Starting phenix.real_space_refine on Tue Mar 12 12:42:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkr_29254/03_2024/8fkr_29254_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkr_29254/03_2024/8fkr_29254.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkr_29254/03_2024/8fkr_29254_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkr_29254/03_2024/8fkr_29254_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkr_29254/03_2024/8fkr_29254_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkr_29254/03_2024/8fkr_29254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkr_29254/03_2024/8fkr_29254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkr_29254/03_2024/8fkr_29254_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkr_29254/03_2024/8fkr_29254_neut_updated.pdb" } resolution = 2.89 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= 0.042 sd= 0.152 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: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 4 7.16 5 Zn 2 6.06 5 P 1993 5.49 5 Mg 54 5.21 5 S 318 5.16 5 C 65634 2.51 5 N 21635 2.21 5 O 26646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BA ASP 44": "OD1" <-> "OD2" Residue "BA ASP 52": "OD1" <-> "OD2" Residue "BA GLU 108": "OE1" <-> "OE2" Residue "BA GLU 161": "OE1" <-> "OE2" Residue "L6 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L6 GLU 79": "OE1" <-> "OE2" Residue "L7 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 GLU 157": "OE1" <-> "OE2" Residue "L7 GLU 182": "OE1" <-> "OE2" Residue "L7 GLU 194": "OE1" <-> "OE2" Residue "L8 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ASP 32": "OD1" <-> "OD2" Residue "L8 ASP 59": "OD1" <-> "OD2" Residue "L8 GLU 96": "OE1" <-> "OE2" Residue "L8 GLU 99": "OE1" <-> "OE2" Residue "L8 GLU 126": "OE1" <-> "OE2" Residue "L9 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 ASP 17": "OD1" <-> "OD2" Residue "L9 GLU 103": "OE1" <-> "OE2" Residue "L9 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 GLU 131": "OE1" <-> "OE2" Residue "LA GLU 9": "OE1" <-> "OE2" Residue "LA GLU 154": "OE1" <-> "OE2" Residue "LC TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC GLU 96": "OE1" <-> "OE2" Residue "LC ASP 99": "OD1" <-> "OD2" Residue "LC GLU 130": "OE1" <-> "OE2" Residue "LC PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE GLU 121": "OE1" <-> "OE2" Residue "LE GLU 137": "OE1" <-> "OE2" Residue "LG ASP 59": "OD1" <-> "OD2" Residue "LG PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 111": "OE1" <-> "OE2" Residue "LG GLU 124": "OE1" <-> "OE2" Residue "LI ASP 10": "OD1" <-> "OD2" Residue "LI ASP 52": "OD1" <-> "OD2" Residue "LI ASP 112": "OD1" <-> "OD2" Residue "LI GLU 120": "OE1" <-> "OE2" Residue "LK PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 214": "OD1" <-> "OD2" Residue "LQ TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ GLU 113": "OE1" <-> "OE2" Residue "LS ASP 22": "OD1" <-> "OD2" Residue "LS TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 100": "OE1" <-> "OE2" Residue "LT GLU 38": "OE1" <-> "OE2" Residue "LT TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 54": "OE1" <-> "OE2" Residue "LU GLU 59": "OE1" <-> "OE2" Residue "LU GLU 88": "OE1" <-> "OE2" Residue "NB TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NE ASP 284": "OD1" <-> "OD2" Residue "NE ASP 285": "OD1" <-> "OD2" Residue "NE ASP 323": "OD1" <-> "OD2" Residue "NF GLU 5": "OE1" <-> "OE2" Residue "NF TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF ASP 158": "OD1" <-> "OD2" Residue "NF PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NG GLU 131": "OE1" <-> "OE2" Residue "NG GLU 190": "OE1" <-> "OE2" Residue "NM ASP 4": "OD1" <-> "OD2" Residue "NM PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NM GLU 88": "OE1" <-> "OE2" Residue "NM TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NM GLU 145": "OE1" <-> "OE2" Residue "NM TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NM TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN GLU 55": "OE1" <-> "OE2" Residue "NN GLU 92": "OE1" <-> "OE2" Residue "NN ASP 120": "OD1" <-> "OD2" Residue "NN PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN ASP 193": "OD1" <-> "OD2" Residue "NN TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NN GLU 288": "OE1" <-> "OE2" Residue "NO GLU 21": "OE1" <-> "OE2" Residue "NO GLU 144": "OE1" <-> "OE2" Residue "NO GLU 171": "OE1" <-> "OE2" Residue "NO GLU 223": "OE1" <-> "OE2" Residue "NO GLU 235": "OE1" <-> "OE2" Residue "NO PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NO GLU 346": "OE1" <-> "OE2" Residue "NQ ASP 179": "OD1" <-> "OD2" Residue "NQ GLU 227": "OE1" <-> "OE2" Residue "NS GLU 56": "OE1" <-> "OE2" Residue "NS ASP 150": "OD1" <-> "OD2" Residue "NS ASP 201": "OD1" <-> "OD2" Residue "NS GLU 241": "OE1" <-> "OE2" Residue "SA TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 146": "OE1" <-> "OE2" Residue "SA ASP 156": "OD1" <-> "OD2" Residue "SA TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA ASP 288": "OD1" <-> "OD2" Residue "SA GLU 297": "OE1" <-> "OE2" Residue "SC TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 81": "OE1" <-> "OE2" Residue "SC ASP 214": "OD1" <-> "OD2" Residue "SC GLU 238": "OE1" <-> "OE2" Residue "SC GLU 244": "OE1" <-> "OE2" Residue "SC ASP 249": "OD1" <-> "OD2" Residue "SD GLU 60": "OE1" <-> "OE2" Residue "SD GLU 86": "OE1" <-> "OE2" Residue "SD GLU 203": "OE1" <-> "OE2" Residue "SD ASP 238": "OD1" <-> "OD2" Residue "SE PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE GLU 119": "OE1" <-> "OE2" Residue "SE ASP 160": "OD1" <-> "OD2" Residue "SE ASP 162": "OD1" <-> "OD2" Residue "SE GLU 220": "OE1" <-> "OE2" Residue "SE ASP 231": "OD1" <-> "OD2" Residue "SG GLU 14": "OE1" <-> "OE2" Residue "SG GLU 44": "OE1" <-> "OE2" Residue "SG GLU 66": "OE1" <-> "OE2" Residue "SG GLU 143": "OE1" <-> "OE2" Residue "SH PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH GLU 163": "OE1" <-> "OE2" Residue "SH ASP 182": "OD1" <-> "OD2" Residue "SI ASP 92": "OD1" <-> "OD2" Residue "SI PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ ASP 686": "OD1" <-> "OD2" Residue "SJ ASP 697": "OD1" <-> "OD2" Residue "SK TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 124": "OE1" <-> "OE2" Residue "SK GLU 126": "OE1" <-> "OE2" Residue "SK GLU 168": "OE1" <-> "OE2" Residue "SL ASP 41": "OD1" <-> "OD2" Residue "SL GLU 77": "OE1" <-> "OE2" Residue "SL PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL ASP 196": "OD1" <-> "OD2" Residue "SM TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM ASP 117": "OD1" <-> "OD2" Residue "SM TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM ASP 379": "OD1" <-> "OD2" Residue "SN GLU 59": "OE1" <-> "OE2" Residue "SN GLU 65": "OE1" <-> "OE2" Residue "SN GLU 183": "OE1" <-> "OE2" Residue "SO GLU 224": "OE1" <-> "OE2" Residue "SO PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 7": "OD1" <-> "OD2" Residue "SQ PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 138": "OD1" <-> "OD2" Residue "SQ ASP 180": "OD1" <-> "OD2" Residue "SR ASP 74": "OD1" <-> "OD2" Residue "SR TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 434": "OE1" <-> "OE2" Residue "SS GLU 129": "OE1" <-> "OE2" Residue "SS ASP 155": "OD1" <-> "OD2" Residue "SS PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST GLU 237": "OE1" <-> "OE2" Residue "SV TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV ASP 25": "OD1" <-> "OD2" Residue "SV GLU 72": "OE1" <-> "OE2" Residue "SV GLU 84": "OE1" <-> "OE2" Residue "SV GLU 97": "OE1" <-> "OE2" Residue "SV PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV ASP 123": "OD1" <-> "OD2" Residue "SV GLU 126": "OE1" <-> "OE2" Residue "SW TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW ASP 552": "OD1" <-> "OD2" Residue "SW PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ ASP 44": "OD1" <-> "OD2" Residue "SZ ASP 96": "OD1" <-> "OD2" Residue "SZ GLU 137": "OE1" <-> "OE2" Residue "SZ TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 116287 Number of models: 1 Model: "" Number of chains: 63 Chain: "BA" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1176 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 147} Chain: "L1" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3274 Classifications: {'RNA': 154} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 11, 'rna3p_pur': 62, 'rna3p_pyr': 67} Link IDs: {'rna2p': 24, 'rna3p': 129} Chain breaks: 1 Chain: "L2" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1468 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 6, 'rna3p_pur': 21, 'rna3p_pyr': 31} Link IDs: {'rna2p': 16, 'rna3p': 52} Chain breaks: 3 Chain: "L3" Number of atoms: 37886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1767, 37886 Classifications: {'RNA': 1767} Modifications used: {'rna2p_pur': 167, 'rna2p_pyr': 103, 'rna3p_pur': 798, 'rna3p_pyr': 699} Link IDs: {'rna2p': 270, 'rna3p': 1496} Chain breaks: 31 Chain: "L6" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 