Starting phenix.real_space_refine on Sun Feb 18 18:56:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/02_2024/5tcu_8402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/02_2024/5tcu_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_8402/02_2024/5tcu_8402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/02_2024/5tcu_8402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/02_2024/5tcu_8402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tcu_8402/02_2024/5tcu_8402_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 27 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: 50.02, 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: 58.96 Conformation dependent library (CDL) restraints added in 5.8 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 for structures that cannot fit in PDB format. 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: 59.13 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: 163.37 Time building geometry restraints manager: 63.68 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: 80882 35.99 - 71.99: 10798 71.99 - 107.98: 1183 107.98 - 143.98: 46 143.98 - 179.97: 65 Dihedral angle restraints: 92974 sinusoidal: 78355 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 92971 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: 3.110 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: 0.110 Extract box with map and model: 18.870 Check model and map are aligned: 1.440 Set scattering table: 0.900 Process input model: 423.790 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 453.500 ------------------------------------------------------------------------------- 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 : 24.562 179.972 83536 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 % Allowed : 9.10 % Favored : 90.02 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRPSE 43 HIS 0.016 0.003 HISLL 65 PHE 0.033 0.004 PHELN 99 TYR 0.042 0.004 TYRS8 36 ARG 0.015 0.002 ARGL2 69 *********************** 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 : 5.286 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. REVERT: SC 58 ARG cc_start: 0.6566 (ttm-80) cc_final: 0.5582 (mmp-170) REVERT: SC 85 ASN cc_start: 0.8532 (t160) cc_final: 0.8267 (m-40) REVERT: SD 70 ASP cc_start: 0.8119 (p0) cc_final: 0.7747 (p0) REVERT: SD 123 ILE cc_start: 0.8828 (mt) cc_final: 0.8624 (mt) REVERT: SG 70 MET cc_start: 0.6640 (ttp) cc_final: 0.6259 (ttm) REVERT: SF 12 THR cc_start: 0.8969 (p) cc_final: 0.8646 (m) REVERT: SF 75 THR cc_start: 0.8135 (p) cc_final: 0.7929 (p) REVERT: SF 80 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8193 (tt) REVERT: SF 110 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7219 (mt-10) REVERT: SH 81 ILE cc_start: 0.8538 (mp) cc_final: 0.8299 (mt) REVERT: S1 80 THR cc_start: 0.6195 (p) cc_final: 0.5780 (m) REVERT: S2 69 THR cc_start: 0.8293 (t) cc_final: 0.7920 (t) REVERT: S3 53 MET cc_start: 0.7125 (pmm) cc_final: 0.6738 (ptp) REVERT: S3 107 ARG cc_start: 0.7883 (mpp80) cc_final: 0.7591 (mtm180) REVERT: S5 16 TYR cc_start: 0.6763 (m-80) cc_final: 0.6446 (m-80) REVERT: S7 40 TYR cc_start: 0.5554 (t80) cc_final: 0.5248 (t80) REVERT: S8 14 VAL cc_start: 0.7693 (m) cc_final: 0.7276 (t) REVERT: S9 23 ILE cc_start: 0.7127 (mp) cc_final: 0.6716 (mm) REVERT: S9 29 LYS cc_start: 0.7538 (mptp) cc_final: 0.6813 (tptp) REVERT: S9 57 GLN cc_start: 0.7233 (mt0) cc_final: 0.7027 (mt0) REVERT: SA 16 LYS cc_start: 0.7934 (tmtm) cc_final: 0.7647 (tptp) REVERT: L2 11 ASN cc_start: 0.8383 (t160) cc_final: 0.7854 (t0) REVERT: LC 187 GLN cc_start: 0.7378 (tm-30) cc_final: 0.7120 (tm-30) REVERT: LK 51 ASP cc_start: 0.6671 (p0) cc_final: 0.6075 (p0) REVERT: LM 25 THR cc_start: 0.8293 (p) cc_final: 0.8055 (p) REVERT: LM 58 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8434 (pt) REVERT: LN 13 ASN cc_start: 0.7853 (p0) cc_final: 0.7599 (p0) REVERT: LO 38 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8025 (tp40) REVERT: LP 57 TYR cc_start: 0.7492 (t80) cc_final: 0.7240 (t80) REVERT: LR 92 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7433 (pt) REVERT: L1 65 LYS cc_start: 0.8901 (ttpm) cc_final: 0.8565 (tttp) REVERT: L3 44 GLN cc_start: 0.8735 (tp-100) cc_final: 0.8502 (tp40) REVERT: L3 52 GLN cc_start: 0.8406 (mt0) cc_final: 0.8029 (mt0) REVERT: L4 98 ASP cc_start: 0.7282 (p0) cc_final: 0.7075 (p0) REVERT: L5 1 MET cc_start: 0.5981 (mpt) cc_final: 0.5581 (mpt) REVERT: L8 86 ILE cc_start: 0.9031 (pp) cc_final: 0.8214 (pt) REVERT: LB 30 PHE cc_start: 0.7958 (t80) cc_final: 0.7651 (t80) REVERT: LD 5 GLN cc_start: 0.7983 (pp30) cc_final: 0.7768 (pp30) REVERT: LD 7 THR cc_start: 0.8468 (m) cc_final: 0.8261 (m) REVERT: LD 40 ASN cc_start: 0.8168 (t0) cc_final: 0.7891 (m-40) REVERT: LH 5 LYS cc_start: 0.9306 (ttmp) cc_final: 0.8927 (ttmm) REVERT: LH 53 SER cc_start: 0.9069 (m) cc_final: 0.8864 (p) REVERT: LH 54 ASP cc_start: 0.7722 (p0) cc_final: 0.7516 (p0) REVERT: LI 1 MET cc_start: 0.7170 (tpp) cc_final: 0.6910 (tpp) REVERT: LI 6 SER cc_start: 0.8502 (t) cc_final: 0.8280 (p) outliers start: 31 outliers final: 14 residues processed: 1327 average time/residue: 1.2105 time to fit residues: 2718.5471 Evaluate side-chains 1024 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1007 time to evaluate : 5.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SF residue 80 ILE Chi-restraints excluded: chain S4 residue 65 VAL Chi-restraints excluded: chain LC residue 27 VAL Chi-restraints excluded: chain LC residue 209 VAL Chi-restraints excluded: chain LC residue 216 LYS Chi-restraints excluded: chain LL residue 175 LYS Chi-restraints excluded: chain LM residue 8 ASN Chi-restraints excluded: chain LM residue 58 ILE Chi-restraints excluded: chain LN residue 122 LEU Chi-restraints excluded: chain LR residue 92 ILE Chi-restraints excluded: chain L3 residue 4 VAL Chi-restraints excluded: chain L3 residue 117 LEU Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain LA residue 60 THR Chi-restraints excluded: chain LB residue 66 LYS Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LH residue 61 LEU 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: 0.9980 chunk 852 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** SD 43 ASN SE 27 ASN SG 28 ASN SG 40 GLN SG 148 ASN ** SF 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 62 ASN S2 40 ASN ** S2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** LN 3 GLN LN 4 GLN LO 54 GLN LO 126 HIS ** LR 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1 31 HIS ** L3 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 44 GLN ** L3 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 145732 Z= 0.210 Angle : 0.723 27.404 219193 Z= 0.366 Chirality : 0.040 2.051 28395 Planarity : 0.005 0.069 11121 Dihedral : 25.275 179.971 75257 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.07 % Favored : 86.89 % Rotamer: Outliers : 4.13 % Allowed : 18.14 % Favored : 77.73 % 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: -4.88 (0.10), residues: 5042 helix: -3.41 (0.11), residues: 1180 sheet: -2.74 (0.17), residues: 751 loop : -3.48 (0.09), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPSE 43 HIS 0.009 0.001 HISSF 22 PHE 0.025 0.002 PHELH 33 TYR 0.022 0.002 TYRS3 65 ARG 0.008 0.001 ARGL6 76 *********************** 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 1289 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1144 time to evaluate : 5.312 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 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: "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: "LEULH 61 " (corrupted residue). Skipping it. REVERT: SB 167 TYR cc_start: 0.6742 (m-10) cc_final: 0.6403 (m-10) REVERT: SC 58 ARG cc_start: 0.6450 (ttm-80) cc_final: 0.5506 (mmp-170) REVERT: SC 85 ASN cc_start: 0.8480 (t160) cc_final: 0.8205 (m110) REVERT: SD 70 ASP cc_start: 0.8069 (p0) cc_final: 0.7707 (p0) REVERT: SG 47 PHE cc_start: 0.6908 (m-80) cc_final: 0.6601 (m-80) REVERT: SG 51 GLU cc_start: 0.5100 (OUTLIER) cc_final: 0.4793 (pt0) REVERT: SH 75 THR cc_start: 0.7822 (p) cc_final: 0.7580 (m) REVERT: SH 90 LEU cc_start: 0.7198 (mp) cc_final: 0.6453 (tt) REVERT: S3 107 ARG cc_start: 0.7741 (mpp80) cc_final: 0.7414 (mtm180) REVERT: S5 16 TYR cc_start: 0.6582 (m-80) cc_final: 0.6191 (m-80) REVERT: S5 22 THR cc_start: 0.6893 (OUTLIER) cc_final: 0.6527 (t) REVERT: S7 40 TYR cc_start: 0.5381 (t80) cc_final: 0.5156 (t80) REVERT: S8 14 VAL cc_start: 0.7780 (m) cc_final: 0.7347 (t) REVERT: S9 23 ILE cc_start: 0.6900 (mp) cc_final: 0.6493 (mm) REVERT: S9 29 LYS cc_start: 0.7337 (mptp) cc_final: 0.6664 (tptp) REVERT: L2 11 ASN cc_start: 0.8273 (t160) cc_final: 0.7800 (t0) REVERT: LJ 96 SER cc_start: 0.8788 (t) cc_final: 0.8538 (m) REVERT: LK 38 MET cc_start: 0.7454 (tmm) cc_final: 0.6831 (tmm) REVERT: LK 51 ASP cc_start: 0.6554 (p0) cc_final: 0.6140 (p0) REVERT: LM 58 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8273 (pt) REVERT: LN 106 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8045 (pp) REVERT: L3 40 MET cc_start: 0.8382 (ttp) cc_final: 0.8118 (ttm) REVERT: L3 52 GLN cc_start: 0.8379 (mt0) cc_final: 0.8152 (mt0) REVERT: L3 94 MET cc_start: 0.7149 (mmt) cc_final: 0.6944 (mmt) REVERT: L5 1 MET cc_start: 0.5994 (mpt) cc_final: 0.5661 (mpt) REVERT: L7 36 GLU cc_start: 0.7164 (mp0) cc_final: 0.6957 (mm-30) REVERT: LD 49 LYS cc_start: 0.9109 (tttt) cc_final: 0.8861 (ttmt) REVERT: LS 3 VAL cc_start: 0.8683 (t) cc_final: 0.8463 (t) REVERT: LF 53 ASP cc_start: 0.6564 (p0) cc_final: 0.5492 (m-30) outliers start: 145 outliers final: 87 residues processed: 1220 average time/residue: 1.2141 time to fit residues: 2581.6249 Evaluate side-chains 1117 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1026 time to evaluate : 5.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 6 ASN Chi-restraints excluded: chain SB residue 30 SER Chi-restraints excluded: chain SB residue 123 LEU Chi-restraints excluded: chain SD residue 134 ILE Chi-restraints excluded: chain SG residue 20 SER Chi-restraints excluded: chain SG residue 51 GLU Chi-restraints excluded: chain SG residue 63 GLU Chi-restraints excluded: chain SG residue 87 VAL Chi-restraints excluded: chain SG residue 101 LEU Chi-restraints excluded: chain SG residue 115 THR Chi-restraints excluded: chain SF residue 103 ILE Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain SF residue 109 SER Chi-restraints excluded: chain SH residue 30 ILE Chi-restraints excluded: chain SH residue 47 ILE Chi-restraints excluded: chain SH residue 50 LEU Chi-restraints excluded: chain SH residue 105 LEU Chi-restraints excluded: chain SH residue 112 MET Chi-restraints excluded: chain S2 residue 25 SER Chi-restraints excluded: chain S2 residue 36 ASP Chi-restraints excluded: chain S2 residue 58 SER Chi-restraints excluded: chain S2 residue 67 SER Chi-restraints excluded: chain S2 residue 71 SER Chi-restraints excluded: chain S3 residue 7 LEU Chi-restraints excluded: chain S3 residue 36 THR Chi-restraints excluded: chain S4 residue 15 VAL Chi-restraints excluded: chain S4 residue 65 VAL Chi-restraints excluded: chain S5 residue 22 THR Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S6 residue 56 LEU Chi-restraints excluded: chain S9 residue 34 LEU Chi-restraints excluded: chain SI residue 11 VAL Chi-restraints excluded: chain SI residue 16 MET Chi-restraints excluded: chain SA residue 13 THR Chi-restraints excluded: chain SA residue 21 ASN Chi-restraints excluded: chain SA residue 37 THR Chi-restraints excluded: chain L2 residue 132 LEU Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain LC residue 5 ILE Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 70 ASN Chi-restraints excluded: chain LC residue 106 SER Chi-restraints excluded: chain LC residue 137 SER Chi-restraints excluded: chain LC residue 209 VAL Chi-restraints excluded: chain LC residue 216 LYS Chi-restraints excluded: chain LJ residue 19 LEU Chi-restraints excluded: chain LJ residue 125 VAL Chi-restraints excluded: chain LK residue 28 VAL Chi-restraints excluded: chain LK residue 67 VAL Chi-restraints excluded: chain LK residue 153 ASP Chi-restraints excluded: chain LL residue 175 LYS Chi-restraints excluded: chain LM residue 31 SER Chi-restraints excluded: chain LM residue 58 ILE Chi-restraints excluded: chain LM residue 71 THR Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 96 THR Chi-restraints excluded: chain LN residue 10 VAL Chi-restraints excluded: chain LN residue 106 LEU Chi-restraints excluded: chain LO residue 79 LEU Chi-restraints excluded: chain LQ residue 117 VAL Chi-restraints excluded: chain LR residue 3 SER Chi-restraints excluded: chain LR residue 51 VAL Chi-restraints excluded: chain LR residue 74 THR Chi-restraints excluded: chain L1 residue 11 THR Chi-restraints excluded: chain L1 residue 27 THR Chi-restraints excluded: chain L3 residue 4 VAL Chi-restraints excluded: chain L3 residue 65 ILE Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L3 residue 117 LEU Chi-restraints excluded: chain L4 residue 27 VAL Chi-restraints excluded: chain L4 residue 81 ASN Chi-restraints excluded: chain L4 residue 96 THR Chi-restraints excluded: chain L4 residue 97 ILE Chi-restraints excluded: chain L6 residue 73 ASN Chi-restraints excluded: chain L7 residue 31 ASP Chi-restraints excluded: chain L7 residue 79 THR Chi-restraints excluded: chain L8 residue 27 VAL Chi-restraints excluded: chain L8 residue 41 VAL Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L9 residue 15 VAL Chi-restraints excluded: chain L9 residue 24 SER Chi-restraints excluded: chain LA residue 60 THR Chi-restraints excluded: chain LB residue 13 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 66 LYS Chi-restraints excluded: chain LD residue 23 VAL Chi-restraints excluded: chain LD residue 55 THR Chi-restraints excluded: chain LE residue 21 LYS Chi-restraints excluded: chain LG residue 7 GLN Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LH residue 61 LEU 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: 30.0000 chunk 709 optimal weight: 10.0000 chunk 580 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 854 optimal weight: 0.0670 chunk 922 optimal weight: 9.9990 chunk 760 optimal weight: 0.4980 chunk 847 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 685 optimal weight: 0.9980 overall best weight: 3.