Starting phenix.real_space_refine on Sat Dec 9 13:37:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcs_6583/12_2023/3jcs_6583_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcs_6583/12_2023/3jcs_6583.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcs_6583/12_2023/3jcs_6583_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcs_6583/12_2023/3jcs_6583_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcs_6583/12_2023/3jcs_6583_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcs_6583/12_2023/3jcs_6583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcs_6583/12_2023/3jcs_6583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcs_6583/12_2023/3jcs_6583_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcs_6583/12_2023/3jcs_6583_updated.pdb" } resolution = 2.8 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= 0.006 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 3419 5.49 5 Mg 109 5.21 5 S 195 5.16 5 C 60318 2.51 5 N 21905 2.21 5 O 31311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 119": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G ARG 226": "NH1" <-> "NH2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "G ARG 277": "NH1" <-> "NH2" Residue "G ARG 310": "NH1" <-> "NH2" Residue "G ARG 315": "NH1" <-> "NH2" Residue "G ARG 316": "NH1" <-> "NH2" Residue "G ARG 332": "NH1" <-> "NH2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H ARG 179": "NH1" <-> "NH2" Residue "I ARG 39": "NH1" <-> "NH2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I ARG 42": "NH1" <-> "NH2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ARG 74": "NH1" <-> "NH2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I ARG 78": "NH1" <-> "NH2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J ARG 89": "NH1" <-> "NH2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K ARG 93": "NH1" <-> "NH2" Residue "K ARG 172": "NH1" <-> "NH2" Residue "L ARG 26": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 71": "NH1" <-> "NH2" Residue "M ARG 105": "NH1" <-> "NH2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M ARG 144": "NH1" <-> "NH2" Residue "M ARG 169": "NH1" <-> "NH2" Residue "M ARG 172": "NH1" <-> "NH2" Residue "M ARG 193": "NH1" <-> "NH2" Residue "M ARG 194": "NH1" <-> "NH2" Residue "M ARG 202": "NH1" <-> "NH2" Residue "N ARG 3": "NH1" <-> "NH2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 7": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 21": "NH1" <-> "NH2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 39": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 88": "NH1" <-> "NH2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N ARG 116": "NH1" <-> "NH2" Residue "N ARG 128": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "N ARG 139": "NH1" <-> "NH2" Residue "N ARG 153": "NH1" <-> "NH2" Residue "N ARG 154": "NH1" <-> "NH2" Residue "N ARG 162": "NH1" <-> "NH2" Residue "N ARG 178": "NH1" <-> "NH2" Residue "N ARG 185": "NH1" <-> "NH2" Residue "N ARG 193": "NH1" <-> "NH2" Residue "N ARG 209": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "O ARG 164": "NH1" <-> "NH2" Residue "O ARG 185": "NH1" <-> "NH2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P ARG 59": "NH1" <-> "NH2" Residue "P ARG 66": "NH1" <-> "NH2" Residue "P ARG 73": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 52": "NH1" <-> "NH2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q ARG 81": "NH1" <-> "NH2" Residue "Q ARG 85": "NH1" <-> "NH2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q ARG 98": "NH1" <-> "NH2" Residue "Q ARG 110": "NH1" <-> "NH2" Residue "Q ARG 121": "NH1" <-> "NH2" Residue "Q ARG 126": "NH1" <-> "NH2" Residue "R ARG 14": "NH1" <-> "NH2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R ARG 91": "NH1" <-> "NH2" Residue "R ARG 97": "NH1" <-> "NH2" Residue "R ARG 119": "NH1" <-> "NH2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S ARG 83": "NH1" <-> "NH2" Residue "S ARG 97": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T ARG 62": "NH1" <-> "NH2" Residue "T ARG 127": "NH1" <-> "NH2" Residue "V ARG 36": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "W ARG 10": "NH1" <-> "NH2" Residue "W ARG 13": "NH1" <-> "NH2" Residue "W ARG 43": "NH1" <-> "NH2" Residue "W ARG 72": "NH1" <-> "NH2" Residue "W ARG 84": "NH1" <-> "NH2" Residue "W ARG 84": "NH1" <-> "NH2" Residue "W ARG 112": "NH1" <-> "NH2" Residue "X ARG 19": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Y ARG 110": "NH1" <-> "NH2" Residue "Z ARG 17": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a GLU 24": "OE1" <-> "OE2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 94": "NH1" <-> "NH2" Residue "a ARG 106": "NH1" <-> "NH2" Residue "a ARG 110": "NH1" <-> "NH2" Residue "b ARG 59": "NH1" <-> "NH2" Residue "b ARG 60": "NH1" <-> "NH2" Residue "b ARG 62": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 119": "NH1" <-> "NH2" Residue "c ARG 161": "NH1" <-> "NH2" Residue "c ARG 228": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "e ARG 148": "NH1" <-> "NH2" Residue "f ARG 14": "NH1" <-> "NH2" Residue "f ARG 22": "NH1" <-> "NH2" Residue "f ARG 37": "NH1" <-> "NH2" Residue "f ARG 62": "NH1" <-> "NH2" Residue "f ARG 73": "NH1" <-> "NH2" Residue "g ARG 28": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "g ARG 133": "NH1" <-> "NH2" Residue "h ARG 5": "NH1" <-> "NH2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h ARG 25": "NH1" <-> "NH2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "h ARG 70": "NH1" <-> "NH2" Residue "i ARG 79": "NH1" <-> "NH2" Residue "i ARG 79": "NH1" <-> "NH2" Residue "j ARG 14": "NH1" <-> "NH2" Residue "j ARG 20": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 57": "NH1" <-> "NH2" Residue "j ARG 58": "NH1" <-> "NH2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "j ARG 73": "NH1" <-> "NH2" Residue "k ARG 37": "NH1" <-> "NH2" Residue "k ARG 40": "NH1" <-> "NH2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l ARG 45": "NH1" <-> "NH2" Residue "m ARG 49": "NH1" <-> "NH2" Residue "m ARG 56": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 117257 Number of models: 1 Model: "" Number of chains: 74 Chain: "1" Number of atoms: 33313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1554, 33313 Classifications: {'RNA': 1554} Modifications used: {'rna2p': 1, 'rna2p_pur': 191, 'rna2p_pyr': 108, 'rna3p': 10, 'rna3p_pur': 683, 'rna3p_pyr': 556} Link IDs: {'rna2p': 300, 'rna3p': 1253} Chain breaks: 20 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 7 Chain: "2" Number of atoms: 23926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 23926 Classifications: {'RNA': 1119} Modifications used: {'rna2p': 3, 'rna2p_pur': 109, 'rna2p_pyr': 87, 'rna3p': 17, 'rna3p_pur': 483, 'rna3p_pyr': 414} Link IDs: {'rna2p': 199, 'rna3p': 919} Chain breaks: 13 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 16 Chain: "3" Number of atoms: 3893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3893 Classifications: {'RNA': 184} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 12, 'rna3p_pur': 74, 'rna3p_pyr': 88} Link IDs: {'rna2p': 21, 'rna3p': 162} Chain breaks: 7 Chain: "4" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3177 Classifications: {'RNA': 149} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 9, 'rna3p_pur': 66, 'rna3p_pyr': 63} Link IDs: {'rna2p': 20, 'rna3p': 128} Chain breaks: 2 Chain: "5" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1708 Classifications: {'RNA': 80} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 36, 'rna3p_pyr': 29} Link IDs: {'rna2p': 15, 'rna3p': 64} Chain breaks: 2 Chain: "6" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1288 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 15, 'rna3p_pur': 16, 'rna3p_pyr': 18} Link IDs: {'rna2p': 27, 'rna3p': 33} Chain: "7" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3280 Classifications: {'RNA': 154} Modifications used: {'5*END': 1, 'rna2p_pur': 15, 'rna2p_pyr': 14, 'rna3p': 1, 'rna3p_pur': 65, 'rna3p_pyr': 58} Link IDs: {'rna2p': 29, 'rna3p': 124} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "8" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2531 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 17, 'rna3p_pur': 46, 'rna3p_pyr': 41} Link IDs: {'rna2p': 31, 'rna3p': 87} Chain breaks: 1 Chain: "A" Number of atoms: 1859 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 245, 1840 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 229} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 6} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 245, 1840 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 229} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 6} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1860 Chain: "B" Number of atoms: 3020 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 396, 3001 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 97 Conformer: "B" Number of residues, atoms: 396, 3001 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 97 bond proxies already assigned to first conformer: 3044 Chain: "C" Number of atoms: 2237 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 301, 2230 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 286} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Conformer: "B" Number of residues, atoms: 301, 2230 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 286} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 2267 Chain: "D" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 799 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 3, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 517 Unresolved non-hydrogen angles: 648 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 15, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 287 Chain: "E" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1509 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "F" Number of atoms: 1002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 137, 993 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 137, 993 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 1004 Chain: "G" Number of atoms: 1772 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 226, 1761 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 1775 Chain: "H" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1596 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 191} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "I" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1061 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 121} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 924 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 120} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1061 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 150} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "L" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1096 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 138} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1714 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 195} Chain: "N" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1714 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 201} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1557 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 11, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 152 Chain: "P" Number of atoms: 1494 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 195, 1485 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 187} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 195, 1485 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 187} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 1500 Chain: "Q" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1162 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 3, 'TRANS': 152} Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 89 Chain: "R" Number of atoms: 1019 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 131, 1012 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 123} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 131, 1012 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 123} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 1029 Chain: "S" Number of atoms: 1112 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1093 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 141} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Conformer: "B" Number of residues, atoms: 149, 1093 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 141} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 bond proxies already assigned to first conformer: 1097 Chain: "T" Number of atoms: 1221 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 154, 1205 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 146} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 154, 1205 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 146} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 1210 Chain: "U" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 541 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 1, 'TRANS': 98} Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 146 Chain: "V" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "W" Number of atoms: 896 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 117, 885 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Conformer: "B" Number of residues, atoms: 117, 885 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 bond proxies already assigned to first conformer: 887 Chain: "X" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 508 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 57} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "Y" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 914 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 4, 'TRANS': 127} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 82 Chain: "Z" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 538 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "a" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 982 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "b" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 