104} Chain: "L7" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1507 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "L8" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "L9" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1546 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "LA" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1161 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain breaks: 2 Chain: "LB" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1223 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "LC" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1461 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain: "LE" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 686 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain breaks: 2 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 4, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "LG" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 844 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "LH" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 284 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain breaks: 1 Chain: "LI" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LK" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 642 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "LN" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3044 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "LQ" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1096 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "LS" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "LT" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "LU" Number of atoms: 840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} bond proxies already assigned to first conformer: 834 Chain: "LW" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 563 Classifications: {'peptide': 69} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Chain: "NB" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 257 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "NE" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1331 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain breaks: 1 Chain: "NF" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1588 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 3 Chain: "NG" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 738 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "NM" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1550 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "NN" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1950 Classifications: {'peptide': 244} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 230} Chain breaks: 2 Chain: "NO" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2487 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain breaks: 1 Chain: "NQ" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2502 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 305} Chain breaks: 1 Chain: "NS" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2529 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 284} Chain: "SA" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2656 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 313} Chain breaks: 1 Chain: "SC" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1627 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 187} Chain breaks: 2 Chain: "SD" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1985 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 229} Chain: "SE" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1498 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 175} Chain: "SG" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "SH" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1267 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "SI" Number of atoms: 1732 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 bond proxies already assigned to first conformer: 1742 Chain: "SJ" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 609 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "SK" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1721 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "SL" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1960 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "SM" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3452 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 