.9990 chunk 566 optimal weight: 10.0000 chunk 551 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 overall best weight: 5.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SE 27 ASN SG 28 ASN ** SG 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 15 ASN ** S2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 6 GLN ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 11 ASN ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 143 HIS LJ 30 ASN ** LJ 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 111 HIS LM 133 HIS ** LR 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 145732 Z= 0.253 Angle : 0.699 27.177 219193 Z= 0.351 Chirality : 0.039 2.059 28395 Planarity : 0.005 0.066 11121 Dihedral : 18.316 179.665 59425 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 15.03 % Favored : 84.93 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.10), residues: 5042 helix: -1.97 (0.14), residues: 1166 sheet: -2.11 (0.18), residues: 778 loop : -3.17 (0.10), residues: 3098 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1049 time to evaluate : 5.544 Fit side-chains TARDY: cannot create tardy model for: "ASPSE 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRPSF 132 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSS4 114 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLQ 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 91 outliers final: 60 residues processed: 1087 average time/residue: 1.2055 time to fit residues: 2287.0214 Evaluate side-chains 1068 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1008 time to evaluate : 5.413 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 60 outliers final: 8 residues processed: 60 average time/residue: 1.0309 time to fit residues: 121.8475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 559 optimal weight: 40.0000 chunk 361 optimal weight: 10.0000 chunk 540 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 177 optimal weight: 50.0000 chunk 175 optimal weight: 5.9990 chunk 575 optimal weight: 10.0000 chunk 616 optimal weight: 10.0000 chunk 447 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 711 optimal weight: 20.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SG 28 ASN ** SG 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 83 HIS ** S2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 6 GLN ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 42 HIS S6 76 GLN ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 11 ASN L2 142 HIS ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 143 HIS ** LJ 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 111 HIS LM 133 HIS ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 20 ASN LE 32 ASN LG 7 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.100 145732 Z= 0.389 Angle : 0.800 27.189 219193 Z= 0.394 Chirality : 0.043 2.053 28395 Planarity : 0.006 0.066 11121 Dihedral : 18.406 179.986 59425 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 16.56 % Favored : 83.40 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.10), residues: 5042 helix: -2.04 (0.13), residues: 1179 sheet: -2.23 (0.18), residues: 780 loop : -3.26 (0.10), residues: 3083 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1011 time to evaluate : 5.473 Fit side-chains TARDY: cannot create tardy model for: "ASPSE 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRPSF 132 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSS4 114 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VALLQ 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 105 outliers final: 69 residues processed: 1059 average time/residue: 1.1553 time to fit residues: 2125.9265 Evaluate side-chains 1052 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 983 time to evaluate : 5.481 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 69 outliers final: 8 residues processed: 69 average time/residue: 1.0065 time to fit residues: 134.8847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 823 optimal weight: 7.9990 chunk 867 optimal weight: 5.9990 chunk 791 optimal weight: 9.9990 chunk 843 optimal weight: 30.0000 chunk 866 optimal weight: 4.9990 chunk 507 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 662 optimal weight: 5.9990 chunk 258 optimal weight: 8.9990 chunk 762 optimal weight: 5.9990 chunk 797 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SG 28 ASN ** SG 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 77 GLN ** S2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 6 GLN ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S9 57 GLN ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 143 HIS ** LJ 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 111 HIS LM 133 HIS ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 145732 Z= 0.250 Angle : 0.703 27.175 219193 Z= 0.352 Chirality : 0.039 2.058 28395 Planarity : 0.005 0.060 11121 Dihedral : 18.308 179.725 59425 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.48 % Favored : 85.48 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.11), residues: 5042 helix: -1.87 (0.14), residues: 1166 sheet: -2.15 (0.18), residues: 797 loop : -3.16 (0.10), residues: 3079 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1050 time to evaluate : 5.501 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASPSE 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TRPSF 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSS4 114 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLQ 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 61 outliers final: 38 residues processed: 1076 average time/residue: 1.1945 time to fit residues: 2231.0195 Evaluate side-chains 1044 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1006 time to evaluate : 5.464 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 38 outliers final: 8 residues processed: 38 average time/residue: 1.0163 time to fit residues: 77.4450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 840 optimal weight: 6.9990 chunk 553 optimal weight: 10.0000 chunk 891 optimal weight: 0.2980 chunk 544 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 619 optimal weight: 10.0000 chunk 935 optimal weight: 10.0000 chunk 861 optimal weight: 9.9990 chunk 744 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 575 optimal weight: 10.0000 overall best weight: 7.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SG 28 ASN ** SH 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 6 GLN S4 91 HIS ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S9 57 GLN L2 11 ASN L2 134 ASN ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 136 GLN LC 143 HIS LC 167 GLN ** LJ 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 169 ASN LL 111 HIS LM 133 HIS ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 32 ASN LG 7 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 145732 Z= 0.309 Angle : 0.737 27.169 219193 Z= 0.367 Chirality : 0.041 2.057 28395 Planarity : 0.005 0.071 11121 Dihedral : 18.328 179.838 59425 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 15.97 % Favored : 83.99 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.10), residues: 5042 helix: -1.90 (0.14), residues: 1174 sheet: -2.20 (0.18), residues: 787 loop : -3.18 (0.10), residues: 3081 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1001 time to evaluate : 5.501 Fit side-chains TARDY: cannot create tardy model for: "ASPSE 95 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRPSF 132 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSS4 114 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLQ 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 36 outliers final: 28 residues processed: 1021 average time/residue: 1.2043 time to fit residues: 2134.2444 Evaluate side-chains 1011 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 983 time to evaluate : 5.445 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLL 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULN 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. outliers start: 28 outliers final: 8 residues processed: 28 average time/residue: 0.9920 time to fit residues: 57.6623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 456 optimal weight: 10.0000 chunk 591 optimal weight: 10.0000 chunk 793 optimal weight: 9.9990 chunk 228 optimal weight: 0.8980 chunk 686 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 746 optimal weight: 0.0980 chunk 312 optimal weight: 50.0000 chunk 766 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SG 28 ASN ** SH 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 6 GLN ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 143 HIS ** LJ 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 111 HIS LM 133 HIS LQ 83 GLN ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101610 restraints weight = 325802.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102523 restraints weight = 165741.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102535 restraints weight = 137273.600| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 145732 Z= 0.215 Angle : 0.674 27.134 219193 Z= 0.339 Chirality : 0.038 2.060 28395 Planarity : 0.005 0.058 11121 Dihedral : 18.179 179.985 59425 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.00 % Favored : 85.96 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.11), residues: 5042 helix: -1.72 (0.14), residues: 1167 sheet: -2.09 (0.18), residues: 792 loop : -3.13 (0.10), residues: 3083 =============================================================================== Job complete usr+sys time: 31283.25 seconds wall clock time: 547 minutes 27.02 seconds (32847.02 seconds total)