503 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 61} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "c" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1732 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 8, 'TRANS': 213} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "d" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 518 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "e" Number of atoms: 824 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 112, 814 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 112, 814 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 815 Chain: "f" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 982 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 118} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "g" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 983 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 119} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 856 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "i" Number of atoms: 494 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 61} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 63, 483 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 61} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 476 Chain: "j" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 639 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "k" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 373 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "l" Number of atoms: 457 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 50, 446 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 50, 446 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 447 Chain: "m" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 668 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "n" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 659 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 51} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "2" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Unusual residues: {' MG': 25} Classifications: {'undetermined': 25} Link IDs: {None: 24} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" 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} Chain: "5" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" 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} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "1" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "4" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N AARG A 60 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 60 " occ=0.50 residue: pdb=" N AHIS B 174 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 174 " occ=0.50 residue: pdb=" N ALYS B 227 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 227 " occ=0.50 residue: pdb=" N APRO C 278 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO C 278 " occ=0.50 residue: pdb=" N ALYS F 90 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS F 90 " occ=0.50 residue: pdb=" N AARG G 301 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG G 301 " occ=0.50 residue: pdb=" N ALYS P 170 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS P 170 " occ=0.50 residue: pdb=" N AVAL R 78 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL R 78 " occ=0.50 residue: pdb=" N AARG S 100 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG S 100 " occ=0.50 residue: pdb=" N AHIS T 133 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS T 133 " occ=0.50 residue: pdb=" N AARG W 84 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG W 84 " occ=0.50 residue: pdb=" N AHIS e 132 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS e 132 " occ=0.50 ... (remaining 2 not shown) Time building chain proxies: 49.18, per 1000 atoms: 0.42 Number of scatterers: 117257 At special positions: 0 Unit cell: (210, 214, 261, 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 195 16.00 P 3419 15.00 Mg 109 11.99 O 31311 8.00 N 21905 7.00 C 60318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 17 " distance=2.04 Simple disulfide: pdb=" SG CYS j 19 " - pdb=" SG CYS j 34 " distance=2.04 Simple disulfide: pdb=" SG CYS m 39 " - pdb=" SG CYS m 42 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 9364 O5' U 1 439 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 50.42 Conformation dependent library (CDL) restraints added in 9.3 seconds 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10952 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: 202 helices and 55 sheets defined 41.3% alpha, 12.3% beta 742 base pairs and 1680 stacking pairs defined. Time for finding SS restraints: 60.48 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.643A pdb=" N LYS A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN A 12 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 removed outlier: 3.739A pdb=" N ARG A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 5.774A pdb=" N THR A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.580A pdb=" N SER A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.748A pdb=" N ARG A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'B' and resid 13 through 18 removed outlier: 4.541A pdb=" N LEU B 17 " --> pdb=" O HIS B 13 " (cutoff:3.500A) Proline residue: B 18 - end of helix No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.758A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 5.851A pdb=" N SER B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ALA B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 126' Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.501A pdb=" N PHE B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 removed outlier: 4.165A pdb=" N THR B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.778A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.681A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 removed outlier: 3.610A pdb=" N VAL B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 379 through 388 removed outlier: 4.484A pdb=" N LYS B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 388 " --> pdb=" O ASN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 398 removed outlier: 3.871A pdb=" N ARG B 396 " --> pdb=" O LYS B 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 30 removed outlier: 4.202A pdb=" N THR C 28 " --> pdb=" O PRO C 24 " (cutoff:3.500A) Proline residue: C 30 - end of helix Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.533A pdb=" N VAL C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS C 45 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER C 47 " --> pdb=" O MET C 43 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 133 removed outlier: 3.818A pdb=" N SER C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix Processing helix chain 'C' and resid 134 through 140 removed outlier: 4.184A pdb=" N ARG C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.404A pdb=" N TYR C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLU C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.773A pdb=" N ALA C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.894A pdb=" N VAL C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 185 " --> pdb=" O ARG C 181 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 197 removed outlier: 6.603A pdb=" N MET C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 197' Processing helix chain 'C' and resid 215 through 220 removed outlier: 4.143A pdb=" N PHE C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 removed outlier: 5.930A pdb=" N ALA C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.679A pdb=" N PHE C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLN C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 3.620A pdb=" N ILE C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER C 293 " --> pdb=" O ARG C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 removed outlier: 3.918A pdb=" N VAL C 299 " --> pdb=" O GLU C 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.573A pdb=" N THR D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ARG D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA D 35 " --> pdb=" O ARG D 31 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LYS D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN D 41 " --> pdb=" O LYS D 37 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N CYS D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 91 removed outlier: 3.675A pdb=" N GLU D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE D 91 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 143 removed outlier: 4.570A pdb=" N ALA D 141 " --> pdb=" O GLY D 137 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 143' Processing helix chain 'D' and resid 157 through 169 removed outlier: 4.265A pdb=" N MET D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU D 166 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 168 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS D 169 " --> pdb=" O PHE D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 85 removed outlier: 3.652A pdb=" N CYS E 68 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU E 69 " --> pdb=" O PRO E 65 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR E 72 " --> pdb=" O CYS E 68 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N MET E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 165 removed outlier: 5.127A pdb=" N GLU E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 162 " --> pdb=" O ALA E 158 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N CYS E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU E 165 " --> pdb=" O HIS E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 175 removed outlier: 5.235A pdb=" N PHE E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 170 through 175' Processing helix chain 'F' and resid 80 through 85 removed outlier: 4.297A pdb=" N VAL F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE F 85 " --> pdb=" O SER F 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 80 through 85' Processing helix chain 'F' and resid 150 through 169 removed outlier: 3.671A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA F 169 " --> pdb=" O ILE F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 181 removed outlier: 3.846A pdb=" N GLY F 176 " --> pdb=" O LYS F 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU F 178 " --> pdb=" O LYS F 174 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL F 181 " --> pdb=" O TYR F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 194 removed outlier: 5.509A pdb=" N ASN F 194 " --> pdb=" O PRO F 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 154 removed outlier: 3.688A pdb=" N ARG G 148 " --> pdb=" O GLN G 144 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG G 152 " --> pdb=" O ARG G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 166 removed outlier: 4.447A pdb=" N GLN G 162 " --> pdb=" O PRO G 158 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR G 164 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS G 165 " --> pdb=" O ASN G 161 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 183 removed outlier: 3.964A pdb=" N ASN G 173 " --> pdb=" O ARG G 169 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLU G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 204 removed outlier: 5.594A pdb=" N ARG G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS G 196 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP G 204 " --> pdb=" O GLU G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 231 removed outlier: 4.457A pdb=" N VAL G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG G 226 " --> pdb=" O GLN G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 259 removed outlier: 4.385A pdb=" N VAL G 248 " --> pdb=" O PRO G 244 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TRP G 250 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N MET G 251 " --> pdb=" O LEU G 247 " (cutoff:3.500A) Proline residue: G 252 - end of helix removed outlier: 3.590A pdb=" N CYS G 255 " --> pdb=" O MET G 251 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG G 256 " --> pdb=" O PRO G 252 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA G 257 " --> pdb=" O ASN G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 276 removed outlier: 3.526A pdb=" N ASP G 273 " --> pdb=" O ALA G 269 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA G 274 " --> pdb=" O ARG G 270 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE G 275 " --> pdb=" O LEU G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 307 removed outlier: 3.798A pdb=" N GLU G 293 " --> pdb=" O ASN G 289 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALA G 294 " --> pdb=" O ALA G 290 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU G 296 " --> pdb=" O ASP G 292 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N AARG G 301 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG G 306 " --> pdb=" O SER G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 317 removed outlier: 3.546A pdb=" N ARG G 316 " --> pdb=" O ASP G 312 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 338 removed outlier: 3.742A pdb=" N ARG G 328 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA G 329 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU G 330 " --> pdb=" O ARG G 326 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU G 331 " --> pdb=" O SER G 327 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG G 337 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN G 338 " --> pdb=" O LYS G 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.929A pdb=" N VAL H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 79 removed outlier: 3.545A pdb=" N TYR H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR H 75 " --> pdb=" O LYS H 71 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS H 78 " --> pdb=" O GLN H 74 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ARG H 79 " --> pdb=" O TYR H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 93 through 107 removed outlier: 3.571A pdb=" N VAL