4 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 90 Chain: "SN" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1350 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "SO" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2544 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 284} Chain: "SQ" Number of atoms: 1778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Conformer: "B" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} bond proxies already assigned to first conformer: 1797 Chain: "SR" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3524 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 19, 'TRANS': 408} Chain breaks: 2 Chain: "SS" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1955 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 25, 'TRANS': 209} Chain breaks: 2 Chain: "ST" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "SV" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1171 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "SW" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3560 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 19, 'TRANS': 425} Chain breaks: 1 Chain: "SZ" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1338 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain breaks: 1 Chain: "L1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L3" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Unusual residues: {' MG': 45} Classifications: {'undetermined': 45} Link IDs: {None: 44} Chain: "L9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "NM" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "SA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SR" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' K': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "SV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 63238 SG CYSLW 19 97.633 146.628 147.097 1.00 72.90 S ATOM 63266 SG CYSLW 22 98.354 143.883 149.671 1.00 69.07 S ATOM 63357 SG CYSLW 34 100.107 147.176 149.982 1.00 75.08 S ATOM 63376 SG CYSLW 37 100.975 144.951 147.070 1.00 69.48 S ATOM 67909 SG CYSNM 29 115.829 77.160 191.946 1.00 29.08 S ATOM 68025 SG CYSNM 44 121.834 75.543 190.422 1.00 26.26 S ATOM 67988 SG CYSNM 39 120.360 81.138 193.277 1.00 32.06 S ATOM 67809 SG CYSNM 17 118.348 80.101 187.184 1.00 27.63 S ATOM A07UO SG CYSSV 6 63.133 209.056 250.101 1.00 37.93 S ATOM A07VH SG CYSSV 9 59.553 207.700 249.821 1.00 40.25 S ATOM A080L SG CYSSV 32 62.393 205.295 249.617 1.00 37.47 S ATOM A081F SG CYSSV 36 61.862 207.601 246.787 1.00 40.81 S Time building chain proxies: 45.50, per 1000 atoms: 0.39 Number of scatterers: 116287 At special positions: 0 Unit cell: (214.4, 256.208, 335.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 Fe 4 26.01 K 1 19.00 S 318 16.00 P 1993 15.00 Mg 54 11.99 O 26646 8.00 N 21635 7.00 C 65634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.70 Conformation dependent library (CDL) restraints added in 10.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4NM 401 " pdb="FE1 SF4NM 401 " - pdb=" SG CYSNM 29 " pdb="FE4 SF4NM 401 " - pdb=" SG CYSNM 17 " pdb="FE2 SF4NM 401 " - pdb=" SG CYSNM 44 " pdb="FE3 SF4NM 401 " - pdb=" SG CYSNM 39 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 12 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17210 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: 326 helices and 79 sheets defined 49.1% alpha, 13.9% beta 630 base pairs and 970 stacking pairs defined. Time for finding SS restraints: 68.06 Creating SS restraints... Processing helix chain 'BA' and resid 24 through 36 Proline residue: BA 30 - end of helix Proline residue: BA 34 - end of helix Processing helix chain 'BA' and resid 38 through 51 removed outlier: 3.731A pdb=" N GLYBA 51 " --> pdb=" O ALABA 47 " (cutoff:3.500A) Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.721A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 91 through 96 removed outlier: 3.959A pdb=" N GLNBA 95 " --> pdb=" O ASPBA 91 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYSBA 96 " --> pdb=" O ARGBA 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'BA' and resid 91 through 96' Processing helix chain 'BA' and resid 105 through 121 removed outlier: 5.038A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.616A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 removed outlier: 3.633A pdb=" N ILEBA 151 " --> pdb=" O HISBA 147 " (cutoff:3.500A) Processing helix chain 'L6' and resid 27 through 