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 125 ASN SD 145 GLN SG 28 ASN SG 148 ASN ** SF 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 101 GLN ** S3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 31 GLN ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 11 ASN ** 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 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 75 GLN ** LJ 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 15 ASN ** LL 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LM 8 ASN LM 11 ASN LM 136 GLN ** LN 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 37 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 7 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 145732 Z= 0.190 Angle : 0.674 27.178 219193 Z= 0.340 Chirality : 0.038 2.062 28395 Planarity : 0.005 0.066 11121 Dihedral : 25.079 179.946 75243 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.98 % Favored : 85.98 % Rotamer: Outliers : 5.76 % Allowed : 20.13 % Favored : 74.11 % 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: -4.43 (0.10), residues: 5042 helix: -2.78 (0.12), residues: 1176 sheet: -2.48 (0.17), residues: 774 loop : -3.29 (0.10), residues: 3092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPSI 34 HIS 0.010 0.001 HISSF 22 PHE 0.031 0.002 PHEL3 106 TYR 0.025 0.002 TYRSB 183 ARG 0.010 0.001 ARGS3 63 *********************** 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 1282 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1080 time to evaluate : 5.457 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 TARDY: cannot create tardy model for: "LYSLC 216 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLL 175 " (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: "LEULH 61 " (corrupted residue). Skipping it. REVERT: SC 58 ARG cc_start: 0.6423 (ttm-80) cc_final: 0.5630 (mmt-90) REVERT: SC 85 ASN cc_start: 0.8427 (t160) cc_final: 0.8164 (m110) REVERT: SD 70 ASP cc_start: 0.8137 (p0) cc_final: 0.7668 (p0) REVERT: SE 29 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8910 (tp) REVERT: S1 23 GLU cc_start: 0.6929 (mm-30) cc_final: 0.5670 (tt0) REVERT: S2 116 VAL cc_start: 0.8664 (t) cc_final: 0.8374 (p) REVERT: S3 107 ARG cc_start: 0.7642 (mpp80) cc_final: 0.7298 (mtm180) REVERT: S7 40 TYR cc_start: 0.5345 (t80) cc_final: 0.5128 (t80) REVERT: S9 23 ILE cc_start: 0.6909 (mp) cc_final: 0.6453 (mm) REVERT: S9 39 SER cc_start: 0.7456 (p) cc_final: 0.7146 (t) REVERT: S9 41 ARG cc_start: 0.7320 (mmm-85) cc_final: 0.7051 (mmm-85) REVERT: SA 36 LYS cc_start: 0.7812 (pmtt) cc_final: 0.7573 (pmtt) REVERT: L2 11 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.7858 (t0) REVERT: L2 145 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7499 (mm-30) REVERT: LJ 78 ILE cc_start: 0.9113 (tp) cc_final: 0.8862 (tp) REVERT: LJ 96 SER cc_start: 0.8781 (t) cc_final: 0.8566 (m) REVERT: LK 38 MET cc_start: 0.7505 (tmm) cc_final: 0.6709 (tmm) REVERT: LK 51 ASP cc_start: 0.6488 (p0) cc_final: 0.6085 (p0) REVERT: LM 58 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8339 (pt) REVERT: LO 10 GLU cc_start: 0.7881 (mp0) cc_final: 0.7609 (pm20) REVERT: LO 90 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8178 (mm-30) REVERT: LR 13 LYS cc_start: 0.8449 (tptt) cc_final: 0.8143 (tppp) REVERT: L1 65 LYS cc_start: 0.9170 (ttpt) cc_final: 0.8291 (ptmm) REVERT: L3 52 GLN cc_start: 0.8302 (mt0) cc_final: 0.7958 (mt0) REVERT: L5 1 MET cc_start: 0.5933 (mpt) cc_final: 0.5654 (mpt) REVERT: L7 80 ARG cc_start: 0.7873 (mtt180) cc_final: 0.7113 (ptt-90) REVERT: L7 92 ARG cc_start: 0.6784 (mtm180) cc_final: 0.6511 (mtm-85) REVERT: LB 5 GLU cc_start: 0.6647 (pm20) cc_final: 0.6351 (tp30) REVERT: LD 49 LYS cc_start: 0.9153 (tttt) cc_final: 0.8902 (ttmt) REVERT: LS 3 VAL cc_start: 0.8631 (t) cc_final: 0.8422 (t) REVERT: LG 37 ARG cc_start: 0.7731 (ttt180) cc_final: 0.7382 (ttt180) REVERT: LF 53 ASP cc_start: 0.6269 (p0) cc_final: 0.5522 (m-30) outliers start: 202 outliers final: 133 residues processed: 1188 average time/residue: 1.1669 time to fit residues: 2422.1377 Evaluate side-chains 1151 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1015 time to evaluate : 5.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 6 ASN Chi-restraints excluded: chain SB residue 17 ASP Chi-restraints excluded: chain SB residue 86 LEU Chi-restraints excluded: chain SB residue 100 ILE Chi-restraints excluded: chain SB residue 114 LEU Chi-restraints excluded: chain SB residue 119 ILE Chi-restraints excluded: chain SB residue 123 LEU Chi-restraints excluded: chain SB residue 138 THR Chi-restraints excluded: chain SC residue 60 LEU Chi-restraints excluded: chain SD residue 117 LEU Chi-restraints excluded: chain SE residue 29 ILE Chi-restraints excluded: chain SE residue 52 ILE Chi-restraints excluded: chain SE residue 79 LEU Chi-restraints excluded: chain SG residue 20 SER Chi-restraints excluded: chain SG residue 63 GLU Chi-restraints excluded: chain SG residue 87 VAL Chi-restraints excluded: chain SG residue 101 LEU Chi-restraints excluded: chain SF residue 25 LEU Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 103 ILE Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain SF residue 109 SER Chi-restraints excluded: chain SH residue 30 ILE Chi-restraints excluded: chain SH residue 47 ILE Chi-restraints excluded: chain SH residue 50 LEU Chi-restraints excluded: chain SH residue 105 LEU Chi-restraints excluded: chain SH residue 106 LEU Chi-restraints excluded: chain SH residue 112 MET Chi-restraints excluded: chain S2 residue 25 SER Chi-restraints excluded: chain S2 residue 36 ASP Chi-restraints excluded: chain S2 residue 58 SER Chi-restraints excluded: chain S2 residue 95 SER Chi-restraints excluded: chain S3 residue 8 VAL Chi-restraints excluded: chain S3 residue 46 VAL Chi-restraints excluded: chain S4 residue 15 VAL Chi-restraints excluded: chain S4 residue 65 VAL Chi-restraints excluded: chain S6 residue 39 VAL Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S6 residue 56 LEU Chi-restraints excluded: chain S6 residue 65 HIS Chi-restraints excluded: chain S9 residue 34 LEU Chi-restraints excluded: chain SI residue 11 VAL Chi-restraints excluded: chain SI residue 15 LEU Chi-restraints excluded: chain SA residue 13 THR Chi-restraints excluded: chain SA residue 37 THR Chi-restraints excluded: chain SA residue 39 VAL Chi-restraints excluded: chain L2 residue 11 ASN Chi-restraints excluded: chain L2 residue 116 VAL Chi-restraints excluded: chain L2 residue 132 LEU Chi-restraints excluded: chain L2 residue 137 VAL Chi-restraints excluded: chain L2 residue 141 VAL Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain LC residue 5 ILE Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 70 ASN Chi-restraints excluded: chain LC residue 106 SER Chi-restraints excluded: chain LC residue 137 SER Chi-restraints excluded: chain LC residue 195 ILE Chi-restraints excluded: chain LC residue 209 VAL Chi-restraints excluded: chain LC residue 216 LYS Chi-restraints excluded: chain LJ residue 19 LEU Chi-restraints excluded: chain LJ residue 125 VAL Chi-restraints excluded: chain LJ residue 131 PHE Chi-restraints excluded: chain LK residue 4 LEU Chi-restraints excluded: chain LK residue 6 GLU Chi-restraints excluded: chain LK residue 67 VAL Chi-restraints excluded: chain LK residue 153 ASP Chi-restraints excluded: chain LL residue 175 LYS Chi-restraints excluded: chain LM residue 51 THR Chi-restraints excluded: chain LM residue 53 ASP Chi-restraints excluded: chain LM residue 55 VAL Chi-restraints excluded: chain LM residue 56 ILE Chi-restraints excluded: chain LM residue 58 ILE Chi-restraints excluded: chain LM residue 59 ASN Chi-restraints excluded: chain LM residue 71 THR Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 96 THR Chi-restraints excluded: chain LN residue 10 VAL Chi-restraints excluded: chain LN residue 62 ILE Chi-restraints excluded: chain LO residue 69 ILE Chi-restraints excluded: chain LO residue 79 LEU Chi-restraints excluded: chain LO residue 91 VAL Chi-restraints excluded: chain LO residue 123 VAL Chi-restraints excluded: chain LP residue 25 ASN Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 64 VAL Chi-restraints excluded: chain LP residue 75 THR Chi-restraints excluded: chain LQ residue 66 LEU Chi-restraints excluded: chain LQ residue 80 THR Chi-restraints excluded: chain LQ residue 117 VAL Chi-restraints excluded: chain LR residue 3 SER Chi-restraints excluded: chain LR residue 31 LEU Chi-restraints excluded: chain LR residue 51 VAL Chi-restraints excluded: chain L1 residue 11 THR Chi-restraints excluded: chain L1 residue 17 THR Chi-restraints excluded: chain L1 residue 27 THR Chi-restraints excluded: chain L3 residue 4 VAL Chi-restraints excluded: chain L3 residue 42 SER Chi-restraints excluded: chain L3 residue 65 ILE Chi-restraints excluded: chain L3 residue 109 LEU Chi-restraints excluded: chain L3 residue 117 LEU Chi-restraints excluded: chain L4 residue 7 THR Chi-restraints excluded: chain L4 residue 27 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L4 residue 96 THR Chi-restraints excluded: chain L4 residue 97 ILE Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 50 VAL Chi-restraints excluded: chain L6 residue 31 THR Chi-restraints excluded: chain L6 residue 37 GLN Chi-restraints excluded: chain L6 residue 55 ILE Chi-restraints excluded: chain L6 residue 73 ASN Chi-restraints excluded: chain L7 residue 31 ASP Chi-restraints excluded: chain L7 residue 45 GLN Chi-restraints excluded: chain L7 residue 59 THR Chi-restraints excluded: chain L7 residue 70 LEU Chi-restraints excluded: chain L7 residue 76 ASN Chi-restraints excluded: chain L7 residue 79 THR Chi-restraints excluded: chain L8 residue 27 VAL Chi-restraints excluded: chain L8 residue 41 VAL Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L9 residue 15 VAL Chi-restraints excluded: chain L9 residue 24 SER Chi-restraints excluded: chain L9 residue 44 ILE Chi-restraints excluded: chain LA residue 19 SER Chi-restraints excluded: chain LA residue 50 SER Chi-restraints excluded: chain LA residue 60 THR Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 66 LYS Chi-restraints excluded: chain LD residue 55 THR Chi-restraints excluded: chain LE residue 21 LYS Chi-restraints excluded: chain LS residue 25 ASN Chi-restraints excluded: chain LS residue 48 THR Chi-restraints excluded: chain LG residue 7 GLN Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LF residue 18 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 844 optimal weight: 0.0570 chunk 642 optimal weight: 9.9990 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: 7.9990 chunk 907 optimal weight: 8.9990 chunk 447 optimal weight: 20.0000 chunk 812 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 overall best weight: 7.4108 ------------------------------------------------------------------------------- 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 ** SF 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 6 GLN S3 77 ASN ** 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 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 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 111 HIS LM 11 ASN LR 48 ASN ** L3 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 88 HIS L4 90 GLN ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 7 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 145732 Z= 0.325 Angle : 0.756 27.230 219193 Z= 0.377 Chirality : 0.042 2.051 28395 Planarity : 0.005 0.064 11121 Dihedral : 25.074 179.878 75243 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 15.35 % Favored : 84.61 % Rotamer: Outliers : 7.07 % Allowed : 21.50 % Favored : 71.43 % 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: -4.28 (0.10), residues: 5042 helix: -2.49 (0.13), residues: 1169 sheet: -2.43 (0.17), residues: 805 loop : -3.26 (0.10), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPSE 43 HIS 0.010 0.001 HISSF 22 PHE 0.019 0.002 PHELB 26 TYR 0.025 0.002 TYRSB 183 ARG 0.009 0.001 ARGS4 92 *********************** 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 1293 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1045 time to evaluate : 5.333 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 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: "LEULH 61 " (corrupted residue). Skipping it. REVERT: SC 58 ARG cc_start: 0.6433 (ttm-80) cc_final: 0.5617 (mmt-90) REVERT: SC 85 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8204 (m110) REVERT: SD 70 ASP cc_start: 0.8255 (p0) cc_final: 0.7856 (p0) REVERT: SD 96 MET cc_start: 0.7670 (mmm) cc_final: 0.7240 (mtp) REVERT: SE 22 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7708 (tt) REVERT: SE 29 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8900 (tp) REVERT: SG 96 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.5274 (ptp90) REVERT: S2 116 VAL cc_start: 0.8668 (t) cc_final: 0.8408 (p) REVERT: S3 107 ARG cc_start: 0.7726 (mpp80) cc_final: 0.7394 (mtm180) REVERT: S9 23 ILE cc_start: 0.6858 (mp) cc_final: 0.6471 (mm) REVERT: SI 51 VAL cc_start: 0.7536 (OUTLIER) cc_final: 0.7315 (m) REVERT: L2 11 ASN cc_start: 0.8531 (t160) cc_final: 0.8055 (t0) REVERT: LJ 45 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8043 (ppt-90) REVERT: LJ 78 ILE cc_start: 0.9078 (tp) cc_final: 0.8806 (tp) REVERT: LJ 96 SER cc_start: 0.8872 (t) cc_final: 0.8607 (m) REVERT: LK 38 MET cc_start: 0.7533 (tmm) cc_final: 0.6733 (tmm) REVERT: LK 51 ASP cc_start: 0.6552 (p0) cc_final: 0.6127 (p0) REVERT: LN 2 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8805 (tt) REVERT: LO 10 GLU cc_start: 0.7842 (mp0) cc_final: 0.7586 (pm20) REVERT: LO 90 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8186 (mm-30) REVERT: LP 101 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7472 (ppp80) REVERT: LR 13 LYS cc_start: 0.8458 (tptt) cc_final: 0.8215 (tppp) REVERT: L3 44 GLN cc_start: 0.8681 (tp40) cc_final: 0.8271 (tp40) REVERT: L3 52 GLN cc_start: 0.8422 (mt0) cc_final: 0.8064 (mt0) REVERT: L4 88 HIS cc_start: 0.8215 (t-90) cc_final: 0.7913 (t70) REVERT: L5 72 LYS cc_start: 0.8004 (mttm) cc_final: 0.7745 (mttm) REVERT: L6 83 LYS cc_start: 0.5271 (OUTLIER) cc_final: 0.4905 (pttt) REVERT: LB 5 GLU cc_start: 0.6546 (pm20) cc_final: 0.6154 (tp30) REVERT: LD 49 LYS cc_start: 0.9128 (tttt) cc_final: 0.8916 (ttmt) REVERT: LG 15 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8837 (tppp) REVERT: LG 37 ARG cc_start: 0.7737 (ttt180) cc_final: 0.7466 (ttt180) REVERT: LF 53 ASP cc_start: 0.6105 (p0) cc_final: 0.5446 (m-30) outliers start: 248 outliers final: 185 residues processed: 1182 average time/residue: 1.2172 time to fit residues: 2480.5044 Evaluate side-chains 1202 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1008 time to evaluate : 5.