H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL H 99 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Proline residue: H 107 - end of helix Processing helix chain 'H' and resid 110 through 120 removed outlier: 3.989A pdb=" N LEU H 120 " --> pdb=" O ALA H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 134 removed outlier: 4.185A pdb=" N ARG H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR H 133 " --> pdb=" O ASN H 129 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLY H 134 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 165 removed outlier: 4.248A pdb=" N HIS H 163 " --> pdb=" O ASN H 159 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL H 164 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 208 removed outlier: 3.770A pdb=" N LYS H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS H 186 " --> pdb=" O LYS H 182 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU H 188 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN H 190 " --> pdb=" O HIS H 186 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA H 191 " --> pdb=" O HIS H 187 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG H 194 " --> pdb=" O GLN H 190 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU H 195 " --> pdb=" O ALA H 191 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA H 196 " --> pdb=" O LYS H 192 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TRP H 197 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA H 200 " --> pdb=" O ALA H 196 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ALA H 206 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS H 207 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N MET H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 220 removed outlier: 4.458A pdb=" N VAL H 215 " --> pdb=" O HIS H 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 52 removed outlier: 3.695A pdb=" N LYS I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS I 50 " --> pdb=" O LEU I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 removed outlier: 3.750A pdb=" N LEU I 85 " --> pdb=" O SER I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 99 removed outlier: 3.577A pdb=" N ALA I 96 " --> pdb=" O PRO I 92 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR I 97 " --> pdb=" O GLN I 93 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE I 98 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 128 removed outlier: 3.567A pdb=" N MET I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL I 116 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN I 117 " --> pdb=" O GLY I 113 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS I 122 " --> pdb=" O VAL I 118 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR I 124 " --> pdb=" O ARG I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 73 removed outlier: 3.722A pdb=" N ARG J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS J 73 " --> pdb=" O PRO J 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 68 through 73' Processing helix chain 'J' and resid 121 through 129 removed outlier: 4.663A pdb=" N LEU J 127 " --> pdb=" O GLU J 123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP J 128 " --> pdb=" O SER J 124 " (cutoff:3.500A) Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 130 through 136 removed outlier: 4.786A pdb=" N HIS J 134 " --> pdb=" O LYS J 130 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA J 135 " --> pdb=" O ILE J 131 " (cutoff:3.500A) Proline residue: J 136 - end of helix No H-bonds generated for 'chain 'J' and resid 130 through 136' Processing helix chain 'K' and resid 61 through 66 removed outlier: 3.763A pdb=" N ILE K 65 " --> pdb=" O LYS K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 115 removed outlier: 4.881A pdb=" N GLU K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 141 removed outlier: 5.001A pdb=" N LYS K 140 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA K 141 " --> pdb=" O ALA K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 148 Processing helix chain 'K' and resid 149 through 163 removed outlier: 6.163A pdb=" N ARG K 153 " --> pdb=" O ARG K 149 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL K 154 " --> pdb=" O THR K 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU K 155 " --> pdb=" O ALA K 151 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA K 156 " --> pdb=" O ALA K 152 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA K 161 " --> pdb=" O LYS K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 192 removed outlier: 3.837A pdb=" N TYR K 169 " --> pdb=" O ASP K 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 12 removed outlier: 3.969A pdb=" N ARG L 12 " --> pdb=" O CYS L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 48 removed outlier: 3.696A pdb=" N LYS L 47 " --> pdb=" O ILE L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 69 removed outlier: 3.623A pdb=" N MET L 68 " --> pdb=" O LYS L 64 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 64 through 69' Processing helix chain 'L' and resid 74 through 83 removed outlier: 3.660A pdb=" N LEU L 78 " --> pdb=" O ASN L 74 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER L 79 " --> pdb=" O LEU L 75 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ARG L 80 " --> pdb=" O ASN L 76 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU L 81 " --> pdb=" O ASN L 77 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA L 83 " --> pdb=" O SER L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 74 through 83' Processing helix chain 'L' and resid 84 through 94 removed outlier: 3.526A pdb=" N ALA L 90 " --> pdb=" O GLU L 86 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 105 removed outlier: 4.100A pdb=" N SER L 104 " --> pdb=" O ASP L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 138 removed outlier: 3.769A pdb=" N ARG L 135 " --> pdb=" O ASP L 131 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY L 138 " --> pdb=" O ILE L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 14 removed outlier: 4.092A pdb=" N TYR M 6 " --> pdb=" O GLY M 2 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU M 7 " --> pdb=" O ALA M 3 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS M 14 " --> pdb=" O LEU M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 34 removed outlier: 3.914A pdb=" N TRP M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG M 31 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS M 32 " --> pdb=" O TRP M 28 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N HIS M 34 " --> pdb=" O PHE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 52 removed outlier: 3.599A pdb=" N LEU M 51 " --> pdb=" O LYS M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 88 removed outlier: 4.185A pdb=" N SER M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY M 88 " --> pdb=" O PRO M 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 83 through 88' Processing helix chain 'M' and resid 97 through 110 removed outlier: 3.504A pdb=" N GLY M 107 " --> pdb=" O GLU M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 146 removed outlier: 3.577A pdb=" N ASP M 145 " --> pdb=" O THR M 141 " (cutoff:3.500A) Proline residue: M 146 - end of helix Processing helix chain 'M' and resid 148 through 153 removed outlier: 4.457A pdb=" N VAL M 152 " --> pdb=" O ILE M 148 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN M 153 " --> pdb=" O ASN M 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 148 through 153' Processing helix chain 'M' and resid 158 through 163 Processing helix chain 'M' and resid 165 through 173 removed outlier: 4.231A pdb=" N GLY M 173 " --> pdb=" O ARG M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 183 removed outlier: 4.001A pdb=" N SER M 182 " --> pdb=" O GLY M 178 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS M 183 " --> pdb=" O HIS M 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 178 through 183' Processing helix chain 'M' and resid 187 through 197 Processing helix chain 'N' and resid 6 through 11 removed outlier: 4.641A pdb=" N ARG N 10 " --> pdb=" O SER N 6 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE N 11 " --> pdb=" O ARG N 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 6 through 11' Processing helix chain 'N' and resid 61 through 80 removed outlier: 4.050A pdb=" N LEU N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE N 70 " --> pdb=" O GLU N 66 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN N 73 " --> pdb=" O ARG N 69 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR N 75 " --> pdb=" O GLN N 71 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N MET N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL N 77 " --> pdb=" O ASN N 73 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS N 78 " --> pdb=" O LYS N 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG N 79 " --> pdb=" O TYR N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 86 removed outlier: 4.031A pdb=" N PHE N 85 " --> pdb=" O ASN N 81 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N HIS N 86 " --> pdb=" O LYS N 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 81 through 86' Processing helix chain 'N' and resid 141 through 160 removed outlier: 3.892A pdb=" N VAL N 145 " --> pdb=" O LYS N 141 " (cutoff:3.500A) Proline residue: N 146 - end of helix removed outlier: 4.983A pdb=" N PHE N 149 " --> pdb=" O VAL N 145 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLU N 150 " --> pdb=" O PRO N 146 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA N 151 " --> pdb=" O GLN N 147 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG N 153 " --> pdb=" O PHE N 149 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS N 158 " --> pdb=" O ARG N 154 " (cutoff:3.500A) Proline residue: N 160 - end of helix Processing helix chain 'N' and resid 178 through 188 removed outlier: 4.076A pdb=" N ALA N 183 " --> pdb=" O THR N 179 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP N 186 " --> pdb=" O GLU N 182 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA N 187 " --> pdb=" O ALA N 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 16 removed outlier: 8.184A pdb=" N PHE O 13 " --> pdb=" O ASN O 9 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS O 14 " --> pdb=" O LYS O 10 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 26 removed outlier: 3.861A pdb=" N GLU O 25 " --> pdb=" O ARG O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 38 removed outlier: 4.332A pdb=" N ARG O 34 " --> pdb=" O TYR O 30 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN O 35 " --> pdb=" O HIS O 31 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU O 38 " --> pdb=" O ARG O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 87 removed outlier: 4.002A pdb=" N LEU O 83 " --> pdb=" O TYR O 79 " (cutoff:3.500A) Proline residue: O 84 - end of helix Processing helix chain 'O' and resid 94 through 114 removed outlier: 3.715A pdb=" N ARG O 108 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR O 109 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 120 removed outlier: 3.946A pdb=" N PHE O 119 " --> pdb=" O ILE O 115 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLN O 120 " --> pdb=" O ALA O 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 115 through 120' Processing helix chain 'O' and resid 163 through 176 removed outlier: 3.759A pdb=" N LEU O 169 " --> pdb=" O VAL O 165 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY O 175 " --> pdb=" O GLY O 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 205 removed outlier: 3.650A pdb=" N VAL O 200 " --> pdb=" O LEU O 196 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS O 201 " --> pdb=" O ASP O 197 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG O 202 " --> pdb=" O ALA O 198 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 221 removed outlier: 4.591A pdb=" N TYR O 213 " --> pdb=" O HIS O 209 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS O 215 " --> pdb=" O ALA O 211 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLN O 216 " --> pdb=" O GLU O 212 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS O 218 " --> pdb=" O LEU O 214 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLU O 219 " --> pdb=" O LYS O 215 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU O 220 " --> pdb=" O GLN O 216 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA O 221 " --> pdb=" O VAL O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 241 through 259 removed outlier: 5.315A pdb=" N GLU O 246 " --> pdb=" O PRO O 242 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLY O 247 " --> pdb=" O GLU O 243 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR O 249 " --> pdb=" O ILE O 245 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA O 252 " --> pdb=" O MET O 248 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA O 254 " --> pdb=" O LYS O 250 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA O 258 " --> pdb=" O ALA O 254 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 39 removed outlier: 3.819A pdb=" N LEU P 28 " --> pdb=" O PRO P 24 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU P 29 " --> pdb=" O TYR P 25 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA P 37 " --> pdb=" O TYR P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 55 removed outlier: 3.523A pdb=" N LYS P 46 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU P 52 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 79 removed outlier: 4.589A pdb=" N PHE P 77 " --> pdb=" O ARG P 73 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR P 78 " --> pdb=" O LYS P 74 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA P 79 " --> pdb=" O ALA P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 124 removed outlier: 3.592A pdb=" N GLN P 118 " --> pdb=" O LYS P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 137 removed outlier: 4.416A pdb=" N MET P 135 " --> pdb=" O ASP P 131 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE P 136 " --> pdb=" O GLN P 132 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA P 137 " --> pdb=" O LEU P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 