47 removed outlier: 3.545A pdb=" N ALAL6 47 " --> pdb=" O ALAL6 43 " (cutoff:3.500A) Processing helix chain 'L6' and resid 77 through 85 Processing helix chain 'L6' and resid 87 through 95 removed outlier: 4.013A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.747A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.596A pdb=" N GLYL7 30 " --> pdb=" O GLNL7 26 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 56 removed outlier: 4.059A pdb=" N ALAL7 56 " --> pdb=" O LEUL7 52 " (cutoff:3.500A) Processing helix chain 'L7' and resid 75 through 89 Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 5.331A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.802A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYSL7 116 " --> pdb=" O TYRL7 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L7' and resid 110 through 116' Processing helix chain 'L7' and resid 124 through 129 Processing helix chain 'L7' and resid 137 through 146 Processing helix chain 'L7' and resid 149 through 190 removed outlier: 3.695A pdb=" N THRL7 153 " --> pdb=" O TYRL7 149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLUL7 186 " --> pdb=" O GLUL7 182 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.973A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLNL8 56 " --> pdb=" O PHEL8 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'L8' and resid 51 through 56' Processing helix chain 'L8' and resid 69 through 81 removed outlier: 3.510A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.588A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 4.136A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.993A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 4.888A pdb=" N SERL9 34 " --> pdb=" O TYRL9 30 " (cutoff:3.500A) Processing helix chain 'L9' and resid 44 through 52 Processing helix chain 'L9' and resid 97 through 111 removed outlier: 3.731A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.688A pdb=" N ASNL9 145 " --> pdb=" O ALAL9 141 " (cutoff:3.500A) Proline residue: L9 146 - end of helix Processing helix chain 'L9' and resid 147 through 153 removed outlier: 6.235A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYSL9 153 " --> pdb=" O GLNL9 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 147 through 153' Processing helix chain 'L9' and resid 158 through 163 removed outlier: 3.543A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 4.070A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLYL9 173 " --> pdb=" O ARGL9 169 " (cutoff:3.500A) Processing helix chain 'L9' and resid 187 through 197 Processing helix chain 'LA' and resid 25 through 37 Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LA' and resid 108 through 113 removed outlier: 3.876A pdb=" N LEULA 112 " --> pdb=" O ASPLA 108 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VALLA 113 " --> pdb=" O VALLA 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 108 through 113' Processing helix chain 'LA' and resid 159 through 176 removed outlier: 3.724A pdb=" N VALLA 164 " --> pdb=" O PROLA 160 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLNLA 166 " --> pdb=" O GLULA 162 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYSLA 167 " --> pdb=" O GLULA 163 " (cutoff:3.500A) Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.120A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.682A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 Processing helix chain 'LB' and resid 122 through 130 Processing helix chain 'LB' and resid 146 through 152 removed outlier: 3.941A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.557A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLNLC 125 " --> pdb=" O ALALC 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 120 through 125' Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.541A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASPLC 147 " --> pdb=" O LYSLC 143 " (cutoff:3.500A) Processing helix chain 'LC' and resid 161 through 166 Proline residue: LC 165 - end of helix No H-bonds generated for 'chain 'LC' and resid 161 through 166' Processing helix chain 'LE' and resid 92 through 97 removed outlier: 3.869A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYSLE 97 " --> pdb=" O ILELE 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 92 through 97' Processing helix chain 'LE' and resid 100 through 121 removed outlier: 3.706A pdb=" N SERLE 104 " --> pdb=" O LYSLE 100 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) Processing helix chain 