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 6 ASN Chi-restraints excluded: chain SB residue 17 ASP Chi-restraints excluded: chain SB residue 30 SER Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 86 LEU Chi-restraints excluded: chain SB residue 100 ILE Chi-restraints excluded: chain SB residue 114 LEU Chi-restraints excluded: chain SB residue 119 ILE Chi-restraints excluded: chain SB residue 123 LEU Chi-restraints excluded: chain SB residue 138 THR Chi-restraints excluded: chain SC residue 60 LEU Chi-restraints excluded: chain SC residue 85 ASN Chi-restraints excluded: chain SD residue 17 THR Chi-restraints excluded: chain SD residue 117 LEU Chi-restraints excluded: chain SD residue 134 ILE Chi-restraints excluded: chain SE residue 22 LEU Chi-restraints excluded: chain SE residue 29 ILE Chi-restraints excluded: chain SE residue 52 ILE Chi-restraints excluded: chain SE residue 79 LEU Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SG residue 12 VAL Chi-restraints excluded: chain SG residue 20 SER Chi-restraints excluded: chain SG residue 63 GLU Chi-restraints excluded: chain SG residue 80 VAL Chi-restraints excluded: chain SG residue 87 VAL Chi-restraints excluded: chain SG residue 96 ARG Chi-restraints excluded: chain SG residue 101 LEU Chi-restraints excluded: chain SG residue 115 THR Chi-restraints excluded: chain SG residue 117 GLU Chi-restraints excluded: chain SF residue 25 LEU Chi-restraints excluded: chain SF residue 74 ILE Chi-restraints excluded: chain SF residue 75 THR Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 103 ILE Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain SF residue 109 SER Chi-restraints excluded: chain SF residue 112 VAL Chi-restraints excluded: chain SH residue 30 ILE Chi-restraints excluded: chain SH residue 47 ILE Chi-restraints excluded: chain SH residue 50 LEU Chi-restraints excluded: chain SH residue 75 THR Chi-restraints excluded: chain SH residue 105 LEU Chi-restraints excluded: chain SH residue 106 LEU Chi-restraints excluded: chain SH residue 112 MET Chi-restraints excluded: chain S2 residue 23 ILE Chi-restraints excluded: chain S2 residue 25 SER Chi-restraints excluded: chain S2 residue 55 SER Chi-restraints excluded: chain S2 residue 58 SER Chi-restraints excluded: chain S2 residue 67 SER Chi-restraints excluded: chain S2 residue 71 SER Chi-restraints excluded: chain S2 residue 95 SER Chi-restraints excluded: chain S2 residue 119 ASN Chi-restraints excluded: chain S3 residue 8 VAL Chi-restraints excluded: chain S3 residue 46 VAL Chi-restraints excluded: chain S3 residue 80 ILE Chi-restraints excluded: chain S3 residue 92 VAL Chi-restraints excluded: chain S4 residue 65 VAL Chi-restraints excluded: chain S6 residue 39 VAL Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S6 residue 56 LEU Chi-restraints excluded: chain S6 residue 57 LEU Chi-restraints excluded: chain S6 residue 65 HIS Chi-restraints excluded: chain S8 residue 63 ILE Chi-restraints excluded: chain S9 residue 34 LEU Chi-restraints excluded: chain SI residue 11 VAL Chi-restraints excluded: chain SI residue 15 LEU Chi-restraints excluded: chain SI residue 16 MET Chi-restraints excluded: chain SI residue 51 VAL Chi-restraints excluded: chain SA residue 13 THR Chi-restraints excluded: chain SA residue 21 ASN Chi-restraints excluded: chain SA residue 37 THR Chi-restraints excluded: chain SA residue 39 VAL Chi-restraints excluded: chain L2 residue 104 ILE Chi-restraints excluded: chain L2 residue 116 VAL Chi-restraints excluded: chain L2 residue 130 LEU Chi-restraints excluded: chain L2 residue 132 LEU Chi-restraints excluded: chain L2 residue 137 VAL Chi-restraints excluded: chain L2 residue 141 VAL Chi-restraints excluded: chain L2 residue 146 LEU Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain LC residue 5 ILE Chi-restraints excluded: chain LC residue 13 THR Chi-restraints excluded: chain LC residue 49 ILE Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 70 ASN Chi-restraints excluded: chain LC residue 106 SER Chi-restraints excluded: chain LC residue 137 SER Chi-restraints excluded: chain LC residue 194 VAL Chi-restraints excluded: chain LC residue 195 ILE Chi-restraints excluded: chain LC residue 209 VAL Chi-restraints excluded: chain LC residue 216 LYS Chi-restraints excluded: chain LJ residue 19 LEU Chi-restraints excluded: chain LJ residue 45 ARG Chi-restraints excluded: chain LJ residue 125 VAL Chi-restraints excluded: chain LJ residue 131 PHE Chi-restraints excluded: chain LJ residue 154 VAL Chi-restraints excluded: chain LK residue 4 LEU Chi-restraints excluded: chain LK residue 6 GLU Chi-restraints excluded: chain LK residue 28 VAL Chi-restraints excluded: chain LK residue 67 VAL Chi-restraints excluded: chain LK residue 153 ASP Chi-restraints excluded: chain LL residue 105 LEU Chi-restraints excluded: chain LL residue 107 VAL Chi-restraints excluded: chain LL residue 175 LYS Chi-restraints excluded: chain LM residue 51 THR Chi-restraints excluded: chain LM residue 53 ASP Chi-restraints excluded: chain LM residue 55 VAL Chi-restraints excluded: chain LM residue 59 ASN Chi-restraints excluded: chain LM residue 71 THR Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 96 THR Chi-restraints excluded: chain LN residue 2 ILE Chi-restraints excluded: chain LN residue 10 VAL Chi-restraints excluded: chain LN residue 40 VAL Chi-restraints excluded: chain LN residue 62 ILE Chi-restraints excluded: chain LN residue 122 LEU Chi-restraints excluded: chain LO residue 69 ILE Chi-restraints excluded: chain LO residue 70 ASN Chi-restraints excluded: chain LO residue 79 LEU Chi-restraints excluded: chain LO residue 123 VAL Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 25 ASN Chi-restraints excluded: chain LP residue 38 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 64 VAL Chi-restraints excluded: chain LP residue 72 THR Chi-restraints excluded: chain LP residue 101 ARG Chi-restraints excluded: chain LQ residue 66 LEU Chi-restraints excluded: chain LQ residue 80 THR Chi-restraints excluded: chain LQ residue 117 VAL Chi-restraints excluded: chain LQ residue 119 ILE Chi-restraints excluded: chain LR residue 3 SER Chi-restraints excluded: chain LR residue 31 LEU Chi-restraints excluded: chain LR residue 39 HIS Chi-restraints excluded: chain LR residue 51 VAL Chi-restraints excluded: chain L1 residue 11 THR Chi-restraints excluded: chain L1 residue 17 THR Chi-restraints excluded: chain L1 residue 19 LEU Chi-restraints excluded: chain L3 residue 4 VAL Chi-restraints excluded: chain L3 residue 42 SER Chi-restraints excluded: chain L3 residue 65 ILE Chi-restraints excluded: chain L3 residue 109 LEU Chi-restraints excluded: chain L3 residue 117 LEU Chi-restraints excluded: chain L4 residue 7 THR Chi-restraints excluded: chain L4 residue 27 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L4 residue 81 ASN Chi-restraints excluded: chain L4 residue 96 THR Chi-restraints excluded: chain L4 residue 97 ILE Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 50 VAL Chi-restraints excluded: chain L6 residue 31 THR Chi-restraints excluded: chain L6 residue 33 VAL Chi-restraints excluded: chain L6 residue 37 GLN Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L6 residue 55 ILE Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 73 ASN Chi-restraints excluded: chain L6 residue 83 LYS Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 31 ASP Chi-restraints excluded: chain L7 residue 45 GLN Chi-restraints excluded: chain L7 residue 59 THR Chi-restraints excluded: chain L7 residue 76 ASN Chi-restraints excluded: chain L7 residue 79 THR Chi-restraints excluded: chain L7 residue 81 VAL Chi-restraints excluded: chain L8 residue 18 LEU Chi-restraints excluded: chain L8 residue 27 VAL Chi-restraints excluded: chain L8 residue 41 VAL Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L9 residue 15 VAL Chi-restraints excluded: chain L9 residue 24 SER Chi-restraints excluded: chain L9 residue 44 ILE Chi-restraints excluded: chain L9 residue 88 SER Chi-restraints excluded: chain LA residue 14 THR Chi-restraints excluded: chain LA residue 19 SER Chi-restraints excluded: chain LA residue 50 SER Chi-restraints excluded: chain LA residue 60 THR Chi-restraints excluded: chain LB residue 13 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 66 LYS Chi-restraints excluded: chain LD residue 5 GLN Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 23 VAL Chi-restraints excluded: chain LD residue 55 THR Chi-restraints excluded: chain LE residue 21 LYS Chi-restraints excluded: chain LE residue 23 SER Chi-restraints excluded: chain LS residue 25 ASN Chi-restraints excluded: chain LS residue 48 THR Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LH residue 58 VAL Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LI residue 27 CYS Chi-restraints excluded: chain LF residue 18 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 755 optimal weight: 10.0000 chunk 515 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 675 optimal weight: 8.9990 chunk 374 optimal weight: 10.0000 chunk 774 optimal weight: 6.9990 chunk 627 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 463 optimal weight: 40.0000 chunk 814 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SE 70 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 15 ASN S4 31 GLN S5 31 HIS ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 70 ASN 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 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 111 HIS LM 11 ASN LO 27 ASN LP 123 HIS L1 79 HIS ** L3 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 40 ASN LG 7 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 145732 Z= 0.366 Angle : 0.794 27.285 219193 Z= 0.394 Chirality : 0.043 2.049 28395 Planarity : 0.006 0.072 11121 Dihedral : 25.095 179.963 75241 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 16.30 % Favored : 83.66 % Rotamer: Outliers : 7.70 % Allowed : 21.96 % Favored : 70.35 % 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: -4.25 (0.10), residues: 5042 helix: -2.38 (0.13), residues: 1177 sheet: -2.42 (0.17), residues: 793 loop : -3.27 (0.10), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPSE 43 HIS 0.010 0.002 HISSF 22 PHE 0.043 0.002 PHELJ 90 TYR 0.034 0.002 TYRSB 183 ARG 0.012 0.001 ARGSE 47 *********************** 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 1295 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1025 time to evaluate : 5.395 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: "LEULH 61 " (corrupted residue). Skipping it. REVERT: SC 58 ARG cc_start: 0.6512 (ttm-80) cc_final: 0.5602 (mmt-90) REVERT: SC 85 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8202 (m110) REVERT: SD 70 ASP cc_start: 0.8248 (p0) cc_final: 0.7855 (p0) REVERT: SD 96 MET cc_start: 0.7643 (mmm) cc_final: 0.7385 (mtp) REVERT: SE 22 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7780 (tt) REVERT: SG 96 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.5242 (ptp90) REVERT: SH 121 LYS cc_start: 0.8486 (mttm) cc_final: 0.8278 (mtpp) REVERT: S1 23 GLU cc_start: 0.7042 (mm-30) cc_final: 0.5690 (tt0) REVERT: S2 116 VAL cc_start: 0.8646 (t) cc_final: 0.8369 (p) REVERT: S3 107 ARG cc_start: 0.7681 (mpp80) cc_final: 0.7428 (mtm180) REVERT: S9 23 ILE cc_start: 0.6796 (mp) cc_final: 0.6432 (mm) REVERT: L2 11 ASN cc_start: 0.8617 (t160) cc_final: 0.8187 (t0) REVERT: L2 110 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8123 (pp) REVERT: LJ 45 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8610 (ppt-90) REVERT: LJ 78 ILE cc_start: 0.9092 (tp) cc_final: 0.8831 (tp) REVERT: LJ 96 SER cc_start: 0.8812 (t) cc_final: 0.8572 (m) REVERT: LJ 99 TYR cc_start: 0.9020 (p90) cc_final: 0.8747 (p90) REVERT: LJ 169 ASN cc_start: 0.7722 (t0) cc_final: 0.7425 (t0) REVERT: LK 11 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.5223 (tt0) REVERT: LK 38 MET cc_start: 0.7549 (tmm) cc_final: 0.6730 (tmm) REVERT: LK 51 ASP cc_start: 0.6629 (p0) cc_final: 0.6209 (p0) REVERT: LN 2 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8770 (tt) REVERT: LN 106 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7972 (pp) REVERT: LP 101 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7568 (ppp80) REVERT: LR 13 LYS cc_start: 0.8465 (tptt) cc_final: 0.8221 (tppp) REVERT: L3 44 GLN cc_start: 0.8715 (tp40) cc_final: 0.8373 (tp40) REVERT: L3 52 GLN cc_start: 0.8443 (mt0) cc_final: 0.8082 (mt0) REVERT: L3 91 ASN cc_start: 0.6698 (m110) cc_final: 0.6430 (m110) REVERT: L6 83 LYS cc_start: 0.5378 (OUTLIER) cc_final: 0.5030 (pttt) REVERT: LE 7 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7624 (ptp90) REVERT: LS 21 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8357 (ttmt) REVERT: LG 15 LYS cc_start: 0.9107 (ttmm) cc_final: 0.8857 (tppp) REVERT: LF 10 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6527 (p90) REVERT: LF 53 ASP cc_start: 0.6049 (p0) cc_final: 0.5311 (m-30) outliers start: 270 outliers final: 203 residues processed: 1176 average time/residue: 1.1670 time to fit residues: 2400.3570 Evaluate side-chains 1203 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 987 time to evaluate : 5.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 6 ASN Chi-restraints excluded: chain SB residue 17 ASP Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 86 LEU Chi-restraints excluded: chain SB residue 100 ILE Chi-restraints excluded: chain SB residue 114 LEU Chi-restraints excluded: chain SB residue 119 ILE Chi-restraints excluded: chain SB residue 123 LEU Chi-restraints excluded: chain SB residue 138 THR Chi-restraints excluded: chain SB residue 148 ILE Chi-restraints excluded: chain SB residue 192 TYR Chi-restraints excluded: chain SC residue 60 LEU Chi-restraints excluded: chain SC residue 85 ASN Chi-restraints excluded: chain SD residue 17 THR Chi-restraints excluded: chain SD residue 117 LEU Chi-restraints excluded: chain SE residue 22 LEU Chi-restraints excluded: chain SE residue 52 ILE Chi-restraints excluded: chain SE residue 74 ASP Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SG residue 12 VAL Chi-restraints excluded: chain SG residue 20 SER Chi-restraints excluded: chain SG residue 87 VAL Chi-restraints excluded: chain SG residue 96 ARG Chi-restraints excluded: chain SG residue 101 LEU Chi-restraints excluded: chain SG residue 104 LEU Chi-restraints excluded: chain SG residue 106 ASN Chi-restraints excluded: chain SG residue 115 THR Chi-restraints excluded: chain SG residue 117 GLU Chi-restraints excluded: chain SF residue 7 ILE Chi-restraints excluded: chain SF residue 25 LEU Chi-restraints excluded: chain SF residue 75 THR Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 103 ILE Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain SF residue 109 SER Chi-restraints excluded: chain SH residue 30 ILE Chi-restraints excluded: chain SH residue 47 ILE Chi-restraints excluded: chain SH residue 50 LEU Chi-restraints excluded: chain SH residue 75 THR Chi-restraints excluded: chain SH residue 112 MET Chi-restraints excluded: chain S1 residue 76 ILE Chi-restraints excluded: chain S2 residue 25 SER Chi-restraints excluded: chain S2 residue 26 THR Chi-restraints excluded: chain S2 residue 55 SER Chi-restraints excluded: chain S2 residue 58 SER Chi-restraints excluded: chain S2 residue 59 THR Chi-restraints excluded: chain S2 residue 67 SER Chi-restraints excluded: chain S2 residue 71 SER Chi-restraints excluded: chain S2 residue 95 SER Chi-restraints excluded: chain S2 residue 112 ASP Chi-restraints excluded: chain S3 residue 8 VAL Chi-restraints excluded: chain S3 residue 46 VAL Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 80 ILE Chi-restraints excluded: chain S3 residue 92 VAL Chi-restraints excluded: chain S4 residue 16 VAL Chi-restraints excluded: chain S4 residue 34 LEU Chi-restraints excluded: chain S4 residue 65 VAL Chi-restraints excluded: chain S6 residue 39 VAL Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S6 residue 56 LEU Chi-restraints excluded: chain S6 residue 57 LEU Chi-restraints excluded: chain S6 residue 60 VAL Chi-restraints excluded: chain S6 residue 65 HIS Chi-restraints excluded: chain S7 residue 30 ASP Chi-restraints excluded: chain S8 residue 11 VAL Chi-restraints excluded: chain S8 residue 63 ILE Chi-restraints excluded: chain S9 residue 34 LEU Chi-restraints excluded: chain S9 residue 39 SER Chi-restraints excluded: chain SI residue 11 VAL Chi-restraints excluded: chain SI residue 16 MET Chi-restraints excluded: chain SI residue 44 PHE Chi-restraints excluded: chain SA residue 13 THR Chi-restraints excluded: chain SA residue 21 ASN Chi-restraints excluded: chain SA residue 37 THR Chi-restraints excluded: chain SA residue 39 VAL Chi-restraints excluded: chain L2 residue 104 ILE Chi-restraints excluded: chain L2 residue 110 LEU Chi-restraints excluded: chain L2 residue 116 VAL Chi-restraints excluded: chain L2 residue 130 LEU Chi-restraints excluded: chain L2 residue 132 LEU Chi-restraints excluded: chain L2 residue 137 VAL Chi-restraints excluded: chain L2 residue 141 VAL Chi-restraints excluded: chain L2 residue 146 LEU Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain LC residue 5 ILE Chi-restraints excluded: chain LC residue 13 THR Chi-restraints excluded: chain LC residue 49 ILE Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 70 ASN Chi-restraints excluded: chain LC residue 106 SER Chi-restraints excluded: chain LC residue 137 SER Chi-restraints excluded: chain LC residue 194 VAL Chi-restraints