160 removed outlier: 3.603A pdb=" N HIS P 158 " --> pdb=" O GLU P 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE P 159 " --> pdb=" O SER P 155 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLY P 160 " --> pdb=" O VAL P 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 16 Processing helix chain 'Q' and resid 28 through 36 removed outlier: 4.324A pdb=" N ILE Q 32 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN Q 36 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 48 removed outlier: 3.545A pdb=" N LEU Q 44 " --> pdb=" O SER Q 40 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 73 removed outlier: 3.508A pdb=" N MET Q 66 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP Q 71 " --> pdb=" O LYS Q 67 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET Q 72 " --> pdb=" O GLU Q 68 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 113 Proline residue: Q 90 - end of helix removed outlier: 6.741A pdb=" N GLU Q 93 " --> pdb=" O MET Q 89 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU Q 94 " --> pdb=" O PRO Q 90 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET Q 96 " --> pdb=" O LYS Q 92 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU Q 102 " --> pdb=" O ARG Q 98 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU Q 106 " --> pdb=" O LEU Q 102 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS Q 108 " --> pdb=" O ARG Q 104 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA Q 111 " --> pdb=" O ARG Q 107 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASP Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS Q 113 " --> pdb=" O TYR Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 130 removed outlier: 3.502A pdb=" N ARG Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP Q 122 " --> pdb=" O HIS Q 118 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU Q 123 " --> pdb=" O VAL Q 119 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL Q 125 " --> pdb=" O ARG Q 121 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG Q 126 " --> pdb=" O ASP Q 122 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS Q 128 " --> pdb=" O TYR Q 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN Q 130 " --> pdb=" O ARG Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 156 removed outlier: 3.546A pdb=" N GLU Q 140 " --> pdb=" O ARG Q 136 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS Q 141 " --> pdb=" O ASN Q 137 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN Q 147 " --> pdb=" O HIS Q 143 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU Q 148 " --> pdb=" O LYS Q 144 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG Q 153 " --> pdb=" O LYS Q 149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN Q 154 " --> pdb=" O LYS Q 150 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA Q 156 " --> pdb=" O GLU Q 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 50 removed outlier: 3.650A pdb=" N ALA R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 59 removed outlier: 5.094A pdb=" N ASP R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 116 removed outlier: 3.855A pdb=" N SER R 114 " --> pdb=" O HIS R 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 16 removed outlier: 3.532A pdb=" N PHE S 15 " --> pdb=" O THR S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 32 removed outlier: 3.787A pdb=" N ILE S 30 " --> pdb=" O SER S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 97 removed outlier: 4.456A pdb=" N VAL S 96 " --> pdb=" O ARG S 92 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG S 97 " --> pdb=" O PHE S 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 92 through 97' Processing helix chain 'S' and resid 102 through 121 removed outlier: 3.943A pdb=" N LYS S 108 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN S 111 " --> pdb=" O ALA S 107 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA S 114 " --> pdb=" O HIS S 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 38 removed outlier: 4.031A pdb=" N GLU T 31 " --> pdb=" O LYS T 27 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE T 36 " --> pdb=" O THR T 32 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLY T 38 " --> pdb=" O ASN T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 54 removed outlier: 3.681A pdb=" N ALA T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 106 removed outlier: 3.546A pdb=" N MET T 91 " --> pdb=" O SER T 87 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER T 93 " --> pdb=" O VAL T 89 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU T 94 " --> pdb=" O ALA T 90 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS T 105 " --> pdb=" O ASN T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 113 removed outlier: 3.735A pdb=" N MET T 112 " --> pdb=" O ASP T 108 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL T 113 " --> pdb=" O PRO T 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 108 through 113' Processing helix chain 'U' and resid 31 through 36 removed outlier: 3.748A pdb=" N ALA U 35 " --> pdb=" O SER U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 53 removed outlier: 4.564A pdb=" N ASN U 46 " --> pdb=" O ASP U 42 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE U 51 " --> pdb=" O PHE U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 102 removed outlier: 4.928A pdb=" N PHE U 90 " --> pdb=" O ARG U 86 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR U 92 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP U 102 " --> pdb=" O LEU U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 103 through 108 removed outlier: 3.801A pdb=" N ILE U 107 " --> pdb=" O LEU U 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ARG U 108 " --> pdb=" O ARG U 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 103 through 108' Processing helix chain 'V' and resid 57 through 67 removed outlier: 5.150A pdb=" N ALA V 61 " --> pdb=" O SER V 57 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA V 62 " --> pdb=" O LYS V 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER V 64 " --> pdb=" O ILE V 60 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N VAL V 65 " --> pdb=" O ALA V 61 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE V 66 " --> pdb=" O ALA V 62 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG V 67 " --> pdb=" O PHE V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 72 through 81 removed outlier: 3.811A pdb=" N ILE V 79 " --> pdb=" O ALA V 75 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU V 80 " --> pdb=" O MET V 76 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 106 removed outlier: 3.674A pdb=" N LYS V 99 " --> pdb=" O LYS V 95 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 143 removed outlier: 3.696A pdb=" N THR V 138 " --> pdb=" O ASP V 134 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN V 140 " --> pdb=" O LEU V 136 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS V 141 " --> pdb=" O ASP V 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 19 removed outlier: 3.554A pdb=" N ALA W 12 " --> pdb=" O SER W 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG W 14 " --> pdb=" O ARG W 10 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE W 17 " --> pdb=" O ARG W 13 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA W 19 " --> pdb=" O ALA W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 29 removed outlier: 4.266A pdb=" N VAL W 26 " --> pdb=" O HIS W 22 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET W 28 " --> pdb=" O ARG W 24 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER W 29 " --> pdb=" O ARG W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 41 removed outlier: 4.966A pdb=" N ALA W 38 " --> pdb=" O LYS W 34 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS W 39 " --> pdb=" O GLU W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 102 removed outlier: 3.886A pdb=" N VAL W 101 " --> pdb=" O HIS W 97 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU W 102 " --> pdb=" O PRO W 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 97 through 102' Processing helix chain 'W' and resid 109 through 124 removed outlier: 4.858A pdb=" N SER W 114 " --> pdb=" O HIS W 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE W 115 " --> pdb=" O HIS W 111 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER W 122 " --> pdb=" O ARG W 118 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER W 123 " --> pdb=" O LYS W 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 47 removed outlier: 3.831A pdb=" N TYR X 44 " --> pdb=" O CYS X 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG X 46 " --> pdb=" O ALA X 42 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS X 47 " --> pdb=" O LEU X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 54 removed outlier: 4.454A pdb=" N ILE X 53 " --> pdb=" O ASN X 49 " (cutoff:3.500A) Proline residue: X 54 - end of helix No H-bonds generated for 'chain 'X' and resid 49 through 54' Processing helix chain 'X' and resid 56 through 64 removed outlier: 3.905A pdb=" N ARG X 60 " --> pdb=" O THR X 56 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG X 64 " --> pdb=" O ARG X 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 59 through 67 removed outlier: 3.624A pdb=" N ALA Y 63 " --> pdb=" O LYS Y 59 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN Y 67 " --> pdb=" O ALA Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 81 removed outlier: 4.015A pdb=" N PHE Y 80 " --> pdb=" O ASN Y 76 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU Y 81 " --> pdb=" O HIS Y 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 76 through 81' Processing helix chain 'Y' and resid 92 through 99 removed outlier: 5.207A pdb=" N LYS Y 96 " --> pdb=" O GLU Y 92 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE Y 97 " --> pdb=" O LEU Y 93 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN Y 98 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL Y 99 " --> pdb=" O GLY Y 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 92 through 99' Processing helix chain 'Y' and resid 101 through 123 removed outlier: 3.574A pdb=" N ARG Y 105 " --> pdb=" O ASP Y 101 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER Y 106 " --> pdb=" O ALA Y 102 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS Y 109 " --> pdb=" O ARG Y 105 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG Y 110 " --> pdb=" O SER Y 106 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU Y 111 " --> pdb=" O ARG Y 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL Y 112 " --> pdb=" O SER Y 108 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA Y 118 " --> pdb=" O HIS Y 114 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY Y 123 " --> pdb=" O ARG Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 125 through 131 removed outlier: 6.463A pdb=" N PHE Y 129 " --> pdb=" O SER Y 125 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN Y 130 " --> pdb=" O MET Y 126 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG Y 131 " --> pdb=" O TRP Y 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 125 through 131' Processing helix chain 'Z' and resid 4 through 13 removed outlier: 3.569A pdb=" N ILE Z 10 " --> pdb=" O ASP Z 6 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL Z 12 " --> pdb=" O GLN Z 8 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 48 removed outlier: 3.634A pdb=" N ASN Z 47 " --> pdb=" O CYS Z 43 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU Z 48 " --> pdb=" O GLY Z 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 43 through 48' Processing helix chain 'Z' and resid 106 through 122 removed outlier: 4.637A pdb=" N ARG Z 113 " --> pdb=" O ARG Z 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET Z 114 " --> pdb=" O ARG Z 110 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA Z 118 " --> pdb=" O MET Z 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 14 removed outlier: 5.344A pdb=" N GLU a 12 " --> pdb=" O LYS a 8 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS a 13 " --> pdb=" O ASP a 9 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER a 14 " --> pdb=" O LEU a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 15 through 39 removed outlier: 3.557A pdb=" N LYS a 20 " --> pdb=" O ASP a 16 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU a 24 " --> pdb=" O LYS a 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR a 25 " --> pdb=" O THR a 21 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN a 37 " --> pdb=" O ARG a 33 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR a 38 " --> pdb=" O VAL a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 75 removed outlier: 3.587A pdb=" N GLY a 46 " --> pdb=" O GLU a 42 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ARG a 47 " --> pdb=" O THR a 43 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE a 48 " --> pdb=" O ARG a 44 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ARG a 49 " --> pdb=" O LEU a 45 " (cutoff:3.500A) Proline residue: a 50 - end of helix removed outlier: 3.608A pdb=" N LYS a 53 " --> pdb=" O ARG a 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE a 55 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA a 56 " --> pdb=" O ARG a 52 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL a 61 " --> pdb=" O ARG a 57 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER a 68 " --> pdb=" O GLN a 64 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE a 73 " --> pdb=" O ASN a 69 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR a 74 " --> pdb=" O LEU a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 89 removed outlier: 6.049A pdb=" N ALA a 89 " --> pdb=" O LYS a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 98 Processing helix chain 'a' and resid 100 through 106 removed outlier: 4.370A pdb=" N LYS a 104 " --> pdb=" O LYS a 100 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN a 105 " --> pdb=" O GLU a 101 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG a 106 " --> pdb=" O ASN a 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 100 through 106' Processing