'LG' and resid 122 through 130 Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 137 removed outlier: 3.705A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALALG 136 " --> pdb=" O ILELG 132 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLYLG 137 " --> pdb=" O ALALG 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 131 through 137' Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 3.736A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SERLI 31 " --> pdb=" O ARGLI 27 " (cutoff:3.500A) Processing helix chain 'LI' and resid 35 through 43 Processing helix chain 'LI' and resid 100 through 105 removed outlier: 4.108A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VALLI 105 " --> pdb=" O PROLI 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 100 through 105' Processing helix chain 'LI' and resid 112 through 134 Processing helix chain 'LK' and resid 6 through 12 removed outlier: 3.921A pdb=" N LYSLK 10 " --> pdb=" O ARGLK 6 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARGLK 12 " --> pdb=" O THRLK 8 " (cutoff:3.500A) Processing helix chain 'LK' and resid 60 through 67 removed outlier: 3.526A pdb=" N ASNLK 66 " --> pdb=" O HISLK 62 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLNLK 67 " --> pdb=" O LEULK 63 " (cutoff:3.500A) Processing helix chain 'LK' and resid 74 through 83 removed outlier: 4.802A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 94 removed outlier: 4.938A pdb=" N LYSLK 94 " --> pdb=" O ALALK 90 " (cutoff:3.500A) Processing helix chain 'LK' and resid 102 through 107 Processing helix chain 'LK' and resid 130 through 141 Processing helix chain 'LN' and resid 111 through 120 removed outlier: 4.097A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 3.847A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 156 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 3.853A pdb=" N LEULN 171 " --> pdb=" O GLNLN 167 " (cutoff:3.500A) Proline residue: LN 172 - end of helix No H-bonds generated for 'chain 'LN' and resid 167 through 172' Processing helix chain 'LN' and resid 189 through 201 Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.950A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 244 through 251 removed outlier: 3.592A pdb=" N VALLN 251 " --> pdb=" O GLYLN 247 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 4.282A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLULN 361 " --> pdb=" O ARGLN 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 356 through 361' Processing helix chain 'LN' and resid 381 through 390 Processing helix chain 'LN' and resid 392 through 403 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 5.156A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 43 through 48 Processing helix chain 'LQ' and resid 81 through 90 removed outlier: 3.847A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.842A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.421A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 removed outlier: 4.042A pdb=" N GLYLS 38 " --> pdb=" O ALALS 34 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 4.299A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VALLS 49 " --> pdb=" O SERLS 45 " (cutoff:3.500A) Processing helix chain 'LS' and resid 80 through 85 Proline residue: LS 85 - end of helix Processing helix chain 'LS' and resid 88 through 95 removed outlier: 5.703A pdb=" N LEULS 95 " --> pdb=" O METLS 91 " (cutoff:3.500A) Processing helix chain 'LS' and resid 96 through 102 Processing helix chain 'LS' and resid 104 through 115 Proline residue: LS 115 - end of helix Processing helix chain 'LT' and resid 35 through 40 removed outlier: 3.851A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLULT 40 " --> pdb=" O ARGLT 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 35 through 40' Processing helix chain 'LU' and resid 25 through 30 removed outlier: 4.040A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARGLU 30 " --> pdb=" O HISLU 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 25 through 30' Processing helix chain 'LU' and resid 34 through 49 removed outlier: 3.549A pdb=" N GLULU 46 " --> pdb=" O ASPLU 42 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLYLU 49 " --> pdb=" O ARGLU 45 " (cutoff:3.500A) Processing helix chain 'LU' and resid 51 through 64 removed outlier: 3.524A pdb=" N VALLU 63 " --> pdb=" O GLULU 59 " (cutoff:3.500A) Processing helix chain 'LU' and resid 65 through 78 Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LW' and