excluded: chain LC residue 195 ILE Chi-restraints excluded: chain LC residue 209 VAL Chi-restraints excluded: chain LC residue 216 LYS Chi-restraints excluded: chain LJ residue 19 LEU Chi-restraints excluded: chain LJ residue 45 ARG Chi-restraints excluded: chain LJ residue 89 VAL Chi-restraints excluded: chain LJ residue 125 VAL Chi-restraints excluded: chain LJ residue 131 PHE Chi-restraints excluded: chain LJ residue 154 VAL Chi-restraints excluded: chain LK residue 4 LEU Chi-restraints excluded: chain LK residue 6 GLU Chi-restraints excluded: chain LK residue 11 GLU Chi-restraints excluded: chain LK residue 12 VAL Chi-restraints excluded: chain LK residue 67 VAL Chi-restraints excluded: chain LK residue 153 ASP Chi-restraints excluded: chain LL residue 105 LEU Chi-restraints excluded: chain LL residue 107 VAL Chi-restraints excluded: chain LL residue 175 LYS Chi-restraints excluded: chain LM residue 51 THR Chi-restraints excluded: chain LM residue 53 ASP Chi-restraints excluded: chain LM residue 55 VAL Chi-restraints excluded: chain LM residue 56 ILE Chi-restraints excluded: chain LM residue 59 ASN Chi-restraints excluded: chain LM residue 71 THR Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 96 THR Chi-restraints excluded: chain LN residue 2 ILE Chi-restraints excluded: chain LN residue 10 VAL Chi-restraints excluded: chain LN residue 40 VAL Chi-restraints excluded: chain LN residue 62 ILE Chi-restraints excluded: chain LN residue 106 LEU Chi-restraints excluded: chain LN residue 122 LEU Chi-restraints excluded: chain LO residue 69 ILE Chi-restraints excluded: chain LO residue 79 LEU Chi-restraints excluded: chain LO residue 123 VAL Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 25 ASN Chi-restraints excluded: chain LP residue 38 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 64 VAL Chi-restraints excluded: chain LP residue 72 THR Chi-restraints excluded: chain LP residue 101 ARG Chi-restraints excluded: chain LQ residue 8 ARG Chi-restraints excluded: chain LQ residue 30 ILE Chi-restraints excluded: chain LQ residue 66 LEU Chi-restraints excluded: chain LQ residue 80 THR Chi-restraints excluded: chain LQ residue 117 VAL Chi-restraints excluded: chain LQ residue 119 ILE Chi-restraints excluded: chain LR residue 3 SER Chi-restraints excluded: chain LR residue 31 LEU Chi-restraints excluded: chain LR residue 39 HIS Chi-restraints excluded: chain LR residue 44 ILE Chi-restraints excluded: chain LR residue 51 VAL Chi-restraints excluded: chain L1 residue 11 THR Chi-restraints excluded: chain L1 residue 17 THR Chi-restraints excluded: chain L1 residue 44 VAL Chi-restraints excluded: chain L3 residue 4 VAL Chi-restraints excluded: chain L3 residue 27 SER Chi-restraints excluded: chain L3 residue 42 SER Chi-restraints excluded: chain L3 residue 65 ILE Chi-restraints excluded: chain L3 residue 109 LEU Chi-restraints excluded: chain L3 residue 117 LEU Chi-restraints excluded: chain L4 residue 7 THR Chi-restraints excluded: chain L4 residue 25 LEU Chi-restraints excluded: chain L4 residue 27 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L4 residue 81 ASN Chi-restraints excluded: chain L4 residue 96 THR Chi-restraints excluded: chain L4 residue 97 ILE Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 50 VAL Chi-restraints excluded: chain L5 residue 107 VAL Chi-restraints excluded: chain L6 residue 31 THR Chi-restraints excluded: chain L6 residue 33 VAL Chi-restraints excluded: chain L6 residue 37 GLN Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L6 residue 55 ILE Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 73 ASN Chi-restraints excluded: chain L6 residue 83 LYS Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 31 ASP Chi-restraints excluded: chain L7 residue 45 GLN Chi-restraints excluded: chain L7 residue 59 THR Chi-restraints excluded: chain L7 residue 76 ASN Chi-restraints excluded: chain L7 residue 79 THR Chi-restraints excluded: chain L7 residue 81 VAL Chi-restraints excluded: chain L8 residue 18 LEU Chi-restraints excluded: chain L8 residue 27 VAL Chi-restraints excluded: chain L8 residue 41 VAL Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L8 residue 92 LEU Chi-restraints excluded: chain L9 residue 15 VAL Chi-restraints excluded: chain L9 residue 24 SER Chi-restraints excluded: chain L9 residue 29 LEU Chi-restraints excluded: chain L9 residue 44 ILE Chi-restraints excluded: chain L9 residue 88 SER Chi-restraints excluded: chain LA residue 14 THR Chi-restraints excluded: chain LA residue 19 SER Chi-restraints excluded: chain LA residue 36 VAL Chi-restraints excluded: chain LA residue 50 SER Chi-restraints excluded: chain LA residue 60 THR Chi-restraints excluded: chain LB residue 13 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 66 LYS Chi-restraints excluded: chain LD residue 5 GLN Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 9 THR Chi-restraints excluded: chain LD residue 13 ILE Chi-restraints excluded: chain LD residue 23 VAL Chi-restraints excluded: chain LD residue 55 THR Chi-restraints excluded: chain LE residue 7 ARG Chi-restraints excluded: chain LE residue 21 LYS Chi-restraints excluded: chain LE residue 23 SER Chi-restraints excluded: chain LS residue 21 LYS Chi-restraints excluded: chain LS residue 25 ASN Chi-restraints excluded: chain LG residue 5 THR Chi-restraints excluded: chain LH residue 7 HIS Chi-restraints excluded: chain LH residue 58 VAL Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LI residue 27 CYS Chi-restraints excluded: chain LF residue 10 HIS Chi-restraints excluded: chain LF residue 18 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 305 optimal weight: 5.9990 chunk 817 optimal weight: 6.9990 chunk 179 optimal weight: 50.0000 chunk 532 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 908 optimal weight: 7.9990 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: 6.7990 ------------------------------------------------------------------------------- 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** SG 148 ASN ** SH 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 15 ASN S5 31 HIS ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 61 GLN ** L2 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 70 ASN 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 11 ASN ** LR 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 40 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 145732 Z= 0.301 Angle : 0.744 27.228 219193 Z= 0.372 Chirality : 0.041 2.059 28395 Planarity : 0.005 0.069 11121 Dihedral : 25.048 179.978 75241 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 15.15 % Favored : 84.81 % Rotamer: Outliers : 7.93 % Allowed : 23.50 % Favored : 68.58 % 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: -4.11 (0.10), residues: 5042 helix: -2.15 (0.13), residues: 1166 sheet: -2.40 (0.17), residues: 796 loop : -3.22 (0.10), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPSE 43 HIS 0.019 0.001 HISSG 18 PHE 0.023 0.002 PHELJ 90 TYR 0.030 0.002 TYRSB 183 ARG 0.015 0.001 ARGS3 69 *********************** 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 1321 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1043 time to evaluate : 5.333 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 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: "LEULH 61 " (corrupted residue). Skipping it. REVERT: SC 58 ARG cc_start: 0.6317 (ttm-80) cc_final: 0.5526 (mmt-90) REVERT: SC 85 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8117 (m110) REVERT: SD 70 ASP cc_start: 0.8269 (p0) cc_final: 0.7868 (p0) REVERT: SG 96 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.5094 (ptp90) REVERT: SH 44 GLU cc_start: 0.6289 (tp30) cc_final: 0.5552 (tp30) REVERT: SH 81 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8063 (pt) REVERT: S2 116 VAL cc_start: 0.8636 (t) cc_final: 0.8363 (p) REVERT: S3 107 ARG cc_start: 0.7614 (mpp80) cc_final: 0.7365 (mtm180) REVERT: S9 23 ILE cc_start: 0.6783 (mp) cc_final: 0.6430 (mm) REVERT: S9 39 SER cc_start: 0.7564 (p) cc_final: 0.7265 (t) REVERT: SI 51 VAL cc_start: 0.7630 (OUTLIER) cc_final: 0.7410 (m) REVERT: SA 36 LYS cc_start: 0.7912 (pmtt) cc_final: 0.7683 (pmtt) REVERT: L2 11 ASN cc_start: 0.8656 (t160) cc_final: 0.8153 (t0) REVERT: L2 110 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8150 (pp) REVERT: LC 131 ILE cc_start: 0.9394 (pp) cc_final: 0.9187 (pt) REVERT: LJ 45 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8515 (ppt-90) REVERT: LJ 78 ILE cc_start: 0.9054 (tp) cc_final: 0.8817 (tp) REVERT: LJ 96 SER cc_start: 0.8836 (t) cc_final: 0.8590 (m) REVERT: LJ 99 TYR cc_start: 0.9022 (p90) cc_final: 0.8776 (p90) REVERT: LJ 169 ASN cc_start: 0.7772 (t0) cc_final: 0.7265 (t0) REVERT: LK 38 MET cc_start: 0.7598 (tmm) cc_final: 0.6806 (tmm) REVERT: LK 51 ASP cc_start: 0.6749 (p0) cc_final: 0.6358 (p0) REVERT: LN 2 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8606 (tt) REVERT: LP 46 GLN cc_start: 0.8409 (mp10) cc_final: 0.8205 (pm20) REVERT: LP 101 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7649 (ppp80) REVERT: L3 44 GLN cc_start: 0.8689 (tp40) cc_final: 0.8337 (tp40) REVERT: L3 52 GLN cc_start: 0.8414 (mt0) cc_final: 0.8102 (mt0) REVERT: L3 91 ASN cc_start: 0.6859 (m110) cc_final: 0.6522 (m110) REVERT: L3 94 MET cc_start: 0.7537 (mmt) cc_final: 0.7236 (mmt) REVERT: L4 90 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: L6 20 MET cc_start: 0.9150 (mmm) cc_final: 0.8838 (tpp) REVERT: L6 56 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8419 (pmt) REVERT: L6 83 LYS cc_start: 0.5442 (OUTLIER) cc_final: 0.5077 (pttt) REVERT: LS 21 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8376 (ttmt) REVERT: LG 15 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8866 (tppp) REVERT: LG 37 ARG cc_start: 0.7793 (ttt180) cc_final: 0.7294 (ttt180) REVERT: LF 53 ASP cc_start: 0.6039 (p0) cc_final: 0.5612 (m-30) outliers start: 278 outliers final: 212 residues processed: 1190 average time/residue: 1.1359 time to fit residues: 2341.2290 Evaluate side-chains 1226 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1002 time to evaluate : 5.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 6 ASN Chi-restraints excluded: chain SB residue 30 SER Chi-restraints excluded: chain SB residue 41 PHE Chi-restraints excluded: chain SB residue 100 ILE Chi-restraints excluded: chain SB residue 114 LEU Chi-restraints excluded: chain SB residue 119 ILE Chi-restraints excluded: chain SB residue 123 LEU Chi-restraints excluded: chain SB residue 138 THR Chi-restraints excluded: chain SB residue 148 ILE Chi-restraints excluded: chain SB residue 150 THR Chi-restraints excluded: chain SB residue 192 TYR Chi-restraints excluded: chain SC residue 60 LEU Chi-restraints excluded: chain SC residue 85 ASN Chi-restraints excluded: chain SD residue 17 THR Chi-restraints excluded: chain SD residue 117 LEU Chi-restraints excluded: chain SE residue 22 LEU Chi-restraints excluded: chain SE residue 52 ILE Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SG residue 12 VAL Chi-restraints excluded: chain SG residue 20 SER Chi-restraints excluded: chain SG residue 42 ILE Chi-restraints excluded: chain SG residue 45 SER Chi-restraints excluded: chain SG residue 80 VAL Chi-restraints excluded: chain SG residue 87 VAL Chi-restraints excluded: chain SG residue 96 ARG Chi-restraints excluded: chain SG residue 101 LEU Chi-restraints excluded: chain SG residue 115 THR Chi-restraints excluded: chain SG residue 117 GLU Chi-restraints excluded: chain SF residue 7 ILE Chi-restraints excluded: chain SF residue 25 LEU Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 74 ILE Chi-restraints excluded: chain SF residue 75 THR Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 103 ILE Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain SF residue 109 SER Chi-restraints excluded: chain SH residue 30 ILE Chi-restraints excluded: chain SH residue 47 ILE Chi-restraints excluded: chain SH residue 50 LEU Chi-restraints excluded: chain SH residue 69 VAL Chi-restraints excluded: chain SH residue 75 THR Chi-restraints excluded: chain SH residue 81 ILE Chi-restraints excluded: chain SH residue 105 LEU Chi-restraints excluded: chain SH residue 106 LEU Chi-restraints excluded: chain SH residue 112 MET Chi-restraints excluded: chain S1 residue 8 ILE Chi-restraints excluded: chain S1 residue 15 HIS Chi-restraints excluded: chain S1 residue 76 ILE Chi-restraints excluded: chain S2 residue 15 ASN Chi-restraints excluded: chain S2 residue 25 SER Chi-restraints excluded: chain S2 residue 26 THR Chi-restraints excluded: chain S2 residue 55 SER Chi-restraints excluded: chain S2 residue 58 SER Chi-restraints excluded: chain S2 residue 67 SER Chi-restraints excluded: chain S2 residue 71 SER Chi-restraints excluded: chain S2 residue 84 VAL Chi-restraints excluded: chain S2 residue 95 SER Chi-restraints excluded: chain S3 residue 8 VAL Chi-restraints excluded: chain S3 residue 46 VAL Chi-restraints excluded: chain S3 residue 69 ARG Chi-restraints excluded: chain S3 residue 80 ILE Chi-restraints excluded: chain S3 residue 92 VAL Chi-restraints excluded: chain S4 residue 16 VAL Chi-restraints excluded: chain S4 residue 32 LYS Chi-restraints excluded: chain S4 residue 34 LEU Chi-restraints excluded: chain S4 residue 65 VAL Chi-restraints excluded: chain S5 residue 18 VAL Chi-restraints excluded: chain S6 residue 39 VAL Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S6 residue 56 LEU Chi-restraints excluded: chain S6 residue 57 LEU Chi-restraints excluded: chain S6 residue 60 VAL Chi-restraints excluded: chain S6 residue 65 HIS Chi-restraints excluded: chain S8 residue 14 VAL Chi-restraints excluded: chain S8 residue 32 THR Chi-restraints excluded: chain S9 residue 34 LEU Chi-restraints excluded: chain SI residue 11 VAL Chi-restraints excluded: chain SI residue 16 MET Chi-restraints excluded: chain SI residue 44 PHE Chi-restraints excluded: chain SI residue 51 VAL Chi-restraints excluded: chain SA residue 13 THR Chi-restraints excluded: chain SA residue 37 THR Chi-restraints excluded: chain SA residue 39 VAL Chi-restraints excluded: chain L2 residue 104 ILE Chi-restraints excluded: chain L2 residue 110 LEU Chi-restraints excluded: chain L2 residue 116 VAL Chi-restraints excluded: chain L2 residue 130 LEU Chi-restraints excluded: chain L2 residue 132 LEU Chi-restraints excluded: chain L2 residue 137 VAL Chi-restraints excluded: chain L2 residue 141 VAL Chi-restraints excluded: chain L2 residue 146 LEU Chi-restraints excluded: chain L2 residue 176 LEU Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain LC residue 5 ILE Chi-restraints excluded: chain LC residue 13 THR Chi-restraints excluded: chain LC residue 49 ILE Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 106 SER Chi-restraints excluded: chain LC residue 137 SER Chi-restraints excluded: chain LC residue 194 VAL Chi-restraints excluded: chain LC residue 195 ILE Chi-restraints excluded: chain LC residue 209 VAL Chi-restraints excluded: chain LC residue 216 LYS Chi-restraints excluded: chain LJ residue 19 LEU Chi-restraints excluded: chain LJ residue 45 ARG Chi-restraints excluded: chain LJ residue 125 VAL Chi-restraints excluded: chain LJ residue 126 VAL Chi-restraints excluded: chain LJ residue 131 PHE Chi-restraints excluded: chain LJ residue 154 VAL Chi-restraints excluded: chain LK residue 4 LEU Chi-restraints excluded: chain LK residue 6 GLU Chi-restraints excluded: chain LK residue 12 VAL Chi-restraints excluded: chain LK residue 28 VAL Chi-restraints excluded: chain LK residue 67 VAL Chi-restraints excluded: chain LK residue 153 ASP Chi-restraints excluded: chain LL residue 105 LEU Chi-restraints excluded: chain LL residue 107 VAL Chi-restraints excluded: chain LL residue 175 LYS Chi-restraints excluded: chain LM residue 53 ASP Chi-restraints excluded: chain LM residue 55 VAL Chi-restraints excluded: chain LM residue 59 ASN Chi-restraints excluded: chain LM residue 71 THR Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 96 THR Chi-restraints excluded: chain LN residue 2 ILE Chi-restraints excluded: chain LN residue 10 VAL Chi-restraints excluded: chain LN residue 40 VAL Chi-restraints excluded: chain LN residue 62 ILE Chi-restraints excluded: chain LN residue 65 THR Chi-restraints excluded: chain LN residue 98 ILE Chi-restraints excluded: chain LN residue 122 LEU Chi-restraints excluded: chain LO residue 69 ILE Chi-restraints excluded: chain LO residue 123 VAL Chi-restraints excluded: chain LP residue 25 ASN Chi-restraints excluded: chain LP residue 38 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 59 LYS Chi-restraints excluded: chain LP residue 64 VAL Chi-restraints excluded: chain LP residue 72 THR Chi-restraints excluded: chain LP residue 101 ARG Chi-restraints excluded: chain LQ residue 8 ARG Chi-restraints excluded: chain LQ residue 30 ILE Chi-restraints excluded: chain LQ residue 80 THR Chi-restraints excluded: chain LQ residue 117 VAL Chi-restraints excluded: chain LQ residue 119 ILE Chi-restraints excluded: chain LR residue 3 SER Chi-restraints excluded: chain LR residue 31 LEU Chi-restraints excluded: chain LR residue 39 HIS Chi-restraints excluded: chain LR residue 44 ILE Chi-restraints excluded: chain LR residue 51 VAL Chi-restraints excluded: chain L1 residue 19 LEU Chi-restraints excluded: chain L1 residue 44 VAL Chi-restraints excluded: chain L1 residue 65 LYS Chi-restraints excluded: chain L3 residue 27 SER Chi-restraints excluded: chain L3 residue 31 LEU Chi-restraints excluded: chain L3 residue 34 VAL Chi-restraints excluded: chain L3 residue 42 SER Chi-restraints excluded: chain L3 residue 65 ILE Chi-restraints excluded: chain L3 residue 109 LEU Chi-restraints excluded: chain L3 residue 117 LEU Chi-restraints excluded: chain L4 residue 7 THR Chi-restraints excluded: chain L4 residue 25 LEU Chi-restraints excluded: chain L4 residue 27 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L4 residue 81 ASN Chi-restraints excluded: chain L4 residue 90 GLN Chi-restraints excluded: chain L4 residue 96 THR Chi-restraints excluded: chain L4 residue 97 ILE Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 50 VAL Chi-restraints excluded: chain L6 residue 31 THR Chi-restraints excluded: chain L6 residue 33 VAL Chi-restraints excluded: chain L6 residue 37 GLN Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L6 residue 55 ILE Chi-restraints excluded: chain L6 residue 56 MET Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 73 ASN Chi-restraints excluded: chain L6 residue 83 LYS Chi-restraints excluded: chain L7 residue 11 VAL Chi-restraints excluded: chain L7 residue 31 ASP Chi-restraints excluded: chain L7 residue 45 GLN Chi-restraints excluded: chain L7 residue 59 THR Chi-restraints excluded: chain L7 residue 76 ASN Chi-restraints excluded: chain L7 residue 79 THR Chi-restraints excluded: chain L7 residue 81 VAL Chi-restraints excluded: chain L8 residue 27 VAL Chi-restraints excluded: chain L8 residue 41 VAL Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L8 residue 82 LEU Chi-restraints excluded: chain L9 residue 15 VAL Chi-restraints excluded: chain L9 residue 24 SER Chi-restraints excluded: chain L9 residue 29 LEU Chi-restraints excluded: chain L9 residue 44 ILE Chi-restraints excluded: chain L9 residue 88 SER Chi-restraints excluded: chain LA residue 14 THR Chi-restraints excluded: chain LA residue 19 SER Chi-restraints excluded: chain LA residue 50 SER Chi-restraints excluded: chain LA residue 54 LEU Chi-restraints excluded: chain LA residue 60 THR Chi-restraints excluded: chain LB residue 13 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 66 LYS Chi-restraints excluded: chain LD residue 5 GLN Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 9 THR Chi-restraints excluded: chain LD residue 13 ILE Chi-restraints excluded: chain LD residue 23 VAL Chi-restraints excluded: chain LD residue 55 THR Chi-restraints excluded: chain LE residue 21 LYS Chi-restraints excluded: chain LE residue 23 SER Chi-restraints excluded: chain LS residue 21 LYS Chi-restraints excluded: chain LS residue 25 ASN Chi-restraints excluded: chain LS residue 39 LEU Chi-restraints excluded: chain LS residue 43 THR Chi-restraints excluded: chain LG residue 5 THR Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LH residue 58 VAL Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LI residue 27 CYS Chi-restraints excluded: chain LF residue 18 THR Chi-restraints excluded: chain LF residue 50 ILE Chi-restraints excluded: chain LF residue 55 HIS 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: 0.9990 chunk 566 optimal weight: 10.0000 chunk 551 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 overall best weight: 3.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SG 28 ASN SG 142 HIS ** SH 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 83 HIS S3 6 GLN S3 42 GLN S5 31 HIS ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 11 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** ** LJ 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 111 HIS ** LR 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** LB 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 40 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 145732 Z= 0.190 Angle : 0.658 27.140 219193 Z= 0.332 Chirality : 0.038 2.065 28395 Planarity : 0.005 0.069 11121 Dihedral : 24.920 179.867 75240 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.59 % Favored : 86.37 % Rotamer: Outliers : 6.39 % Allowed : 26.03 % Favored : 67.58 % 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: -3.89 (0.11), residues: 5042 helix: -1.88 (0.14), residues: 1176 sheet: -2.19 (0.17), residues: 824 loop : -3.14 (0.10), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPLA 48 HIS 0.009 0.001 HISSG 18 PHE 0.021 0.002 PHES5 37 TYR 0.029 0.002 TYRSB 183 ARG 0.013 0.001 ARGSE 47 *********************** 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 1284 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1060 time to evaluate : 5.358 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 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: "LEULH 61 " (corrupted residue). Skipping it. REVERT: SC 58 ARG cc_start: 0.6270 (ttm-80) cc_final: 0.5380 (mmt-90) REVERT: SC 85 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8174 (m110) REVERT: SD 70 ASP cc_start: 0.8182 (p0) cc_final: 0.7780 (p0) REVERT: SG 107 TYR cc_start: 0.7010 (m-80) cc_final: 0.6716 (m-10) REVERT: SH 44 GLU cc_start: 0.6112 (tp30) cc_final: 0.5460 (tp30) REVERT: S1 23 GLU cc_start: 0.6862 (mm-30) cc_final: 0.5623 (tt0) REVERT: S2 116 VAL cc_start: 0.8643 (t) cc_final: 0.8324 (p) REVERT: S3 107 ARG cc_start: 0.7627 (mpp80) cc_final: 0.7406 (mtm180) REVERT: S9 23 ILE cc_start: 0.6724 (mp) cc_final: 0.6320 (mm) REVERT: SI 51 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7301 (m) REVERT: SI 55 ARG cc_start: 0.5457 (ppt170) cc_final: 0.5079 (ppt170) REVERT: L2 11 ASN cc_start: 0.8579 (t160) cc_final: 0.8211 (t0) REVERT: L2 110 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8127 (pp) REVERT: LJ 45 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8751 (ptt90) REVERT: LJ 78 ILE cc_start: 0.9016 (tp) cc_final: 0.8781 (tp) REVERT: LJ 96 SER cc_start: 0.8870 (t) cc_final: 0.8596 (m) REVERT: LJ 169 ASN cc_start: 0.7729 (t0) cc_final: 0.7250 (t0) REVERT: LK 38 MET cc_start: 0.7535 (tmm) cc_final: 0.6713 (tmm) REVERT: LK 51 ASP cc_start: 0.6655 (p0) cc_final: 0.6323 (p0) REVERT: LN 2 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8529 (tt) REVERT: LN 106 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7954 (pp) REVERT: LN 120 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7710 (tm-30) REVERT: LO 10 GLU cc_start: 0.7589 (mp0) cc_final: 0.7267 (pm20) REVERT: LP 46 GLN cc_start: 0.8439 (mp10) cc_final: 0.8230 (pm20) REVERT: LP 101 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7356 (ppp80) REVERT: LR 53 LEU cc_start: 0.8958 (mm) cc_final: 0.8750 (mt) REVERT: L3 44 GLN cc_start: 0.8554 (tp40) cc_final: 0.8149 (tp40) REVERT: L3 91 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6543 (m110) REVERT: L3 94 MET cc_start: 0.7449 (mmt) cc_final: 0.7103 (mmt) REVERT: L6 20 MET cc_start: 0.9065 (mmm) cc_final: 0.8835 (tpp) REVERT: L6 56 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8284 (pmt) REVERT: L6 83 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4907 (pttt) REVERT: L7 71 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7197 (pt) REVERT: LS 26 ASN cc_start: 0.8372 (p0) cc_final: 0.8009 (p0) REVERT: LG 15 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8865 (tppp) REVERT: LF 10 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6416 (p90) REVERT: LF 53 ASP cc_start: 0.5747 (p0) cc_final: 0.5261 (m-30) REVERT: LF 55 HIS cc_start: 0.6841 (OUTLIER) cc_final: 0.6373 (t-90) outliers start: 224 outliers final: 167 residues processed: 1187 average time/residue: 1.1672 time to fit residues: 2412.2932 Evaluate side-chains 1188 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1008 time to evaluate : 5.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 6 ASN Chi-restraints excluded: chain SB residue 41 PHE Chi-restraints excluded: chain SB residue 100 ILE Chi-restraints excluded: chain SB residue 114 LEU Chi-restraints excluded: chain SB residue 119 ILE Chi-restraints excluded: chain SB residue 150 THR Chi-restraints excluded: chain SB residue 191 THR Chi-restraints excluded: chain SB residue 192 TYR Chi-restraints excluded: chain SC residue 60 LEU Chi-restraints excluded: chain SC residue 85 ASN Chi-restraints excluded: chain SD residue 17 THR Chi-restraints excluded: chain SD residue 117 LEU Chi-restraints excluded: chain SD residue 127 SER Chi-restraints excluded: chain SD residue 131 ASN Chi-restraints excluded: chain SE residue 52 ILE Chi-restraints excluded: chain SE residue 79 LEU Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SG residue 12 VAL Chi-restraints excluded: chain SG residue 20 SER Chi-restraints excluded: chain SG residue 42 ILE Chi-restraints excluded: chain SG residue 80 VAL Chi-restraints excluded: chain SG residue 87 VAL Chi-restraints excluded: chain SG residue 101 LEU Chi-restraints excluded: chain SG residue 115 THR Chi-restraints excluded: chain SF residue 25 LEU Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 74 ILE Chi-restraints excluded: chain SF residue 75 THR Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 103 ILE Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain SF residue 109 SER Chi-restraints excluded: chain SH residue 30 ILE Chi-restraints excluded: chain SH residue 47 ILE Chi-restraints excluded: chain SH residue 50 LEU Chi-restraints excluded: chain SH residue 69 VAL Chi-restraints excluded: chain SH residue 106 LEU Chi-restraints excluded: chain SH residue 112 MET Chi-restraints excluded: chain S1 residue 8 ILE Chi-restraints excluded: chain S2 residue 25 SER Chi-restraints excluded: chain S2 residue 58 SER Chi-restraints excluded: chain S2 residue 67 SER Chi-restraints excluded: chain S2 residue 71 SER Chi-restraints excluded: chain S2 residue 94 GLU Chi-restraints excluded: chain S2 residue 95 SER Chi-restraints excluded: chain S3 residue 8 VAL Chi-restraints excluded: chain S3 residue 46 VAL Chi-restraints excluded: chain S3 residue 80 ILE Chi-restraints excluded: chain S3 residue 92 VAL Chi-restraints excluded: chain S4 residue 16 VAL Chi-restraints excluded: chain S4 residue 32 LYS Chi-restraints excluded: chain S4 residue 34 LEU Chi-restraints excluded: chain S4 residue 65 VAL Chi-restraints excluded: chain S4 residue 80 LEU Chi-restraints excluded: chain S5 residue 18 VAL Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S6 residue 56 LEU Chi-restraints excluded: chain S6 residue 57 LEU Chi-restraints excluded: chain S6 residue 65 HIS Chi-restraints excluded: chain S6 residue 68 ASN Chi-restraints excluded: chain S8 residue 41 LYS Chi-restraints excluded: chain S9 residue 34 LEU Chi-restraints excluded: chain SI residue 11 VAL Chi-restraints excluded: chain SI residue 16 MET Chi-restraints excluded: chain SI residue 44 PHE Chi-restraints excluded: chain SI residue 51 VAL Chi-restraints excluded: chain SA residue 13 THR Chi-restraints excluded: chain SA residue 37 THR Chi-restraints excluded: chain SA residue 39 VAL Chi-restraints excluded: chain L2 residue 104 ILE Chi-restraints excluded: chain L2 residue 110 LEU Chi-restraints excluded: chain L2 residue 130 LEU Chi-restraints excluded: chain L2 residue 132 LEU Chi-restraints excluded: chain L2 residue 137 VAL Chi-restraints excluded: chain L2 residue 176 LEU Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain LC residue 5 ILE Chi-restraints excluded: chain LC residue 49 ILE Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 106 SER Chi-restraints excluded: chain LC residue 137 SER Chi-restraints excluded: chain LC residue 209 VAL Chi-restraints excluded: chain LC residue 216 LYS Chi-restraints excluded: chain LJ residue 19 LEU Chi-restraints excluded: chain LJ residue 45 ARG Chi-restraints excluded: chain LJ residue 89 VAL Chi-restraints excluded: chain LJ residue 125 VAL Chi-restraints excluded: chain LJ residue 131 PHE Chi-restraints excluded: chain LJ residue 154 VAL Chi-restraints excluded: chain LK residue 4 LEU Chi-restraints excluded: chain LK residue 6 GLU Chi-restraints excluded: chain LK residue 12 VAL Chi-restraints excluded: chain LK residue 67 VAL Chi-restraints excluded: chain LK residue 122 PHE Chi-restraints excluded: chain LK residue 153 ASP Chi-restraints excluded: chain LL residue 107 VAL Chi-restraints excluded: chain LL residue 175 LYS Chi-restraints excluded: chain LM residue 51 THR Chi-restraints excluded: chain LM residue 53 ASP Chi-restraints excluded: chain LM residue 55 VAL Chi-restraints excluded: chain LM residue 59 ASN Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 96 THR Chi-restraints excluded: chain LN residue 2 ILE Chi-restraints excluded: chain LN residue 10 VAL Chi-restraints excluded: chain LN residue 62 ILE Chi-restraints excluded: chain LN residue 106 LEU Chi-restraints excluded: chain LN residue 122 LEU Chi-restraints excluded: chain LO residue 69 ILE Chi-restraints excluded: chain LO residue 123 VAL Chi-restraints excluded: chain LP residue 25 ASN Chi-restraints excluded: chain LP residue 38 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 64 VAL Chi-restraints excluded: chain LP residue 72 THR Chi-restraints excluded: chain LP residue 101 ARG Chi-restraints excluded: chain LQ residue 8 ARG Chi-restraints excluded: chain LQ residue 9 THR Chi-restraints excluded: chain LQ residue 20 LEU Chi-restraints excluded: chain LQ residue 117 VAL Chi-restraints excluded: chain LQ residue 119 ILE Chi-restraints excluded: chain LR residue 3 SER Chi-restraints excluded: chain LR residue 31 LEU Chi-restraints excluded: chain LR residue 39 HIS Chi-restraints excluded: chain LR residue 44 ILE Chi-restraints excluded: chain LR residue 51 VAL Chi-restraints excluded: chain L1 residue 11 THR Chi-restraints excluded: chain L1 residue 19 LEU Chi-restraints