helix chain 'a' and resid 108 through 118 removed outlier: 6.436A pdb=" N ARG a 113 " --> pdb=" O SER a 109 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN a 114 " --> pdb=" O ARG a 110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA a 115 " --> pdb=" O GLN a 111 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS a 116 " --> pdb=" O MET a 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 20 removed outlier: 3.562A pdb=" N ARG b 18 " --> pdb=" O SER b 14 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY b 20 " --> pdb=" O ASN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 31 removed outlier: 5.419A pdb=" N HIS b 30 " --> pdb=" O PRO b 26 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN b 31 " --> pdb=" O LEU b 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 26 through 31' Processing helix chain 'b' and resid 37 through 70 removed outlier: 3.870A pdb=" N ASN b 43 " --> pdb=" O PRO b 39 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG b 46 " --> pdb=" O VAL b 42 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG b 48 " --> pdb=" O ALA b 44 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN b 70 " --> pdb=" O PHE b 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 82 removed outlier: 4.023A pdb=" N ASN c 35 " --> pdb=" O GLN c 31 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE c 36 " --> pdb=" O GLN c 32 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS c 37 " --> pdb=" O THR c 33 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL c 41 " --> pdb=" O LYS c 37 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA c 42 " --> pdb=" O LYS c 38 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS c 47 " --> pdb=" O ARG c 43 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR c 53 " --> pdb=" O ALA c 49 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA c 79 " --> pdb=" O LEU c 75 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA c 80 " --> pdb=" O ARG c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 117 Processing helix chain 'c' and resid 130 through 141 removed outlier: 3.630A pdb=" N ASN c 135 " --> pdb=" O LYS c 131 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET c 136 " --> pdb=" O PRO c 132 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL c 140 " --> pdb=" O MET c 136 " (cutoff:3.500A) Processing helix chain 'c' and resid 150 through 160 removed outlier: 3.517A pdb=" N ARG c 155 " --> pdb=" O LEU c 151 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA c 156 " --> pdb=" O ALA c 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 175 through 184 removed outlier: 3.859A pdb=" N ILE c 179 " --> pdb=" O ASP c 175 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP c 181 " --> pdb=" O GLN c 177 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS c 182 " --> pdb=" O MET c 178 " (cutoff:3.500A) Processing helix chain 'c' and resid 190 through 201 removed outlier: 4.889A pdb=" N CYS c 201 " --> pdb=" O GLN c 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 204 through 213 removed outlier: 3.903A pdb=" N VAL c 208 " --> pdb=" O HIS c 204 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS c 210 " --> pdb=" O ARG c 206 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET c 212 " --> pdb=" O VAL c 208 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TRP c 213 " --> pdb=" O THR c 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 242 through 252 removed outlier: 5.015A pdb=" N ARG c 246 " --> pdb=" O THR c 242 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE c 247 " --> pdb=" O LEU c 243 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG c 250 " --> pdb=" O ARG c 246 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET c 251 " --> pdb=" O PHE c 247 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 23 removed outlier: 4.004A pdb=" N LEU d 18 " --> pdb=" O ALA d 14 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL d 19 " --> pdb=" O LYS d 15 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 39 removed outlier: 3.549A pdb=" N LEU d 33 " --> pdb=" O THR d 29 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN d 38 " --> pdb=" O THR d 34 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY d 39 " --> pdb=" O THR d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 66 removed outlier: 4.505A pdb=" N ALA d 56 " --> pdb=" O PRO d 52 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU d 59 " --> pdb=" O ARG d 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 77 removed outlier: 3.662A pdb=" N LYS e 75 " --> pdb=" O ARG e 71 " (cutoff:3.500A) Proline residue: e 76 - end of helix No H-bonds generated for 'chain 'e' and resid 71 through 77' Processing helix chain 'e' and resid 86 through 92 removed outlier: 4.143A pdb=" N LEU e 90 " --> pdb=" O HIS e 86 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS e 92 " --> pdb=" O SER e 88 " (cutoff:3.500A) Processing helix chain 'e' and resid 95 through 116 removed outlier: 4.577A pdb=" N ALA e 100 " --> pdb=" O PHE e 96 " (cutoff:3.500A) Proline residue: e 101 - end of helix removed outlier: 3.567A pdb=" N ILE e 104 " --> pdb=" O ALA e 100 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE e 110 " --> pdb=" O ARG e 106 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 123 through 132 removed outlier: 5.768A pdb=" N ASN e 127 " --> pdb=" O ASP e 123 " (cutoff:3.500A) Processing helix chain 'f' and resid 22 through 27 removed outlier: 3.967A pdb=" N PHE f 26 " --> pdb=" O ARG f 22 " (cutoff:3.500A) Proline residue: f 27 - end of helix No H-bonds generated for 'chain 'f' and resid 22 through 27' Processing helix chain 'f' and resid 41 through 46 Processing helix chain 'f' and resid 79 through 88 removed outlier: 3.712A pdb=" N LEU f 83 " --> pdb=" O ASN f 79 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR f 84 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET f 85 " --> pdb=" O GLU f 81 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N MET f 88 " --> pdb=" O TYR f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 117 removed outlier: 3.714A pdb=" N ALA f 108 " --> pdb=" O ARG f 104 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS f 112 " --> pdb=" O ALA f 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET f 114 " --> pdb=" O ALA f 110 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 72 removed outlier: 5.936A pdb=" N ALA g 67 " --> pdb=" O THR g 63 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR g 68 " --> pdb=" O ARG g 64 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TRP g 69 " --> pdb=" O GLU g 65 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR g 70 " --> pdb=" O ASP g 66 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLY g 72 " --> pdb=" O THR g 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 63 through 72' Processing helix chain 'g' and resid 89 through 94 Proline residue: g 94 - end of helix No H-bonds generated for 'chain 'g' and resid 89 through 94' Processing helix chain 'h' and resid 61 through 68 removed outlier: 3.602A pdb=" N LEU h 67 " --> pdb=" O ILE h 63 " (cutoff:3.500A) Processing helix chain 'h' and resid 69 through 74 removed outlier: 4.749A pdb=" N LYS h 73 " --> pdb=" O SER h 69 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER h 74 " --> pdb=" O ARG h 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 69 through 74' Processing helix chain 'h' and resid 84 through 106 removed outlier: 4.273A pdb=" N ARG h 91 " --> pdb=" O GLN h 87 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL h 93 " --> pdb=" O ARG h 89 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL h 98 " --> pdb=" O ARG h 94 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU h 99 " --> pdb=" O ALA h 95 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS h 105 " --> pdb=" O GLN h 101 " (cutoff:3.500A) Processing helix chain 'i' and resid 38 through 52 removed outlier: 4.056A pdb=" N ALA i 42 " --> pdb=" O LYS i 38 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA i 48 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU i 50 " --> pdb=" O ILE i 46 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL i 51 " --> pdb=" O ILE i 47 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY i 52 " --> pdb=" O ALA i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 54 through 67 removed outlier: 3.677A pdb=" N PHE i 63 " --> pdb=" O ARG i 59 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL i 66 " --> pdb=" O GLU i 62 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY i 67 " --> pdb=" O PHE i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 80 removed outlier: 3.813A pdb=" N LEU i 73 " --> pdb=" O GLU i 69 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS i 74 " --> pdb=" O LYS i 70 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS i 78 " --> pdb=" O LYS i 74 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU i 80 " --> pdb=" O CYS i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 100 removed outlier: 4.137A pdb=" N ALA i 86 " --> pdb=" O ASP i 82 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS i 87 " --> pdb=" O PHE i 83 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS i 88 " --> pdb=" O THR i 84 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS i 89 " --> pdb=" O ALA i 85 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS i 92 " --> pdb=" O LYS i 88 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N HIS i 99 " --> pdb=" O GLU i 95 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR i 100 " --> pdb=" O ALA i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.776A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN j 10 " --> pdb=" O THR j 6 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.522A pdb=" N ARG j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 77 removed outlier: 4.356A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA j 75 " --> pdb=" O ASN j 71 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS j 77 " --> pdb=" O ARG j 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 4.002A pdb=" N PHE k 11 " --> pdb=" O THR k 7 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU k 12 " --> pdb=" O LEU k 8 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 50 through 59 removed outlier: 3.569A pdb=" N ASP k 54 " --> pdb=" O LYS k 50 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU k 57 " --> pdb=" O ALA k 53 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG k 58 " --> pdb=" O ASP k 54 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER k 59 " --> pdb=" O LYS k 55 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 3.590A pdb=" N LYS l 16 " --> pdb=" O LYS l 12 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN l 19 " --> pdb=" O LYS l 15 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS l 21 " --> pdb=" O MET l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.463A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU l 29 " --> pdb=" O TYR l 25 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 19 through 35 removed outlier: 3.500A pdb=" N LYS m 28 " --> pdb=" O LYS m 24 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU m 29 " --> pdb=" O ARG m 25 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN m 33 " --> pdb=" O LEU m 29 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS m 34 " --> pdb=" O GLU m 30 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA m 35 " --> pdb=" O VAL m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 73 through 92 removed outlier: 5.114A pdb=" N THR m 78 " --> pdb=" O PRO m 74 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER m 81 " --> pdb=" O SER m 77 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG m 84 " --> pdb=" O ARG m 80 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU m 89 " --> pdb=" O ARG m 85 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA m 90 " --> pdb=" O LEU m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 14 removed outlier: 3.614A pdb=" N ARG m 13 " --> pdb=" O VAL m 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 48 removed outlier: 4.037A pdb=" N SER n 48 " --> pdb=" O ASP n 44 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.563A pdb=" N SER A 47 " --> pdb=" O AARG A 60 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N AARG A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET A 41 " --> pdb=" O CYS A 90 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A 45 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 111 through 114 removed outlier: 3.997A pdb=" N CYS A 111 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 4, first strand: chain 'A' and resid 146 through 150 removed outlier: 4.293A pdb=" N GLN A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 44 through 50 removed outlier: 7.716A pdb=" N THR B 44 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG B 341 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU B 218 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 53 through 58 removed outlier: 3.854A pdb=" N VAL B 159 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY B 91 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 289 through 292 removed outlier: 3.651A pdb=" N GLY B 291 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 84 through 87 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'B' and resid 77 through 81 removed outlier: 3.581A pdb=" N THR B 77 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B 327 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 160 through 166 removed outlier: 5.173A pdb=" N ILE B 160 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N HIS B 182 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 6 through 9 removed outlier: 3.638A pdb=" N GLY C 19 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 224 through 230 removed outlier: 3.748A pdb=" N ASP C 226 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE C 247 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL C 209 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 18 through 25 removed outlier: 3.633A pdb=" N VAL D 73 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE D 21 " --> pdb=" O