resid 51 through 58 removed outlier: 3.517A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 3.756A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) Processing helix chain 'NB' and resid 345 through 354 Processing helix chain 'NB' and resid 360 through 373 Processing helix chain 'NE' and resid 212 through 224 Processing helix chain 'NE' and resid 235 through 257 Processing helix chain 'NE' and resid 258 through 279 Processing helix chain 'NE' and resid 285 through 348 removed outlier: 3.578A pdb=" N LYSNE 309 " --> pdb=" O ARGNE 305 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARGNE 310 " --> pdb=" O ARGNE 306 " (cutoff:3.500A) Processing helix chain 'NE' and resid 351 through 357 removed outlier: 3.507A pdb=" N GLUNE 356 " --> pdb=" O PRONE 352 " (cutoff:3.500A) Processing helix chain 'NF' and resid 5 through 14 Processing helix chain 'NF' and resid 19 through 42 removed outlier: 4.359A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HISNF 33 " --> pdb=" O SERNF 29 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SERNF 36 " --> pdb=" O ALANF 32 " (cutoff:3.500A) Processing helix chain 'NF' and resid 44 through 72 Processing helix chain 'NF' and resid 97 through 115 Processing helix chain 'NF' and resid 205 through 212 removed outlier: 3.575A pdb=" N THRNF 209 " --> pdb=" O SERNF 205 " (cutoff:3.500A) Processing helix chain 'NF' and resid 247 through 252 Processing helix chain 'NG' and resid 127 through 145 removed outlier: 4.409A pdb=" N METNG 144 " --> pdb=" O LEUNG 140 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N METNG 145 " --> pdb=" O GLUNG 141 " (cutoff:3.500A) Processing helix chain 'NG' and resid 151 through 192 removed outlier: 5.527A pdb=" N GLUNG 157 " --> pdb=" O VALNG 153 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THRNG 158 " --> pdb=" O GLNNG 154 " (cutoff:3.500A) Processing helix chain 'NG' and resid 194 through 206 removed outlier: 5.335A pdb=" N SERNG 206 " --> pdb=" O ILENG 202 " (cutoff:3.500A) Processing helix chain 'NG' and resid 207 through 215 Processing helix chain 'NM' and resid 3 through 12 Processing helix chain 'NM' and resid 44 through 49 removed outlier: 5.255A pdb=" N SERNM 49 " --> pdb=" O PRONM 45 " (cutoff:3.500A) Processing helix chain 'NM' and resid 67 through 72 removed outlier: 3.618A pdb=" N ALANM 71 " --> pdb=" O VALNM 67 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALANM 72 " --> pdb=" O ILENM 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'NM' and resid 67 through 72' Processing helix chain 'NM' and resid 86 through 99 Processing helix chain 'NM' and resid 102 through 129 Processing helix chain 'NM' and resid 138 through 173 removed outlier: 6.223A pdb=" N LEUNM 158 " --> pdb=" O ILENM 154 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ASPNM 159 " --> pdb=" O ALANM 155 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASNNM 160 " --> pdb=" O ALANM 156 " (cutoff:3.500A) Processing helix chain 'NN' and resid 7 through 29 removed outlier: 3.539A pdb=" N ALANN 26 " --> pdb=" O LEUNN 22 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALANN 27 " --> pdb=" O GLUNN 23 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASNNN 28 " --> pdb=" O ALANN 24 " (cutoff:3.500A) Proline residue: NN 29 - end of helix Processing helix chain 'NN' and resid 40 through 55 Processing helix chain 'NN' and resid 69 through 81 removed outlier: 3.703A pdb=" N CYSNN 73 " --> pdb=" O SERNN 69 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLYNN 78 " --> pdb=" O VALNN 74 " (cutoff:3.500A) Proline residue: NN 79 - end of helix Processing helix chain 'NN' and resid 117 through 126 removed outlier: 5.030A pdb=" N ARGNN 126 " --> pdb=" O VALNN 122 " (cutoff:3.500A) Processing helix chain 'NN' and resid 131 through 137 removed outlier: 4.477A pdb=" N PHENN 135 " --> pdb=" O HISNN 131 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALANN 136 " --> pdb=" O GLUNN 132 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HISNN 137 " --> pdb=" O GLNNN 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'NN' and resid 131 through 137' Processing helix chain 'NN' and resid 150 through 165 removed outlier: 3.837A pdb=" N LYSNN 154 " --> pdb=" O GLYNN 150 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHENN 164 " --> pdb=" O PHENN 160 " (cutoff:3.500A) Proline residue: NN 165 - end of helix Processing helix chain 'NN' and resid 246 through 251 removed outlier: 3.507A pdb=" N ILENN 250 " --> pdb=" O GLYNN 