excluded: chain L3 residue 31 LEU Chi-restraints excluded: chain L3 residue 42 SER Chi-restraints excluded: chain L3 residue 65 ILE Chi-restraints excluded: chain L3 residue 91 ASN Chi-restraints excluded: chain L3 residue 117 LEU Chi-restraints excluded: chain L4 residue 7 THR Chi-restraints excluded: chain L4 residue 25 LEU Chi-restraints excluded: chain L4 residue 80 LYS Chi-restraints excluded: chain L4 residue 81 ASN Chi-restraints excluded: chain L4 residue 96 THR Chi-restraints excluded: chain L4 residue 97 ILE Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L6 residue 31 THR Chi-restraints excluded: chain L6 residue 37 GLN Chi-restraints excluded: chain L6 residue 55 ILE Chi-restraints excluded: chain L6 residue 56 MET Chi-restraints excluded: chain L6 residue 73 ASN Chi-restraints excluded: chain L6 residue 83 LYS Chi-restraints excluded: chain L7 residue 31 ASP Chi-restraints excluded: chain L7 residue 59 THR Chi-restraints excluded: chain L7 residue 71 LEU Chi-restraints excluded: chain L7 residue 76 ASN Chi-restraints excluded: chain L7 residue 79 THR Chi-restraints excluded: chain L7 residue 81 VAL Chi-restraints excluded: chain L8 residue 18 LEU Chi-restraints excluded: chain L8 residue 27 VAL Chi-restraints excluded: chain L8 residue 41 VAL Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L9 residue 29 LEU Chi-restraints excluded: chain L9 residue 44 ILE Chi-restraints excluded: chain L9 residue 88 SER Chi-restraints excluded: chain LA residue 19 SER Chi-restraints excluded: chain LA residue 50 SER Chi-restraints excluded: chain LA residue 54 LEU Chi-restraints excluded: chain LA residue 60 THR Chi-restraints excluded: chain LB residue 6 ILE Chi-restraints excluded: chain LB residue 13 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 66 LYS Chi-restraints excluded: chain LD residue 5 GLN Chi-restraints excluded: chain LD residue 13 ILE Chi-restraints excluded: chain LD residue 55 THR Chi-restraints excluded: chain LE residue 21 LYS Chi-restraints excluded: chain LE residue 23 SER Chi-restraints excluded: chain LS residue 40 ASN Chi-restraints excluded: chain LS residue 43 THR Chi-restraints excluded: chain LG residue 5 THR Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LI residue 27 CYS Chi-restraints excluded: chain LF residue 10 HIS Chi-restraints excluded: chain LF residue 55 HIS 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: 0.0870 chunk 177 optimal weight: 40.0000 chunk 175 optimal weight: 7.9990 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: 10.0000 overall best weight: 7.6172 ------------------------------------------------------------------------------- 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 15 ASN S3 6 GLN S5 31 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 ** 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 ** L3 52 GLN ** 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** ** LB 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 40 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 145732 Z= 0.323 Angle : 0.750 27.226 219193 Z= 0.372 Chirality : 0.041 2.057 28395 Planarity : 0.005 0.086 11121 Dihedral : 24.926 179.897 75240 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 15.71 % Favored : 84.25 % Rotamer: Outliers : 7.39 % Allowed : 25.15 % Favored : 67.47 % 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: -3.95 (0.10), residues: 5042 helix: -1.87 (0.14), residues: 1177 sheet: -2.21 (0.18), residues: 792 loop : -3.21 (0.10), residues: 3073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPLA 48 HIS 0.010 0.002 HISL1 79 PHE 0.020 0.002 PHELB 26 TYR 0.034 0.002 TYRS5 16 ARG 0.010 0.001 ARGL2 60 *********************** 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 1269 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1010 time to evaluate : 5.346 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 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. revert: symmetry clash TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. REVERT: SC 58 ARG cc_start: 0.6345 (ttm-80) cc_final: 0.5509 (mmt-90) REVERT: SC 85 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8124 (m110) REVERT: SD 70 ASP cc_start: 0.8257 (p0) cc_final: 0.7860 (p0) REVERT: SG 96 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.5047 (ptp90) REVERT: SH 81 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7995 (pt) REVERT: S1 23 GLU cc_start: 0.7028 (mm-30) cc_final: 0.5682 (tt0) REVERT: S2 116 VAL cc_start: 0.8661 (t) cc_final: 0.8335 (p) REVERT: S3 107 ARG cc_start: 0.7666 (mpp80) cc_final: 0.7434 (mtm180) REVERT: S6 58 LYS cc_start: 0.8497 (tttt) cc_final: 0.8284 (mttm) REVERT: S9 23 ILE cc_start: 0.6726 (mp) cc_final: 0.6321 (mm) REVERT: SI 51 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7411 (m) REVERT: L2 11 ASN cc_start: 0.8688 (t160) cc_final: 0.8190 (t0) REVERT: L2 110 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8097 (pp) REVERT: LJ 45 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8349 (ppt-90) REVERT: LJ 78 ILE cc_start: 0.9041 (tp) cc_final: 0.8799 (tp) REVERT: LJ 96 SER cc_start: 0.8845 (t) cc_final: 0.8586 (m) REVERT: LJ 169 ASN cc_start: 0.7729 (t0) cc_final: 0.7247 (t0) REVERT: LK 5 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7515 (tttp) REVERT: LK 38 MET cc_start: 0.7654 (tmm) cc_final: 0.6839 (tmm) REVERT: LK 51 ASP cc_start: 0.6645 (p0) cc_final: 0.6297 (p0) REVERT: LN 2 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8593 (tt) REVERT: LN 106 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7951 (pp) REVERT: LO 10 GLU cc_start: 0.7640 (mp0) cc_final: 0.7290 (pm20) REVERT: LP 101 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7594 (ppp80) REVERT: LR 53 LEU cc_start: 0.9035 (mm) cc_final: 0.8798 (mt) REVERT: L3 15 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8144 (mttp) REVERT: L3 37 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8525 (mt0) REVERT: L3 44 GLN cc_start: 0.8585 (tp40) cc_final: 0.8265 (tp40) REVERT: L3 52 GLN cc_start: 0.8481 (mt0) cc_final: 0.8167 (tt0) REVERT: L3 91 ASN cc_start: 0.6839 (OUTLIER) cc_final: 0.6505 (m110) REVERT: L3 94 MET cc_start: 0.7499 (mmt) cc_final: 0.7239 (mmt) REVERT: L6 56 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8372 (pmt) REVERT: L6 83 LYS cc_start: 0.5429 (OUTLIER) cc_final: 0.5128 (pttt) REVERT: L7 71 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7314 (pt) REVERT: LG 15 LYS cc_start: 0.9123 (ttmm) cc_final: 0.8878 (tppp) REVERT: LF 10 HIS cc_start: 0.6881 (OUTLIER) cc_final: 0.6534 (p90) REVERT: LF 53 ASP cc_start: 0.6398 (p0) cc_final: 0.5359 (m-30) outliers start: 259 outliers final: 216 residues processed: 1154 average time/residue: 1.1369 time to fit residues: 2288.8949 Evaluate side-chains 1223 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 990 time to evaluate : 5.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 6 ASN Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 41 PHE Chi-restraints excluded: chain SB residue 100 ILE Chi-restraints excluded: chain SB residue 114 LEU Chi-restraints excluded: chain SB residue 119 ILE Chi-restraints excluded: chain SB residue 138 THR Chi-restraints excluded: chain SB residue 148 ILE Chi-restraints excluded: chain SB residue 150 THR Chi-restraints excluded: chain SB residue 161 ILE Chi-restraints excluded: chain SB residue 191 THR Chi-restraints excluded: chain SB residue 192 TYR Chi-restraints excluded: chain SC residue 60 LEU Chi-restraints excluded: chain SC residue 85 ASN Chi-restraints excluded: chain SD residue 17 THR Chi-restraints excluded: chain SD residue 117 LEU Chi-restraints excluded: chain SD residue 127 SER Chi-restraints excluded: chain SE residue 52 ILE Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SG residue 12 VAL Chi-restraints excluded: chain SG residue 20 SER Chi-restraints excluded: chain SG residue 42 ILE Chi-restraints excluded: chain SG residue 45 SER Chi-restraints excluded: chain SG residue 80 VAL Chi-restraints excluded: chain SG residue 87 VAL Chi-restraints excluded: chain SG residue 96 ARG Chi-restraints excluded: chain SG residue 101 LEU Chi-restraints excluded: chain SG residue 115 THR Chi-restraints excluded: chain SF residue 7 ILE Chi-restraints excluded: chain SF residue 25 LEU Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 74 ILE Chi-restraints excluded: chain SF residue 75 THR Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 103 ILE Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain SF residue 109 SER Chi-restraints excluded: chain SH residue 30 ILE Chi-restraints excluded: chain SH residue 47 ILE Chi-restraints excluded: chain SH residue 50 LEU Chi-restraints excluded: chain SH residue 69 VAL Chi-restraints excluded: chain SH residue 81 ILE Chi-restraints excluded: chain SH residue 106 LEU Chi-restraints excluded: chain SH residue 112 MET Chi-restraints excluded: chain S1 residue 8 ILE Chi-restraints excluded: chain S2 residue 15 ASN Chi-restraints excluded: chain S2 residue 23 ILE Chi-restraints excluded: chain S2 residue 25 SER Chi-restraints excluded: chain S2 residue 26 THR Chi-restraints excluded: chain S2 residue 58 SER Chi-restraints excluded: chain S2 residue 71 SER Chi-restraints excluded: chain S2 residue 84 VAL Chi-restraints excluded: chain S2 residue 95 SER Chi-restraints excluded: chain S3 residue 8 VAL Chi-restraints excluded: chain S3 residue 46 VAL Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 80 ILE Chi-restraints excluded: chain S3 residue 92 VAL Chi-restraints excluded: chain S4 residue 16 VAL Chi-restraints excluded: chain S4 residue 32 LYS Chi-restraints excluded: chain S4 residue 34 LEU Chi-restraints excluded: chain S4 residue 65 VAL Chi-restraints excluded: chain S4 residue 80 LEU Chi-restraints excluded: chain S5 residue 18 VAL Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S6 residue 56 LEU Chi-restraints excluded: chain S6 residue 57 LEU Chi-restraints excluded: chain S6 residue 60 VAL Chi-restraints excluded: chain S6 residue 65 HIS Chi-restraints excluded: chain S6 residue 68 ASN Chi-restraints excluded: chain S7 residue 30 ASP Chi-restraints excluded: chain S8 residue 11 VAL Chi-restraints excluded: chain S8 residue 32 THR Chi-restraints excluded: chain S8 residue 41 LYS Chi-restraints excluded: chain S8 residue 63 ILE Chi-restraints excluded: chain S9 residue 34 LEU Chi-restraints excluded: chain SI residue 11 VAL Chi-restraints excluded: chain SI residue 16 MET Chi-restraints excluded: chain SI residue 44 PHE Chi-restraints excluded: chain SI residue 51 VAL Chi-restraints excluded: chain SA residue 13 THR Chi-restraints excluded: chain SA residue 37 THR Chi-restraints excluded: chain SA residue 39 VAL Chi-restraints excluded: chain L2 residue 104 ILE Chi-restraints excluded: chain L2 residue 110 LEU Chi-restraints excluded: chain L2 residue 130 LEU Chi-restraints excluded: chain L2 residue 132 LEU Chi-restraints excluded: chain L2 residue 137 VAL Chi-restraints excluded: chain L2 residue 146 LEU Chi-restraints excluded: chain L2 residue 176 LEU Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain LC residue 5 ILE Chi-restraints excluded: chain LC residue 16 PHE Chi-restraints excluded: chain LC residue 49 ILE Chi-restraints excluded: chain LC residue 54 GLU Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 101 VAL Chi-restraints excluded: chain LC residue 106 SER Chi-restraints excluded: chain LC residue 137 SER Chi-restraints excluded: chain LC residue 194 VAL Chi-restraints excluded: chain LC residue 195 ILE Chi-restraints excluded: chain LC residue 209 VAL Chi-restraints excluded: chain LC residue 216 LYS Chi-restraints excluded: chain LJ residue 19 LEU Chi-restraints excluded: chain LJ residue 45 ARG Chi-restraints excluded: chain LJ residue 89 VAL Chi-restraints excluded: chain LJ residue 125 VAL Chi-restraints excluded: chain LJ residue 126 VAL Chi-restraints excluded: chain LJ residue 131 PHE Chi-restraints excluded: chain LJ residue 154 VAL Chi-restraints excluded: chain LK residue 4 LEU Chi-restraints excluded: chain LK residue 5 LYS Chi-restraints excluded: chain LK residue 6 GLU Chi-restraints excluded: chain LK residue 12 VAL Chi-restraints excluded: chain LK residue 28 VAL Chi-restraints excluded: chain LK residue 67 VAL Chi-restraints excluded: chain LK residue 122 PHE Chi-restraints excluded: chain LK residue 153 ASP Chi-restraints excluded: chain LL residue 107 VAL Chi-restraints excluded: chain LL residue 175 LYS Chi-restraints excluded: chain LM residue 51 THR Chi-restraints excluded: chain LM residue 53 ASP Chi-restraints excluded: chain LM residue 55 VAL Chi-restraints excluded: chain LM residue 59 ASN Chi-restraints excluded: chain LM residue 71 THR Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 96 THR Chi-restraints excluded: chain LN residue 2 ILE Chi-restraints excluded: chain LN residue 10 VAL Chi-restraints excluded: chain LN residue 40 VAL Chi-restraints excluded: chain LN residue 62 ILE Chi-restraints excluded: chain LN residue 98 ILE Chi-restraints excluded: chain LN residue 106 LEU Chi-restraints excluded: chain LN residue 122 LEU Chi-restraints excluded: chain LO residue 3 LEU Chi-restraints excluded: chain LO residue 69 ILE Chi-restraints excluded: chain LO residue 123 VAL Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 25 ASN Chi-restraints excluded: chain LP residue 38 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 64 VAL Chi-restraints excluded: chain LP residue 72 THR Chi-restraints excluded: chain LP residue 101 ARG Chi-restraints excluded: chain LP residue 125 LEU Chi-restraints excluded: chain LQ residue 8 ARG Chi-restraints excluded: chain LQ residue 10 SER Chi-restraints excluded: chain LQ residue 20 LEU Chi-restraints excluded: chain LQ residue 34 GLU Chi-restraints excluded: chain LQ residue 117 VAL Chi-restraints excluded: chain LQ residue 119 ILE Chi-restraints excluded: chain LR residue 2 ILE Chi-restraints excluded: chain LR residue 3 SER Chi-restraints excluded: chain LR residue 31 LEU Chi-restraints excluded: chain LR residue 39 HIS Chi-restraints excluded: chain LR residue 44 ILE Chi-restraints excluded: chain LR residue 51 VAL Chi-restraints excluded: chain L1 residue 11 THR Chi-restraints excluded: chain L1 residue 19 LEU Chi-restraints excluded: chain L1 residue 27 THR Chi-restraints excluded: chain L1 residue 32 VAL Chi-restraints excluded: chain L1 residue 44 VAL Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L3 residue 15 LYS Chi-restraints excluded: chain L3 residue 27 SER Chi-restraints excluded: chain L3 residue 31 LEU Chi-restraints excluded: chain L3 residue 34 VAL Chi-restraints excluded: chain L3 residue 37 GLN Chi-restraints excluded: chain L3 residue 42 SER Chi-restraints excluded: chain L3 residue 65 ILE Chi-restraints excluded: chain L3 residue 74 MET Chi-restraints excluded: chain L3 residue 89 ASP Chi-restraints excluded: chain L3 residue 91 ASN Chi-restraints excluded: chain L3 residue 109 LEU Chi-restraints excluded: chain L3 residue 117 LEU Chi-restraints excluded: chain L4 residue 7 THR Chi-restraints excluded: chain L4 residue 25 LEU Chi-restraints excluded: chain L4 residue 27 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L4 residue 80 LYS Chi-restraints excluded: chain L4 residue 96 THR Chi-restraints excluded: chain L4 residue 97 ILE Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 50 VAL Chi-restraints excluded: chain L6 residue 31 THR Chi-restraints excluded: chain L6 residue 33 VAL Chi-restraints excluded: chain L6 residue 37 GLN Chi-restraints