CYS D 71 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS D 71 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE D 67 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA D 68 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= 15, first strand: chain 'E' and resid 7 through 12 removed outlier: 4.020A pdb=" N CYS E 8 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 12 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG E 52 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR E 53 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 55 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE E 57 " --> pdb=" O ASP E 44 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP E 44 " --> pdb=" O ILE E 57 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 86 through 92 removed outlier: 4.561A pdb=" N TYR E 87 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY E 147 " --> pdb=" O TYR E 87 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 108 through 112 removed outlier: 3.504A pdb=" N VAL E 111 " --> pdb=" O ARG E 121 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 36 through 41 removed outlier: 3.669A pdb=" N VAL F 37 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA F 51 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG F 49 " --> pdb=" O ILE F 41 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 261 through 266 removed outlier: 3.514A pdb=" N MET G 235 " --> pdb=" O ILE G 285 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N THR G 281 " --> pdb=" O ALA G 239 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.696A pdb=" N THR H 52 " --> pdb=" O ILE H 25 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 60 through 64 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'J' and resid 25 through 28 removed outlier: 4.335A pdb=" N ASN J 26 " --> pdb=" O ASN J 100 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA J 28 " --> pdb=" O GLY J 102 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE J 104 " --> pdb=" O ALA J 28 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN J 77 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET J 59 " --> pdb=" O LYS J 42 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 81 through 84 removed outlier: 4.346A pdb=" N ARG J 84 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP J 99 " --> pdb=" O ARG J 84 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 71 through 74 removed outlier: 3.877A pdb=" N ARG K 81 " --> pdb=" O ILE K 73 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 94 through 97 Processing sheet with id= 26, first strand: chain 'L' and resid 119 through 122 Processing sheet with id= 27, first strand: chain 'M' and resid 35 through 39 removed outlier: 6.183A pdb=" N THR M 35 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL M 61 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY M 58 " --> pdb=" O ASP M 136 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR M 126 " --> pdb=" O ARG M 68 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE M 133 " --> pdb=" O LEU M 116 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 117 through 121 removed outlier: 6.672A pdb=" N TRP M 129 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 48 through 52 removed outlier: 4.268A pdb=" N VAL N 52 " --> pdb=" O LEU N 136 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU N 136 " --> pdb=" O VAL N 52 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'N' and resid 97 through 100 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'O' and resid 59 through 66 removed outlier: 3.953A pdb=" N ASP O 59 " --> pdb=" O THR O 56 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL O 65 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP O 153 " --> pdb=" O LEU O 51 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 106 through 109 removed outlier: 4.871A pdb=" N ARG P 106 " --> pdb=" O PRO P 85 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 21 through 25 removed outlier: 5.867A pdb=" N ARG Q 21 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE Q 49 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 26 through 32 removed outlier: 5.900A pdb=" N HIS R 8 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL R 12 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER R 62 " --> pdb=" O VAL R 12 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 122 through 126 removed outlier: 6.115A pdb=" N ASN R 122 " --> pdb=" O TYR R 83 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN R 75 " --> pdb=" O ILE R 131 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS R 129 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 72 through 79 Processing sheet with id= 37, first strand: chain 'T' and resid 13 through 20 removed outlier: 8.212A pdb=" N LYS T 13 " --> pdb=" O GLU T 152 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU T 152 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA T 15 " --> pdb=" O MET T 150 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE T 149 " --> pdb=" O HIS T 116 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS T 116 " --> pdb=" O PHE T 149 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 124 through 131 removed outlier: 6.017A pdb=" N MET T 125 " --> pdb=" O CYS T 141 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG T 127 " --> pdb=" O TYR T 139 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR T 139 " --> pdb=" O ARG T 127 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR T 137 " --> pdb=" O THR T 129 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG T 135 " --> pdb=" O ARG T 131 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 76 through 81 removed outlier: 3.546A pdb=" N LEU U 77 " --> pdb=" O ILE U 28 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE U 28 " --> pdb=" O LEU U 77 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE U 79 " --> pdb=" O PHE U 26 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE U 26 " --> pdb=" O ILE U 79 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR U 81 " --> pdb=" O LYS U 24 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY U 115 " --> pdb=" O VAL U 25 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR U 117 " --> pdb=" O LYS U 27 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU U 119 " --> pdb=" O ASP U 29 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 83 through 88 removed outlier: 7.372A pdb=" N ASN V 83 " --> pdb=" O LEU V 129 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU V 122 " --> pdb=" O ARG V 118 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS V 112 " --> pdb=" O ARG V 128 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 83 through 86 removed outlier: 5.334A pdb=" N SER W 90 " --> pdb=" O LYS W 86 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.629A pdb=" N ILE X 4 " --> pdb=" O VAL X 13 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE X 11 " --> pdb=" O CYS X 6 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'X' and resid 18 through 22 removed outlier: 3.698A pdb=" N PHE X 35 " --> pdb=" O ARG X 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Y' and resid 10 through 14 removed outlier: 4.250A pdb=" N HIS Y 21 " --> pdb=" O VAL Y 13 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Y' and resid 27 through 30 removed outlier: 3.748A pdb=" N SER Y 29 " --> pdb=" O ARG Y 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG Y 40 " --> pdb=" O SER Y 29 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Z' and resid 49 through 52 removed outlier: 5.516A pdb=" N LYS Z 49 " --> pdb=" O GLY Z 59 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS Z 57 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 143 through 148 removed outlier: 7.085A pdb=" N TYR c 143 " --> pdb=" O ILE c 99 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY c 147 " --> pdb=" O VAL c 95 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG c 98 " --> pdb=" O ASN c 123 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN c 123 " --> pdb=" O ARG c 98 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE c 122 " --> pdb=" O LEU c 217 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'd' and resid 68 through 71 removed outlier: 3.861A pdb=" N ILE d 44 " --> pdb=" O PRO d 68 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 119 through 122 removed outlier: 3.518A pdb=" N TYR e 162 " --> pdb=" O LYS e 149 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS e 149 " --> pdb=" O TYR e 162 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN e 147 " --> pdb=" O VAL e 164 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG e 143 " --> pdb=" O VAL e 168 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL e 79 " --> pdb=" O ARG e 148 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER e 80 " --> pdb=" O VAL e 181 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'f' and resid 72 through 76 Processing sheet with id= 51, first strand: chain 'g' and resid 99 through 107 removed outlier: 6.815A pdb=" N THR g 99 " --> pdb=" O GLY g 81 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS g 73 " --> pdb=" O VAL g 107 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG g 74 " --> pdb=" O TYR g 138 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL g 78 " --> pdb=" O ARG g 134 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG g 134 " --> pdb=" O VAL g 78 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU g 55 " --> pdb=" O ALA g 40 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'h' and resid 23 through 26 removed outlier: 4.425A pdb=" N THR h 26 " --> pdb=" O LYS h 30 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'k' and resid 2 through 5 removed outlier: 5.253A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA k 31 " --> pdb=" O ASN k 28 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN k 28 " --> pdb=" O ALA k 31 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS k 35 " --> pdb=" O LYS k 24 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N CYS k 22 " --> pdb=" O ARG k 37 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'm' and resid 47 through 50 removed outlier: 6.912A pdb=" N ILE m 54 " --> pdb=" O LYS m 50 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLY m 53 " --> pdb=" O GLY m 66 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS m 62 " --> pdb=" O CYS m 57 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'n' and resid 23 through 27 removed outlier: 3.913A pdb=" N VAL n 26 " --> pdb=" O LYS n 71 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS n 71 " --> pdb=" O VAL n 26 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE n 68 " --> pdb=" O LEU n 85 " (cutoff:3.500A) 1312 hydrogen bonds defined for protein. 3891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1775 hydrogen bonds 2780 hydrogen bond angles 0 basepair planarities 742 basepair parallelities 1680 stacking parallelities Total time for adding SS restraints: 86.91 Time building geometry restraints manager: 54.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 16741 1.33 - 1.45: 54179 1.45 - 1.58: 48509 1.58 - 1.71: 6740 1.71 - 1.83: 311 Bond restraints: 126480 Sorted by residual: bond pdb=" C2' A2M 7 162 " pdb=" C1' A2M 7 162 " ideal model delta sigma weight residual 1.305 1.517 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C2' A2M 2 591 " pdb=" C1' A2M 2 591 " ideal model delta sigma weight residual 1.305 1.516 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C2' A2M 2 527 " pdb=" C1' A2M 2 527 " ideal model delta sigma weight residual 1.305 1.515 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C2' A2M 2 382 " pdb=" C1' A2M 2 382 " ideal model delta sigma weight residual 1.305 1.514 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C2' A2M 11541 " pdb=" C1' A2M 11541 " ideal model delta sigma weight residual 1.305 1.513 -0.208 2.00e-02 2.50e+03 1.09e+02 ... (remaining 126475 not shown) Histogram of bond angle deviations from ideal: 79.22 - 90.78: 2 90.78 - 102.34: 4619 102.34 - 113.90: 93082 113.90 - 125.46: 77373 125.46 - 137.02: 12595 Bond angle restraints: 187671 Sorted by residual: angle pdb=" C1' A2M 1 955 " pdb=" N9 A2M 1 955 " pdb=" C8 A2M 1 955 " ideal model delta sigma weight residual 88.50 126.83 -38.33 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C1' A2M 1 927 " pdb=" N9 A2M 1 927 " pdb=" C8 A2M 1 927 " ideal model delta sigma weight residual 88.50 126.48 -37.98 3.00e+00 1.11e-01 1.60e+02 angle pdb=" C1' A2M 2 527 " pdb=" N9 A2M 2 527 " pdb=" C8 A2M 2 527 " ideal model delta sigma weight residual 88.50 126.12 -37.62 3.00e+00 1.11e-01 1.57e+02 angle pdb=" C1' A2M 2 572 " pdb=" N9 A2M 2 572 " pdb=" C8 A2M 2 572 " ideal model delta sigma weight residual 88.50 125.91 -37.41 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C1' A2M 2 628 " pdb=" N9 A2M 2 628 " pdb=" C8 A2M 2 628 " ideal model delta sigma weight residual 88.50 125.88 -37.38 3.00e+00 1.11e-01 1.55e+02 ... (remaining 187666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 67791 35.98 - 71.96: 7691 71.96 - 107.93: 1140 107.93 - 143.91: 87 143.91 - 179.89: 103 Dihedral angle restraints: 76812 sinusoidal: 59853 harmonic: 16959 Sorted by residual: dihedral pdb=" CA PRO E 136 " pdb=" C PRO E 136 " pdb=" N SER E 137 " pdb=" CA SER E 137 " ideal model delta harmonic sigma weight residual -180.00 -102.23 -77.77 0 5.00e+00 4.00e-02 2.42e+02 dihedral pdb=" CA GLY B 373 " pdb=" C GLY B 373 " pdb=" N HIS B 374 " pdb=" CA HIS B 374 " ideal model delta harmonic sigma weight residual 180.00 110.02 69.98 0 5.00e+00 4.00e-02 1.96e+02 dihedral pdb=" CD BARG W 84 " pdb=" NE BARG W 84 " pdb=" CZ BARG W 84 " pdb=" NH1BARG W 84 " ideal model delta sinusoidal sigma weight residual 0.00 -179.89 179.89 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 76809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.408: 23723 0.408 - 0.817: 5 0.817 - 1.225: 0 1.225 - 1.633: 0 1.633 - 2.041: 1 Chirality restraints: 23729 Sorted by residual: chirality pdb=" P C 11576 " pdb=" OP1 C 11576 " pdb=" OP2 C 11576 " pdb=" O5' C 11576 " both_signs ideal model delta sigma weight residual True 2.41 0.37 2.04 2.00e-01 2.50e+01 1.04e+02 chirality pdb=" C3' G 6 41 " pdb=" C4' G 6 41 " pdb=" O3' G 6 41 " pdb=" C2' G 6 41 " both_signs ideal model delta sigma weight residual False -2.74 -2.02 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C3' G 8 43 " pdb=" C4' G 8 43 " pdb=" O3' G 8 43 " pdb=" C2' G 8 43 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 23726 not shown) Planarity restraints: 11207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC 2 443 " 0.957 2.00e-02 2.50e+03 6.21e-01 8.66e+03 pdb=" C4' OMC 2 443 " -0.223 2.00e-02 2.50e+03 pdb=" O4' OMC 2 443 " -0.836 2.00e-02 2.50e+03 pdb=" C3' OMC 2 443 " 0.238 2.00e-02 2.50e+03 pdb=" O3' OMC 2 443 " -0.901 2.00e-02 2.50e+03 pdb=" C2' OMC 2 443 " 0.633 2.00e-02 2.50e+03 pdb=" O2' OMC 2 443 " 0.585 2.00e-02 2.50e+03 pdb=" C1' OMC 2 443 " -0.437 2.00e-02 2.50e+03 pdb=" N1 OMC 2 443 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 71 " -0.007 2.00e-02 2.50e+03 6.19e-01 8.62e+03 pdb=" C4' OMG 2 71 " -0.484 2.00e-02 2.50e+03 pdb=" O4' OMG 2 71 " -0.818 2.00e-02 2.50e+03 pdb=" C3' OMG 2 71 " 0.576 2.00e-02 2.50e+03 pdb=" O3' OMG 2 71 " 0.580 2.00e-02 2.50e+03 pdb=" C2' OMG 2 71 " 0.221 2.00e-02 2.50e+03 pdb=" O2' OMG 2 71 " -0.862 2.00e-02 2.50e+03 pdb=" C1' OMG 2 71 " -0.223 2.00e-02 2.50e+03 pdb=" N9 OMG 2 71 " 1.