excluded: chain L6 residue 55 ILE Chi-restraints excluded: chain L6 residue 56 MET Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 73 ASN Chi-restraints excluded: chain L6 residue 83 LYS Chi-restraints excluded: chain L7 residue 11 VAL Chi-restraints excluded: chain L7 residue 31 ASP Chi-restraints excluded: chain L7 residue 59 THR Chi-restraints excluded: chain L7 residue 71 LEU Chi-restraints excluded: chain L7 residue 76 ASN Chi-restraints excluded: chain L7 residue 79 THR Chi-restraints excluded: chain L7 residue 81 VAL Chi-restraints excluded: chain L7 residue 93 ILE Chi-restraints excluded: chain L8 residue 18 LEU Chi-restraints excluded: chain L8 residue 27 VAL Chi-restraints excluded: chain L8 residue 41 VAL Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L9 residue 15 VAL Chi-restraints excluded: chain L9 residue 24 SER Chi-restraints excluded: chain L9 residue 29 LEU Chi-restraints excluded: chain L9 residue 44 ILE Chi-restraints excluded: chain L9 residue 88 SER Chi-restraints excluded: chain LA residue 19 SER Chi-restraints excluded: chain LA residue 36 VAL Chi-restraints excluded: chain LA residue 50 SER Chi-restraints excluded: chain LA residue 54 LEU Chi-restraints excluded: chain LA residue 60 THR Chi-restraints excluded: chain LB residue 6 ILE Chi-restraints excluded: chain LB residue 13 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 66 LYS Chi-restraints excluded: chain LD residue 5 GLN Chi-restraints excluded: chain LD residue 13 ILE Chi-restraints excluded: chain LD residue 55 THR Chi-restraints excluded: chain LE residue 7 ARG Chi-restraints excluded: chain LE residue 21 LYS Chi-restraints excluded: chain LE residue 23 SER Chi-restraints excluded: chain LE residue 24 VAL Chi-restraints excluded: chain LS residue 43 THR Chi-restraints excluded: chain LG residue 5 THR Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LH residue 7 HIS Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LI residue 27 CYS Chi-restraints excluded: chain LF residue 10 HIS Chi-restraints excluded: chain LF residue 55 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 823 optimal weight: 9.9990 chunk 867 optimal weight: 10.0000 chunk 791 optimal weight: 10.0000 chunk 843 optimal weight: 5.9990 chunk 866 optimal weight: 10.0000 chunk 507 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 662 optimal weight: 5.9990 chunk 258 optimal weight: 0.9980 chunk 762 optimal weight: 0.0040 chunk 797 optimal weight: 1.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- 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** S3 6 GLN S5 31 HIS ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 11 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** ** 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3 91 ASN ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 34 GLN ** LB 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 32 ASN LS 40 ASN LH 31 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 145732 Z= 0.172 Angle : 0.640 27.125 219193 Z= 0.322 Chirality : 0.037 2.064 28395 Planarity : 0.004 0.070 11121 Dihedral : 24.833 179.865 75240 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.46 % Favored : 87.50 % Rotamer: Outliers : 6.33 % Allowed : 26.23 % Favored : 67.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.11), residues: 5042 helix: -1.65 (0.14), residues: 1183 sheet: -2.05 (0.18), residues: 815 loop : -3.11 (0.10), residues: 3044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPSI 34 HIS 0.008 0.001 HISSF 22 PHE 0.020 0.001 PHES5 37 TYR 0.029 0.002 TYRSB 183 ARG 0.011 0.001 ARGL2 60 *********************** 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 1254 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1032 time to evaluate : 5.341 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 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. revert: symmetry clash TARDY: cannot create tardy model for: "LYSLB 66 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEULH 61 " (corrupted residue). Skipping it. REVERT: SC 58 ARG cc_start: 0.6306 (ttm-80) cc_final: 0.5412 (mmt-90) REVERT: SC 85 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.8065 (m110) REVERT: SD 70 ASP cc_start: 0.8155 (p0) cc_final: 0.7853 (p0) REVERT: SG 96 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.4960 (ptp90) REVERT: SG 107 TYR cc_start: 0.7035 (m-80) cc_final: 0.6623 (m-10) REVERT: SH 81 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7957 (pt) REVERT: S1 23 GLU cc_start: 0.6801 (mm-30) cc_final: 0.5550 (tt0) REVERT: S2 116 VAL cc_start: 0.8605 (t) cc_final: 0.8274 (p) REVERT: S9 23 ILE cc_start: 0.6785 (mp) cc_final: 0.6363 (mm) REVERT: SI 51 VAL cc_start: 0.7521 (OUTLIER) cc_final: 0.7309 (m) REVERT: SA 23 SER cc_start: 0.7616 (m) cc_final: 0.7400 (t) REVERT: L2 11 ASN cc_start: 0.8550 (t160) cc_final: 0.8192 (t0) REVERT: L2 110 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8204 (pp) REVERT: LJ 45 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8749 (ptt90) REVERT: LJ 78 ILE cc_start: 0.8996 (tp) cc_final: 0.8784 (tp) REVERT: LJ 96 SER cc_start: 0.8861 (t) cc_final: 0.8596 (m) REVERT: LK 5 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7670 (tptp) REVERT: LK 38 MET cc_start: 0.7535 (tmm) cc_final: 0.6781 (tmm) REVERT: LK 51 ASP cc_start: 0.6526 (p0) cc_final: 0.6299 (p0) REVERT: LN 2 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8515 (tt) REVERT: LN 106 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7817 (pp) REVERT: LN 120 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7836 (tm-30) REVERT: LO 10 GLU cc_start: 0.7607 (mp0) cc_final: 0.7352 (pm20) REVERT: LR 53 LEU cc_start: 0.8947 (mm) cc_final: 0.8718 (mt) REVERT: L1 65 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8844 (ptpp) REVERT: L3 15 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8035 (mttp) REVERT: L3 37 GLN cc_start: 0.8708 (mt0) cc_final: 0.8463 (mt0) REVERT: L3 44 GLN cc_start: 0.8351 (tp40) cc_final: 0.8036 (tp40) REVERT: L3 94 MET cc_start: 0.7344 (mmt) cc_final: 0.7126 (mmt) REVERT: L5 4 LYS cc_start: 0.8814 (pttt) cc_final: 0.8611 (pttt) REVERT: L5 49 LYS cc_start: 0.8237 (tppt) cc_final: 0.7808 (tppt) REVERT: L6 56 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8244 (pmt) REVERT: L7 71 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6994 (pt) REVERT: LG 15 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8861 (tppp) REVERT: LF 5 ILE cc_start: 0.8179 (pp) cc_final: 0.7970 (pp) REVERT: LF 10 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.6530 (p90) REVERT: LF 53 ASP cc_start: 0.6080 (p0) cc_final: 0.5167 (m-30) REVERT: LF 55 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6384 (t-90) outliers start: 222 outliers final: 178 residues processed: 1150 average time/residue: 1.1541 time to fit residues: 2319.7698 Evaluate side-chains 1185 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 992 time to evaluate : 5.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 6 ASN Chi-restraints excluded: chain SB residue 41 PHE Chi-restraints excluded: chain SB residue 100 ILE Chi-restraints excluded: chain SB residue 114 LEU Chi-restraints excluded: chain SB residue 119 ILE Chi-restraints excluded: chain SB residue 138 THR Chi-restraints excluded: chain SB residue 148 ILE Chi-restraints excluded: chain SB residue 191 THR Chi-restraints excluded: chain SB residue 192 TYR Chi-restraints excluded: chain SC residue 60 LEU Chi-restraints excluded: chain SC residue 85 ASN Chi-restraints excluded: chain SD residue 17 THR Chi-restraints excluded: chain SD residue 117 LEU Chi-restraints excluded: chain SD residue 127 SER Chi-restraints excluded: chain SE residue 39 GLU Chi-restraints excluded: chain SE residue 52 ILE Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SG residue 20 SER Chi-restraints excluded: chain SG residue 45 SER Chi-restraints excluded: chain SG residue 80 VAL Chi-restraints excluded: chain SG residue 87 VAL Chi-restraints excluded: chain SG residue 96 ARG Chi-restraints excluded: chain SG residue 101 LEU Chi-restraints excluded: chain SF residue 25 LEU Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 74 ILE Chi-restraints excluded: chain SF residue 75 THR Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 103 ILE Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain SF residue 109 SER Chi-restraints excluded: chain SH residue 30 ILE Chi-restraints excluded: chain SH residue 47 ILE Chi-restraints excluded: chain SH residue 50 LEU Chi-restraints excluded: chain SH residue 81 ILE Chi-restraints excluded: chain SH residue 106 LEU Chi-restraints excluded: chain SH residue 112 MET Chi-restraints excluded: chain S1 residue 8 ILE Chi-restraints excluded: chain S2 residue 23 ILE Chi-restraints excluded: chain S2 residue 25 SER Chi-restraints excluded: chain S2 residue 58 SER Chi-restraints excluded: chain S2 residue 67 SER Chi-restraints excluded: chain S2 residue 71 SER Chi-restraints excluded: chain S2 residue 84 VAL Chi-restraints excluded: chain S2 residue 94 GLU Chi-restraints excluded: chain S2 residue 112 ASP Chi-restraints excluded: chain S3 residue 69 ARG Chi-restraints excluded: chain S3 residue 80 ILE Chi-restraints excluded: chain S3 residue 92 VAL Chi-restraints excluded: chain S4 residue 16 VAL Chi-restraints excluded: chain S4 residue 34 LEU Chi-restraints excluded: chain S4 residue 65 VAL Chi-restraints excluded: chain S4 residue 80 LEU Chi-restraints excluded: chain S5 residue 18 VAL Chi-restraints excluded: chain S6 residue 56 LEU Chi-restraints excluded: chain S6 residue 57 LEU Chi-restraints excluded: chain S6 residue 60 VAL Chi-restraints excluded: chain S6 residue 65 HIS Chi-restraints excluded: chain S6 residue 75 ILE Chi-restraints excluded: chain S8 residue 41 LYS Chi-restraints excluded: chain S9 residue 34 LEU Chi-restraints excluded: chain SI residue 11 VAL Chi-restraints excluded: chain SI residue 16 MET Chi-restraints excluded: chain SI residue 44 PHE Chi-restraints excluded: chain SI residue 51 VAL Chi-restraints excluded: chain SA residue 13 THR Chi-restraints excluded: chain SA residue 39 VAL Chi-restraints excluded: chain L2 residue 104 ILE Chi-restraints excluded: chain L2 residue 110 LEU Chi-restraints excluded: chain L2 residue 130 LEU Chi-restraints excluded: chain L2 residue 132 LEU Chi-restraints excluded: chain L2 residue 137 VAL Chi-restraints excluded: chain L2 residue 146 LEU Chi-restraints excluded: chain L2 residue 172 VAL Chi-restraints excluded: chain L2 residue 176 LEU Chi-restraints excluded: chain LC residue 5 ILE Chi-restraints excluded: chain LC residue 13 THR Chi-restraints excluded: chain LC residue 16 PHE Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 106 SER Chi-restraints excluded: chain LC residue 137 SER Chi-restraints excluded: chain LC residue 195 ILE Chi-restraints excluded: chain LC residue 209 VAL Chi-restraints excluded: chain LC residue 216 LYS Chi-restraints excluded: chain LJ residue 19 LEU Chi-restraints excluded: chain LJ residue 45 ARG Chi-restraints excluded: chain LJ residue 89 VAL Chi-restraints excluded: chain LJ residue 125 VAL Chi-restraints excluded: chain LJ residue 131 PHE Chi-restraints excluded: chain LJ residue 154 VAL Chi-restraints excluded: chain LK residue 4 LEU Chi-restraints excluded: chain LK residue 5 LYS Chi-restraints excluded: chain LK residue 6 GLU Chi-restraints excluded: chain LK residue 67 VAL Chi-restraints excluded: chain LK residue 122 PHE Chi-restraints excluded: chain LK residue 153 ASP Chi-restraints excluded: chain LL residue 107 VAL Chi-restraints excluded: chain LL residue 175 LYS Chi-restraints excluded: chain LM residue 51 THR Chi-restraints excluded: chain LM residue 53 ASP Chi-restraints excluded: chain LM residue 55 VAL Chi-restraints excluded: chain LM residue 59 ASN Chi-restraints excluded: chain LM residue 71 THR Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 96 THR Chi-restraints excluded: chain LN residue 2 ILE Chi-restraints excluded: chain LN residue 10 VAL Chi-restraints excluded: chain LN residue 40 VAL Chi-restraints excluded: chain LN residue 62 ILE Chi-restraints excluded: chain LN residue 106 LEU Chi-restraints excluded: chain LN residue 122 LEU Chi-restraints excluded: chain LO residue 69 ILE Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 25 ASN Chi-restraints excluded: chain LP residue 38 THR Chi-restraints excluded: chain LP residue 64 VAL Chi-restraints excluded: chain LP residue 72 THR Chi-restraints excluded: chain LQ residue 8 ARG Chi-restraints excluded: chain LQ residue 9 THR Chi-restraints excluded: chain LQ residue 10 SER Chi-restraints excluded: chain LQ residue 20 LEU Chi-restraints excluded: chain LQ residue 34 GLU Chi-restraints excluded: chain LQ residue 117 VAL Chi-restraints excluded: chain LR residue 2 ILE Chi-restraints excluded: chain LR residue 31 LEU Chi-restraints excluded: chain LR residue 39 HIS Chi-restraints excluded: chain LR residue 44 ILE Chi-restraints excluded: chain L1 residue 11 THR Chi-restraints excluded: chain L1 residue 19 LEU Chi-restraints excluded: chain L1 residue 27 THR Chi-restraints excluded: chain L1 residue 65 LYS Chi-restraints excluded: chain L1 residue 68 SER Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L1 residue 102 LEU Chi-restraints excluded: chain L3 residue 4 VAL Chi-restraints excluded: chain L3 residue 15 LYS Chi-restraints excluded: chain L3 residue 31 LEU Chi-restraints excluded: chain L3 residue 42 SER Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L3 residue 89 ASP Chi-restraints excluded: chain L3 residue 109 LEU Chi-restraints excluded: chain L3 residue 117 LEU Chi-restraints excluded: chain L4 residue 7 THR Chi-restraints excluded: chain L4 residue 25 LEU Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L4 residue 80 LYS Chi-restraints excluded: chain L4 residue 81 ASN Chi-restraints excluded: chain L4 residue 96 THR Chi-restraints excluded: chain L4 residue 97 ILE Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L6 residue 37 GLN Chi-restraints excluded: chain L6 residue 55 ILE Chi-restraints excluded: chain L6 residue 56 MET Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 73 ASN Chi-restraints excluded: chain L7 residue 31 ASP Chi-restraints excluded: chain L7 residue 66 SER Chi-restraints excluded: chain L7 residue 71 LEU Chi-restraints excluded: chain L7 residue 76 ASN Chi-restraints excluded: chain L7 residue 79 THR Chi-restraints excluded: chain L7 residue 81 VAL Chi-restraints excluded: chain L7 residue 93 ILE Chi-restraints excluded: chain L8 residue 18 LEU Chi-restraints excluded: chain L8 residue 27 VAL Chi-restraints excluded: chain L8 residue 41 VAL Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L8 residue 86 ILE Chi-restraints excluded: chain L9 residue 15 VAL Chi-restraints excluded: chain L9 residue 24 SER Chi-restraints excluded: chain L9 residue 44 ILE Chi-restraints excluded: chain L9 residue 88 SER Chi-restraints excluded: chain LA residue 36 VAL Chi-restraints excluded: chain LA residue 50 SER Chi-restraints excluded: chain LA residue 54 LEU Chi-restraints excluded: chain LA residue 60 THR Chi-restraints excluded: chain LB residue 6 ILE Chi-restraints excluded: chain LB residue 13 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 66 LYS Chi-restraints excluded: chain LD residue 5 GLN Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 9 THR Chi-restraints excluded: chain LD residue 13 ILE Chi-restraints excluded: chain LE residue 21 LYS Chi-restraints excluded: chain LE residue 23 SER Chi-restraints excluded: chain LS residue 40 ASN Chi-restraints excluded: chain LS residue 43 THR Chi-restraints excluded: chain LG residue 5 THR Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LI residue 27 CYS Chi-restraints excluded: chain LF residue 10 HIS Chi-restraints excluded: chain LF residue 55 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 939 random chunks: chunk 840 optimal weight: 7.9990 chunk 553 optimal weight: 10.0000 chunk 891 optimal weight: 0.0070 chunk 544 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 619 optimal weight: 10.0000 chunk 935 optimal weight: 6.9990 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: 6.6006 ------------------------------------------------------------------------------- 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** S1 15 HIS S2 28 ASN S3 6 GLN S5 31 HIS ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 226 ASN ** 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 ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 40 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 145732 Z= 0.294 Angle : 0.719 27.215 219193 Z= 0.357 Chirality : 0.039 2.056 28395 Planarity : 0.005 0.109 11121 Dihedral : 24.834 179.863 75240 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 15.47 % Favored : 84.49 % Rotamer: Outliers : 6.05 % Allowed : 26.60 % Favored : 67.35 % 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: -3.78 (0.11), residues: 5042 helix: -1.64 (0.14), residues: 1176 sheet: -2.07 (0.18), residues: 794 loop : -3.15 (0.10), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPLA 48 HIS 0.009 0.001 HISSF 22 PHE 0.030 0.002 PHEL3 25 TYR 0.072 0.002 TYRSF 51 ARG 0.017 0.001 ARGLP 101 ********************** 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 1205 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 993 time to evaluate : 5.369 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. 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. 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. REVERT: SB 18 TRP cc_start: 0.8576 (m-10) cc_final: 0.8236 (m100) REVERT: SB 36 LEU cc_start: 0.8209 (pp) cc_final: 0.7976 (mp) REVERT: SC 58 ARG cc_start: 0.6252 (ttm-80) cc_final: 0.5463 (mmt-90) REVERT: SD 70 ASP cc_start: 0.8266 (p0) cc_final: 0.7889 (p0) REVERT: SE 88 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7355 (mtt90) REVERT: SG 96 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.4995 (ptp90) REVERT: SG 107 TYR cc_start: 0.7077 (m-80) cc_final: 0.6704 (m-10) REVERT: SH 81 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7908 (pt) REVERT: S1 23 GLU cc_start: 0.6964 (mm-30) cc_final: 0.5619 (tt0) REVERT: S2 17 GLU cc_start: 0.5262 (tp30) cc_final: 0.5034 (mt-10) REVERT: S2 98 ARG cc_start: 0.7156 (ptm160) cc_final: 0.6643 (ttp-170) REVERT: S2 116 VAL cc_start: 0.8613 (t) cc_final: 0.8254 (p) REVERT: S8 13 LYS cc_start: 0.6054 (mmmt) cc_final: 0.5355 (mmmt) REVERT: S8 14 VAL cc_start: 0.7897 (m) cc_final: 0.7601 (t) REVERT: S9 23 ILE cc_start: 0.6703 (mp) cc_final: 0.6296 (mm) REVERT: SI 51 VAL cc_start: 0.7616 (OUTLIER) cc_final: 0.7406 (m) REVERT: L2 11 ASN cc_start: 0.8682 (t160) cc_final: 0.8171 (t0) REVERT: L2 110 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8222 (pp) REVERT: LJ 45 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8403 (ppt-90) REVERT: LJ 78 ILE cc_start: 0.9020 (tp) cc_final: 0.8798 (tp) REVERT: LJ 96 SER cc_start: 0.8848 (t) cc_final: 0.8589 (m) REVERT: LJ 169 ASN cc_start: 0.7695 (t0) cc_final: 0.7221 (t0) REVERT: LK 5 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7482 (tttp) REVERT: LK 38 MET cc_start: 0.7620 (tmm) cc_final: 0.6843 (tmm) REVERT: LK 51 ASP cc_start: 0.6604 (p0) cc_final: 0.6326 (p0) REVERT: LN 2 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8519 (tt) REVERT: LN 106 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7852 (pp) REVERT: LN 120 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7797 (tm-30) REVERT: LO 10 GLU cc_start: 0.7645 (mp0) cc_final: 0.7311 (pm20) REVERT: LR 53 LEU cc_start: 0.9020 (mm) cc_final: 0.8780 (mt) REVERT: L3 15 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8052 (mttp) REVERT: L3 37 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8557 (mt0) REVERT: L3 44 GLN cc_start: 0.8535 (tp40) cc_final: 0.8211 (tp40) REVERT: L4 90 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: L6 56 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8373 (pmt) REVERT: L7 71 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7160 (pt) REVERT: LG 15 LYS cc_start: 0.9146 (ttmm) cc_final: 0.8924 (tppp) REVERT: LF 53 ASP cc_start: 0.6109 (p0) cc_final: 0.5231 (m-30) outliers start: 212 outliers final: 176 residues processed: 1112 average time/residue: 1.1215 time to fit residues: 2179.6725 Evaluate side-chains 1172 residues out of total 4346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 983 time to evaluate : 5.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 6 ASN Chi-restraints excluded: chain SB residue 17 ASP Chi-restraints excluded: chain SB residue 41 PHE Chi-restraints excluded: chain SB residue 100 ILE Chi-restraints excluded: chain SB residue 114 LEU Chi-restraints excluded: chain SB residue 119 ILE Chi-restraints excluded: chain SB residue 138 THR Chi-restraints excluded: chain SB residue 148 ILE Chi-restraints excluded: chain SB residue 191 THR Chi-restraints excluded: chain SC residue 60 LEU Chi-restraints excluded: chain SD residue 17 THR Chi-restraints excluded: chain SD residue 117 LEU Chi-restraints excluded: chain SD residue 127 SER Chi-restraints excluded: chain SE residue 52 ILE Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SG residue 20 SER Chi-restraints excluded: chain SG residue 80 VAL Chi-restraints excluded: chain SG residue 87 VAL Chi-restraints excluded: chain SG residue 96 ARG Chi-restraints excluded: chain SG residue 101 LEU Chi-restraints excluded: chain SF residue 25 LEU Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 74 ILE Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain SF residue 109 SER Chi-restraints excluded: chain SH residue 30 ILE Chi-restraints excluded: chain SH residue 47 ILE Chi-restraints excluded: chain SH residue 50 LEU Chi-restraints excluded: chain SH residue 81 ILE Chi-restraints excluded: chain SH residue 106 LEU Chi-restraints excluded: chain SH residue 112 MET Chi-restraints excluded: chain S1 residue 8 ILE Chi-restraints excluded: chain S1 residue 15 HIS Chi-restraints excluded: chain S2 residue 23 ILE Chi-restraints excluded: chain S2 residue 25 SER Chi-restraints excluded: chain S2 residue 26 THR Chi-restraints excluded: chain S2 residue 58 SER Chi-restraints excluded: chain S2 residue 67 SER Chi-restraints excluded: chain S2 residue 71 SER Chi-restraints excluded: chain S2 residue 84 VAL Chi-restraints excluded: chain S2 residue 112 ASP Chi-restraints excluded: chain S3 residue 80 ILE Chi-restraints excluded: chain S3 residue 92 VAL Chi-restraints excluded: chain S4 residue 16 VAL Chi-restraints excluded: chain S4 residue 32 LYS Chi-restraints excluded: chain S4 residue 34 LEU Chi-restraints excluded: chain S4 residue 65 VAL Chi-restraints excluded: chain S5 residue 18 VAL Chi-restraints excluded: chain S6 residue 56 LEU Chi-restraints excluded: chain S6 residue 57 LEU Chi-restraints excluded: chain S6 residue 60 VAL Chi-restraints excluded: chain S6 residue 65 HIS Chi-restraints excluded: chain S9 residue 34 LEU Chi-restraints excluded: chain SI residue 11 VAL Chi-restraints excluded: chain SI residue 16 MET Chi-restraints excluded: chain SI residue 44 PHE Chi-restraints excluded: chain SI residue 51 VAL Chi-restraints excluded: chain SA residue 13 THR Chi-restraints excluded: chain SA residue 37 THR Chi-restraints excluded: chain SA residue 39 VAL Chi-restraints excluded: chain L2 residue 104 ILE Chi-restraints excluded: chain L2 residue 110 LEU Chi-restraints excluded: chain L2 residue 130 LEU Chi-restraints excluded: chain L2 residue 132 LEU Chi-restraints excluded: chain L2 residue 137 VAL Chi-restraints excluded: chain L2 residue 146 LEU Chi-restraints excluded: chain L2 residue 172 VAL Chi-restraints excluded: chain L2 residue 176 LEU Chi-restraints excluded: chain LC residue 5 ILE Chi-restraints excluded: chain LC residue 13 THR Chi-restraints excluded: chain LC residue 16 PHE Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 106 SER Chi-restraints excluded: chain LC residue 137 SER Chi-restraints excluded: chain LC residue 195 ILE Chi-restraints excluded: chain LC residue 209 VAL Chi-restraints excluded: chain LC residue 216 LYS Chi-restraints excluded: chain LJ residue 19 LEU Chi-restraints excluded: chain LJ residue 45 ARG Chi-restraints excluded: chain LJ residue 89 VAL Chi-restraints excluded: chain LJ residue 125 VAL Chi-restraints excluded: chain LJ residue 131 PHE Chi-restraints excluded: chain LJ residue 154 VAL Chi-restraints excluded: chain LK residue 4 LEU Chi-restraints excluded: chain LK residue 5 LYS Chi-restraints excluded: chain LK residue 6 GLU Chi-restraints excluded: chain LK residue 12 VAL Chi-restraints excluded: chain LK residue 28 VAL Chi-restraints excluded: chain LK residue 67 VAL Chi-restraints excluded: chain LK residue 122 PHE Chi-restraints excluded: chain LK residue 153 ASP Chi-restraints excluded: chain LL residue 107 VAL Chi-restraints excluded: chain LL residue 175 LYS Chi-restraints excluded: chain LM residue 53 ASP Chi-restraints excluded: chain LM residue 59 ASN Chi-restraints excluded: chain LM residue 71 THR Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 96 THR Chi-restraints excluded: chain LN residue 2 ILE Chi-restraints excluded: chain LN residue 10 VAL Chi-restraints excluded: chain LN residue 40 VAL Chi-restraints excluded: chain LN residue 62 ILE Chi-restraints excluded: chain LN residue 106 LEU Chi-restraints excluded: chain LN residue 122 LEU Chi-restraints excluded: chain LO residue 69 ILE Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 25 ASN Chi-restraints excluded: chain LP residue 38 THR Chi-restraints excluded: chain LP residue 52 ILE Chi-restraints excluded: chain LP residue 64 VAL Chi-restraints excluded: chain LP residue 72 THR Chi-restraints excluded: chain LQ residue 8 ARG Chi-restraints excluded: chain LQ residue 10 SER Chi-restraints excluded: chain LQ residue 20 LEU Chi-restraints excluded: chain LQ residue 34 GLU Chi-restraints excluded: chain LQ residue 117 VAL Chi-restraints excluded: chain LR residue 2 ILE Chi-restraints excluded: chain LR residue 3 SER Chi-restraints excluded: chain LR residue 31 LEU Chi-restraints excluded: chain LR residue 39 HIS Chi-restraints excluded: chain LR residue 44 ILE Chi-restraints excluded: chain L1 residue 11 THR Chi-restraints excluded: chain L1 residue 19 LEU Chi-restraints excluded: chain L1 residue 27 THR Chi-restraints excluded: chain L1 residue 32 VAL Chi-restraints excluded: chain L1 residue 68 SER Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L3 residue 4 VAL Chi-restraints excluded: chain L3 residue 15 LYS Chi-restraints excluded: chain L3 residue 27 SER Chi-restraints excluded: chain L3 residue 31 LEU Chi-restraints excluded: chain L3 residue 34 VAL Chi-restraints excluded: chain L3 residue 37 GLN Chi-restraints excluded: chain L3 residue 42 SER Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L3 residue 89 ASP Chi-restraints excluded: chain L3 residue 109 LEU Chi-restraints excluded: chain L3 residue 117 LEU Chi-restraints excluded: chain L4 residue 7 THR Chi-restraints excluded: chain L4 residue 25 LEU Chi-restraints excluded: chain L4 residue 80 LYS Chi-restraints excluded: chain L4 residue 81 ASN Chi-restraints excluded: chain L4 residue 90 GLN Chi-restraints excluded: chain L4 residue 96 THR Chi-restraints excluded: chain L4 residue 97 ILE Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L6 residue 37 GLN Chi-restraints excluded: chain L6 residue 55 ILE Chi-restraints excluded: chain L6 residue 56 MET Chi-restraints excluded: chain L6 residue 72 THR Chi-restraints excluded: chain L6 residue 73 ASN Chi-restraints excluded: chain L7 residue 31 ASP Chi-restraints excluded: chain L7 residue 59 THR Chi-restraints excluded: chain L7 residue 66 SER Chi-restraints excluded: chain L7 residue 71 LEU Chi-restraints excluded: chain L7 residue 79 THR Chi-restraints excluded: chain L7 residue 81 VAL Chi-restraints excluded: chain L8 residue 18 LEU Chi-restraints excluded: chain L8 residue 27 VAL Chi-restraints excluded: chain L8 residue 41 VAL Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L9 residue 15 VAL Chi-restraints excluded: chain L9 residue 24 SER Chi-restraints excluded: chain L9 residue 44 ILE Chi-restraints excluded: chain L9 residue 88 SER Chi-restraints excluded: chain LA residue 14 THR Chi-restraints excluded: chain LA residue 36 VAL Chi-restraints excluded: chain LA residue 50 SER Chi-restraints excluded: chain LA residue 60 THR Chi-restraints excluded: chain LB residue 6 ILE Chi-restraints excluded: chain LB residue 13 GLU Chi-restraints excluded: chain LB residue 20 SER Chi-restraints excluded: chain LB residue 66 LYS Chi-restraints excluded: chain LD residue 5 GLN Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 9 THR Chi-restraints excluded: chain LD residue 13 ILE Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LE residue 21 LYS Chi-restraints excluded: chain LE residue 23 SER Chi-restraints excluded: chain LE residue 24 VAL Chi-restraints excluded: chain LS residue 39 LEU Chi-restraints excluded: chain LS residue 43 THR Chi-restraints excluded: chain LG residue 5 THR Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LH residue 61 LEU Chi-restraints excluded: chain LI residue 27 CYS Chi-restraints excluded: chain LF residue 55 HIS 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: 4.9990 chunk 228 optimal weight: 1.9990 chunk 686 optimal weight: 3.9990 chunk 109 optimal weight: 30.0000 chunk 207 optimal weight: 8.9990 chunk 746 optimal weight: 0.2980 chunk 312 optimal weight: 50.0000 chunk 766 optimal weight: 6.9990 chunk 94 optimal weight: 30.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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** S1 15 HIS S2 28 ASN S3 6 GLN S5 31 HIS ** S6 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 11 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** ** 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 ** L5 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN ** L7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 32 ASN LG 7 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102726 restraints weight = 325357.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103598 restraints weight = 165133.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.103672 restraints weight = 134051.030| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 145732 Z= 0.187 Angle : 0.651 27.114 219193 Z= 0.327 Chirality : 0.037 2.059 28395 Planarity : 0.005 0.065 11121 Dihedral : 24.798 179.902 75240 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.77 % Favored : 87.19 % Rotamer: Outliers : 5.90 % Allowed : 27.26 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.11), residues: 5042 helix: -1.52 (0.14), residues: 1180 sheet: -1.98 (0.18), residues: 796 loop : -3.08 (0.10), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPLA 48 HIS 0.016 0.001 HISS1 15 PHE 0.029 0.002 PHEL3 25 TYR 0.051 0.002 TYRSF 51 ARG 0.020 0.001 ARGS9 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31785.86 seconds wall clock time: 555 minutes 51.30 seconds (33351.30 seconds total)