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 2 641 " 0.043 2.00e-02 2.50e+03 5.82e-01 7.62e+03 pdb=" C4' OMG 2 641 " -0.478 2.00e-02 2.50e+03 pdb=" O4' OMG 2 641 " -0.754 2.00e-02 2.50e+03 pdb=" C3' OMG 2 641 " 0.571 2.00e-02 2.50e+03 pdb=" O3' OMG 2 641 " 0.522 2.00e-02 2.50e+03 pdb=" C2' OMG 2 641 " 0.235 2.00e-02 2.50e+03 pdb=" O2' OMG 2 641 " -0.816 2.00e-02 2.50e+03 pdb=" C1' OMG 2 641 " -0.253 2.00e-02 2.50e+03 pdb=" N9 OMG 2 641 " 0.929 2.00e-02 2.50e+03 ... (remaining 11204 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 28 1.85 - 2.62: 3766 2.62 - 3.38: 150574 3.38 - 4.14: 384919 4.14 - 4.90: 558814 Nonbonded interactions: 1098101 Sorted by model distance: nonbonded pdb=" O2' A 6 28 " pdb=" C8 G 6 29 " model vdw 1.093 3.260 nonbonded pdb=" O4 U 2 829 " pdb=" N4 C 2 958 " model vdw 1.097 2.520 nonbonded pdb=" OD1 ASN V 51 " pdb="MG MG V 201 " model vdw 1.405 2.170 nonbonded pdb=" O3' U 7 146 " pdb=" ND2 ASN V 51 " model vdw 1.421 2.520 nonbonded pdb=" N1 G 3 22 " pdb=" N2 G 3 209 " model vdw 1.461 3.200 ... (remaining 1098096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.140 Extract box with map and model: 16.470 Check model and map are aligned: 1.440 Set scattering table: 0.820 Process input model: 337.330 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.290 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 374.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.212 126480 Z= 0.547 Angle : 0.981 38.332 187671 Z= 0.500 Chirality : 0.051 2.041 23729 Planarity : 0.026 0.621 11207 Dihedral : 24.405 179.891 65851 Min Nonbonded Distance : 1.093 Molprobity Statistics. All-atom Clashscore : 24.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.84 % Favored : 87.99 % Rotamer: Outliers : 1.41 % Allowed : 5.34 % Favored : 93.25 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.02 % Twisted Proline : 0.42 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.08), residues: 5796 helix: -4.34 (0.07), residues: 1663 sheet: -3.11 (0.18), residues: 635 loop : -3.37 (0.09), residues: 3498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP j 31 HIS 0.024 0.003 HIS A 19 PHE 0.062 0.004 PHE C 255 TYR 0.059 0.004 TYR W 71 ARG 0.027 0.002 ARG T 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1280 time to evaluate : 5.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 17 residues processed: 1310 average time/residue: 2.0519 time to fit residues: 3665.1639 Evaluate side-chains 976 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 959 time to evaluate : 5.506 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 3 average time/residue: 1.8167 time to fit residues: 13.6952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 905 random chunks: chunk 764 optimal weight: 1.9990 chunk 685 optimal weight: 7.9990 chunk 380 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 462 optimal weight: 0.3980 chunk 366 optimal weight: 1.9990 chunk 709 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 431 optimal weight: 0.0070 chunk 527 optimal weight: 4.9990 chunk 821 optimal weight: 7.9990 overall best weight: 1.6804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 19 HIS A 21 HIS A 65 HIS ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN A 140 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN A 221 HIS A 228 HIS B 55 HIS B 108 HIS B 127 GLN B 174 HIS A B 279 HIS B 282 GLN B 326 ASN ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 197 ASN C 237 HIS E 42 GLN E 51 ASN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 97 HIS E 123 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN F 154 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 HIS G 222 GLN G 253 ASN H 60 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN H 212 ASN I 12 HIS ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 HIS ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 ASN J 26 ASN J 35 ASN J 49 ASN J 83 GLN J 134 HIS K 92 ASN ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN L 60 HIS L 112 ASN M 76 HIS M 95 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 ASN N 71 GLN ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** P 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 ASN P 175 ASN P 197 HIS Q 130 ASN R 10 GLN R 122 ASN S 33 ASN S 58 HIS T 3 HIS T 37 ASN T 78 GLN T 97 ASN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 133 HIS W 18 GLN W 100 ASN W 110 HIS Y 67 GLN ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 117 GLN a 36 GLN a 116 HIS ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 ASN b 30 HIS b 43 ASN c 109 GLN c 120 GLN ** c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 176 ASN c 177 GLN c 196 ASN c 245 ASN d 71 HIS e 120 ASN e 127 ASN f 122 ASN g 47 HIS g 80 HIS g 122 ASN g 143 GLN h 13 HIS h 51 HIS h 62 HIS h 71 HIS j 12 HIS j 16 HIS j 25 ASN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 HIS n 27 GLN n 82 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 126480 Z= 0.240 Angle : 0.886 26.846 187671 Z= 0.463 Chirality : 0.045 2.126 23729 Planarity : 0.008 0.177 11207 Dihedral : 25.585 179.994 56047 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.96 % Favored : 89.99 % Rotamer: Outliers : 3.86 % Allowed : 16.34 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.41 (0.09), residues: 5796 helix: -3.22 (0.09), residues: 1766 sheet: -2.43 (0.18), residues: 699 loop : -2.96 (0.09), residues: 3331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP j 31 HIS 0.013 0.002 HIS e 86 PHE 0.036 0.002 PHE C 255 TYR 0.028 0.002 TYR A 67 ARG 0.046 0.001 ARG H 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1075 time to evaluate : 5.610 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 54 residues processed: 1139 average time/residue: 1.9058 time to fit residues: 3028.8760 Evaluate side-chains 985 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 931 time to evaluate : 5.485 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 26 residues processed: 29 average time/residue: 0.8278 time to fit residues: 51.8318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 905 random chunks: chunk 456 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 684 optimal weight: 1.9990 chunk 559 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 823 optimal weight: 3.9990 chunk 889 optimal weight: 4.9990 chunk 733 optimal weight: 6.9990 chunk 816 optimal weight: 7.9990 chunk 280 optimal weight: 30.0000 chunk 660 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 106 GLN A 205 ASN A 211 HIS A 228 HIS ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 174 HIS B ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 HIS H 74 GLN H 186 HIS I 16 HIS I 23 GLN J 26 ASN ** J 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS L 77 ASN ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 GLN M 95 ASN M 98 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 ASN ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 ASN ** O 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 HIS ** R 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 10 GLN ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN T 78 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS W 18 GLN W 111 HIS ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 130 GLN a 31 GLN a 36 GLN ** a 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 ASN g 122 ASN g 143 GLN h 34 GLN j 71 ASN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 126480 Z= 0.387 Angle : 0.905 27.577 187671 Z= 0.470 Chirality : 0.047 2.086 23729 Planarity : 0.009 0.137 11207 Dihedral : 25.434 179.964 56047 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.00 % Favored : 88.94 % Rotamer: Outliers : 5.15 % Allowed : 19.16 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.02 % 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: -3.93 (0.10), residues: 5796 helix: -2.63 (0.10), residues: 1803 sheet: -2.28 (0.19), residues: 653 loop : -2.74 (0.10), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP j 31 HIS 0.017 0.002 HIS e 86 PHE 0.046 0.003 PHE C 91 TYR 0.034 0.003 TYR T 139 ARG 0.019 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1000 time to evaluate : 5.739 Fit side-chains revert: symmetry clash outliers start: 209 outliers final: 109 residues processed: 1098 average time/residue: 1.9206 time to fit residues: 2948.6907 Evaluate side-chains 1031 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 922 time to evaluate : 5.543 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 54 residues processed: 55 average time/residue: 1.0888 time to fit residues: 108.2675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 905 random chunks: chunk 813 optimal weight: 7.9990 chunk 619 optimal weight: 6.9990 chunk 427 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 392 optimal weight: 4.9990 chunk 552 optimal weight: 9.9990 chunk 826 optimal weight: 0.9980 chunk 874 optimal weight: 0.4980 chunk 431 optimal weight: 10.0000 chunk 783 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 228 HIS ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 282 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN G 253 ASN H 74 GLN I 108 ASN ** K 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN L 144 GLN M 33 GLN M 57 GLN M 95 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 175 ASN ** R 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN a 65 ASN ** b 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 ASN d 38 GLN g 143 GLN h 41 GLN j 71 ASN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 126480 Z= 0.304 Angle : 0.850 27.382 187671 Z= 0.445 Chirality : 0.044 2.085 23729 Planarity : 0.008 0.168 11207 Dihedral : 25.330 179.770 56047 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.19 % Favored : 89.76 % Rotamer: Outliers : 5.56 % Allowed : 20.91 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.57 (0.10), residues: 5796 helix: -2.23 (0.11), residues: 1808 sheet: -2.08 (0.19), residues: 686 loop : -2.58 (0.10), residues: 3302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP j 31 HIS 0.014 0.002 HIS e 86 PHE 0.032 0.002 PHE C 91 TYR 0.034 0.002 TYR T 48 ARG 0.043 0.001 ARG H 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 972 time to evaluate : 5.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 226 outliers final: 121 residues processed: 1088 average time/residue: 1.8788 time to fit residues: 2860.8424 Evaluate side-chains 1033 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 912 time to evaluate : 5.524 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 69 residues processed: 55 average time/residue: 1.1185 time to fit residues: 109.0528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 905 random chunks: chunk 728 optimal weight: 0.0970 chunk 496 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 651 optimal weight: 9.9990 chunk 360 optimal weight: 0.0980 chunk 746 optimal weight: 8.9990 chunk 604 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 446 optimal weight: 30.0000 chunk 785 optimal weight: 0.7980 chunk 220 optimal weight: 30.0000 overall best weight: 2.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 228 HIS ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 282 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN G 151 GLN H 74 GLN I 23 GLN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN ** K 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN M 33 GLN M 57 GLN M 95 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN ** P 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 175 ASN ** R 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 130 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN b 43 ASN d 70 HIS g 25 ASN g 143 GLN j 71 ASN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 126480 Z= 0.296 Angle : 0.840 27.318 187671 Z= 0.440 Chirality : 0.044 2.078 23729 Planarity : 0.008 0.133 11207 Dihedral : 25.253 179.664 56047 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.69 % Favored : 89.26 % Rotamer: Outliers : 5.68 % Allowed : 22.37 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.31 (0.10), residues: 5796 helix: -1.95 (0.11), residues: 1823 sheet: -1.98 (0.19), residues: 659 loop : -2.45 (0.10), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP j 31 HIS 0.012 0.002 HIS e 86 PHE 0.035 0.002 PHE C 91 TYR 0.038 0.002 TYR T 48 ARG 0.011 0.001 ARG X 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 964 time to evaluate : 5.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 231 outliers final: 117 residues processed: 1084 average time/residue: 1.8994 time to fit residues: 2877.7329 Evaluate side-chains 1035 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 918 time to evaluate : 5.489 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 71 residues processed: 46 average time/residue: 0.9936 time to fit residues: 85.8154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 905 random chunks: chunk 294 optimal weight: 30.0000 chunk 787 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 513 optimal weight: 6.9990 chunk 215 optimal weight: 30.0000 chunk 875 optimal weight: 0.9980 chunk 726 optimal weight: 4.9990 chunk 405 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 289 optimal weight: 7.9990 chunk 459 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 228 HIS ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN G 151 GLN G 253 ASN H 74 GLN H 159 ASN I 23 GLN I 36 GLN J 49 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN ** K 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN M 57 GLN M 95 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 175 ASN Q 130 ASN ** R 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 HIS ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN T 78 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN W 83 ASN ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 130 GLN ** Z 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN a 64 GLN b 43 ASN c 167 ASN d 38 GLN ** e 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 143 GLN j 71 ASN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 126480 Z= 0.340 Angle : 0.857 27.276 187671 Z= 0.447 Chirality : 0.045 2.079 23729 Planarity : 0.008 0.135 11207 Dihedral : 25.238 179.888 56047 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.66 % Favored : 89.29 % Rotamer: Outliers : 5.44 % Allowed : 23.56 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.02 % 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: -3.23 (0.10), residues: 5796 helix: -1.82 (0.11), residues: 1829 sheet: -2.04 (0.19), residues: 655 loop : -2.41 (0.10), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 193 HIS 0.013 0.002 HIS e 86 PHE 0.039 0.002 PHE C 91 TYR 0.041 0.002 TYR T 48 ARG 0.017 0.001 ARG O 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 942 time to evaluate : 5.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 221 outliers final: 139 residues processed: 1065 average time/residue: 1.9149 time to fit residues: 2842.6920 Evaluate side-chains 1054 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 915 time to evaluate : 5.513 Switching outliers to nearest non-outliers outliers start: 139 outliers final: 89 residues processed: 51 average time/residue: 1.1038 time to fit residues: 100.6494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 905 random chunks: chunk 844 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 498 optimal weight: 0.9980 chunk 639 optimal weight: 0.7980 chunk 495 optimal weight: 0.9980 chunk 737 optimal weight: 2.9990 chunk 488 optimal weight: 20.0000 chunk 872 optimal weight: 0.9980 chunk 545 optimal weight: 4.9990 chunk 531 optimal weight: 7.9990 chunk 402 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 228 HIS ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 187 GLN B 282 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN ** F 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN G 151 GLN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN ** K 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN M 57 GLN M 95 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 175 ASN Q 130 ASN S 22 HIS S 54 HIS ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN T 78 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 117 GLN ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN b 43 ASN b 50 HIS d 38 GLN g 143 GLN l 19 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 126480 Z= 0.182 Angle : 0.787 27.269 187671 Z= 0.416 Chirality : 0.040 2.070 23729 Planarity : 0.007 0.126 11207 Dihedral : 25.122 179.984 56047 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.25 % Favored : 90.70 % Rotamer: Outliers : 4.93 % Allowed : 24.70 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.10), residues: 5796 helix: -1.41 (0.12), residues: 1820 sheet: -1.90 (0.19), residues: 660 loop : -2.25 (0.10), residues: 3316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 193 HIS 0.007 0.001 HIS e 86 PHE 0.018 0.001 PHE C 169 TYR 0.037 0.002 TYR T 48 ARG 0.030 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 973 time to evaluate : 5.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 200 outliers final: 120 residues processed: 1091 average time/residue: 1.8736 time to fit residues: 2867.8289 Evaluate side-chains 1027 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 907 time to evaluate : 5.593 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 84 residues processed: 39 average time/residue: 1.1422 time to fit residues: 81.3881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 905 random chunks: chunk 539 optimal weight: 0.9980 chunk 348 optimal weight: 0.4980 chunk 520 optimal weight: 0.9980 chunk 262 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 554 optimal weight: 0.4980 chunk 594 optimal weight: 1.9990 chunk 431 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 685 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 228 HIS B 121 ASN B 173 ASN B 282 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS F 152 GLN F 191 HIS F 194 ASN G 151 GLN G 253 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN J 49 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN ** K 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN M 57 GLN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 HIS M 161 GLN N 73 ASN ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS O 181 HIS ** R 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 HIS ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN W 22 HIS W 83 ASN ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN a 64 GLN b 43 ASN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 GLN e 147 GLN g 122 ASN j 25 ASN l 19 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 27 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 126480 Z= 0.161 Angle : 0.760 27.296 187671 Z= 0.403 Chirality : 0.039 2.066 23729 Planarity : 0.007 0.123 11207 Dihedral : 24.910 179.870 56047 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.66 % Favored : 91.29 % Rotamer: Outliers : 3.67 % Allowed : 27.08 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.10), residues: 5796 helix: -0.97 (0.12), residues: 1806 sheet: -1.68 (0.19), residues: 656 loop : -2.07 (0.10), residues: 3334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 193 HIS 0.011 0.001 HIS R 8 PHE 0.021 0.001 PHE a 73 TYR 0.036 0.002 TYR O 189 ARG 0.016 0.001 ARG Q 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1015 time to evaluate : 5.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 87 residues processed: 1109 average time/residue: 1.9039 time to fit residues: 3004.9165 Evaluate side-chains 990 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 903 time to evaluate : 5.539 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 67 residues processed: 20 average time/residue: 1.2175 time to fit residues: 46.8493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 905 random chunks: chunk 793 optimal weight: 3.9990 chunk 835 optimal weight: 4.9990 chunk 762 optimal weight: 0.9990 chunk 812 optimal weight: 2.9990 chunk 489 optimal weight: 0.9990 chunk 354 optimal weight: 9.9990 chunk 638 optimal weight: 20.0000 chunk 249 optimal weight: 30.0000 chunk 734 optimal weight: 4.9990 chunk 768 optimal weight: 5.9990 chunk 810 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 228 HIS B 121 ASN B 173 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN F 152 GLN G 151 GLN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 HIS I 23 GLN I 36 GLN J 35 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN ** K 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN M 57 GLN M 95 ASN M 149 ASN N 73 ASN ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 GLN ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 ASN ** P 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 121 GLN ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 133 HIS W 22 HIS ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN b 43 ASN ** c 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 GLN l 19 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 126480 Z= 0.292 Angle : 0.818 27.247 187671 Z= 0.427 Chirality : 0.042 2.073 23729 Planarity : 0.008 0.128 11207 Dihedral : 24.933 179.695 56047 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.79 % Favored : 90.16 % Rotamer: Outliers : 3.86 % Allowed : 27.95 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.10), residues: 5796 helix: -1.08 (0.12), residues: 1819 sheet: -1.69 (0.20), residues: 643 loop : -2.08 (0.10), residues: 3334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 193 HIS 0.011 0.002 HIS e 86 PHE 0.032 0.002 PHE a 73 TYR 0.045 0.002 TYR T 48 ARG 0.017 0.001 ARG L 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 935 time to evaluate : 5.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 156 outliers final: 106 residues processed: 1033 average time/residue: 1.8639 time to fit residues: 2711.5073 Evaluate side-chains 1012 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 906 time to evaluate : 5.463 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 79 residues processed: 29 average time/residue: 1.0064 time to fit residues: 57.5590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 905 random chunks: chunk 533 optimal weight: 2.9990 chunk 859 optimal weight: 0.6980 chunk 524 optimal weight: 0.7980 chunk 407 optimal weight: 0.8980 chunk 597 optimal weight: 0.9980 chunk 901 optimal weight: 10.0000 chunk 829 optimal weight: 7.9990 chunk 717 optimal weight: 40.0000 chunk 74 optimal weight: 8.9990 chunk 554 optimal weight: 0.0070 chunk 440 optimal weight: 0.0470 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS B 121 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 GLN C 234 ASN C 243 HIS ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN G 151 GLN G 253 ASN ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 HIS I 36 GLN J 35 ASN J 49 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS K 109 GLN K 170 GLN ** K 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN M 57 GLN M 95 ASN M 149 ASN N 73 ASN ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 HIS ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 GLN ** T 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 133 HIS W 22 HIS W 83 ASN ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN b 43 ASN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 GLN d 49 ASN g 143 GLN l 19 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 126480 Z= 0.151 Angle : 0.764 27.308 187671 Z= 0.404 Chirality : 0.038 2.060 23729 Planarity : 0.007 0.122 11207 Dihedral : 24.862 179.731 56047 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.13 % Favored : 91.83 % Rotamer: Outliers : 2.79 % Allowed : 29.67 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.11), residues: 5796 helix: -0.74 (0.12), residues: 1804 sheet: -1.50 (0.20), residues: 652 loop : -1.99 (0.10), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 193 HIS 0.008 0.001 HIS c 204 PHE 0.023 0.002 PHE a 73 TYR 0.035 0.002 TYR O 189 ARG 0.017 0.001 ARG L 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11592 Ramachandran restraints generated. 5796 Oldfield, 0 Emsley, 5796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 931 time to evaluate : 5.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 79 residues processed: 1017 average time/residue: 1.8907 time to fit residues: 2708.1113 Evaluate side-chains 967 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 888 time to evaluate : 5.509 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 71 residues processed: 9 average time/residue: 1.2385 time to fit residues: 23.9864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 905 random chunks: chunk 570 optimal weight: 0.0470 chunk 764 optimal weight: 6.9990 chunk 219 optimal weight: 30.0000 chunk 661 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 719 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 738 optimal weight: 0.4980 chunk 91 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 overall best weight: 3.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS B 121 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** B 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 GLN C 197 ASN C 234 ASN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN G 151 GLN H 74 GLN I 10 HIS I 23 GLN J 35 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS ** K 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN ** K 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN M 149 ASN M 196 ASN N 73 ASN ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 ASN ** P 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 HIS ** T 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 133 HIS W 22 HIS ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 79 HIS ** Z 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 GLN g 143 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 3 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.204042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.164062 restraints weight = 311026.675| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.86 r_work: 0.3846 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 126480 Z= 0.354 Angle : 0.847 27.191 187671 Z= 0.439 Chirality : 0.044 2.077 23729 Planarity : 0.008 0.134 11207 Dihedral : 24.918 179.644 56047 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.99 % Favored : 89.95 % Rotamer: Outliers : 3.28 % Allowed : 29.60 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.10), residues: 5796 helix: -1.03 (0.12), residues: 1820 sheet: -1.62 (0.19), residues: 667 loop : -2.05 (0.10), residues: 3309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP F 193 HIS 0.013 0.002 HIS e 86 PHE 0.033 0.002 PHE C 91 TYR 0.047 0.003 TYR F 83 ARG 0.020 0.001 ARG c 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40043.82 seconds wall clock time: 693 minutes 31.24 seconds (41611.24 seconds total)