246 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THRNN 251 " --> pdb=" O ASPNN 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'NN' and resid 246 through 251' Processing helix chain 'NN' and resid 173 through 178 removed outlier: 3.655A pdb=" N ILENN 177 " --> pdb=" O LEUNN 174 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYSNN 178 " --> pdb=" O ASNNN 175 " (cutoff:3.500A) Processing helix chain 'NO' and resid 8 through 19 Processing helix chain 'NO' and resid 21 through 43 removed outlier: 5.485A pdb=" N ALANO 43 " --> pdb=" O ARGNO 39 " (cutoff:3.500A) Processing helix chain 'NO' and resid 48 through 67 removed outlier: 3.501A pdb=" N GLYNO 58 " --> pdb=" O LYSNO 54 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASPNO 67 " --> pdb=" O METNO 63 " (cutoff:3.500A) Processing helix chain 'NO' and resid 68 through 86 removed outlier: 3.862A pdb=" N GLUNO 74 " --> pdb=" O LEUNO 70 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VALNO 83 " --> pdb=" O ILENO 79 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N HISNO 84 " --> pdb=" O SERNO 80 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALANO 85 " --> pdb=" O GLNNO 81 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHENO 86 " --> pdb=" O LEUNO 82 " (cutoff:3.500A) Processing helix chain 'NO' and resid 88 through 107 Processing helix chain 'NO' and resid 111 through 137 removed outlier: 4.099A pdb=" N ASPNO 116 " --> pdb=" O ARGNO 112 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYSNO 117 " --> pdb=" O LEUNO 113 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHENO 118 " --> pdb=" O ARGNO 114 " (cutoff:3.500A) Processing helix chain 'NO' and resid 139 through 154 Processing helix chain 'NO' and resid 162 through 181 removed outlier: 4.749A pdb=" N LEUNO 174 " --> pdb=" O ILENO 170 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLUNO 175 " --> pdb=" O GLUNO 171 " (cutoff:3.500A) Processing helix chain 'NO' and resid 186 through 204 Proline residue: NO 196 - end of helix removed outlier: 3.528A pdb=" N ARGNO 199 " --> pdb=" O ASPNO 195 " (cutoff:3.500A) Processing helix chain 'NO' and resid 206 through 247 removed outlier: 3.512A pdb=" N PHENO 218 " --> pdb=" O THRNO 214 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLUNO 219 " --> pdb=" O ARGNO 215 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THRNO 220 " --> pdb=" O GLYNO 216 " (cutoff:3.500A) Proline residue: NO 226 - end of helix Processing helix chain 'NO' and resid 299 through 314 removed outlier: 3.562A pdb=" N METNO 310 " --> pdb=" O ARGNO 306 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARGNO 313 " --> pdb=" O GLUNO 309 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLNNO 314 " --> pdb=" O METNO 310 " (cutoff:3.500A) Processing helix chain 'NO' and resid 317 through 337 removed outlier: 3.527A pdb=" N VALNO 327 " --> pdb=" O ARGNO 323 " (cutoff:3.500A) Processing helix chain 'NO' and resid 345 through 353 Processing helix chain 'NQ' and resid 1 through 9 removed outlier: 3.727A pdb=" N ARGNQ 7 " --> pdb=" O ALANQ 3 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRPNQ 8 " --> pdb=" O ALANQ 4 " (cutoff:3.500A) Processing helix chain 'NS' and resid 59 through 93 removed outlier: 3.500A pdb=" N LYSNS 83 " --> pdb=" O LEUNS 79 " (cutoff:3.500A) Processing helix chain 'NS' and resid 104 through 109 Processing helix chain 'NS' and resid 120 through 130 removed outlier: 3.722A pdb=" N ALANS 124 " --> pdb=" O ASPNS 120 " (cutoff:3.500A) Processing helix chain 'NS' and resid 132 through 138 removed outlier: 3.563A pdb=" N PHENS 136 " --> pdb=" O PHENS 132 " (cutoff:3.500A) Processing helix chain 'NS' and resid 153 through 168 Proline residue: NS 168 - end of helix Processing helix chain 'NS' and resid 179 through 191 Proline residue: NS 185 - end of helix Processing helix chain 'NS' and resid 228 through 233 removed outlier: 5.225A pdb=" N LYSNS 233 " --> pdb=" O ARGNS 229 " (cutoff:3.500A) Processing helix chain 'NS' and resid 253 through 268 removed outlier: 3.940A pdb=" N LEUNS 266 " --> pdb=" O METNS 262 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHENS 267 " --> pdb=" O PHENS 263 " (cutoff:3.500A) Proline residue: NS 268 - end of helix Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.360A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALASA 30 " --> pdb=" O ALASA 26 " (cutoff:3.500A) Proline residue: SA 31 - end of helix No H-bonds generated for 'chain 'SA' and resid 25 through 31' Processing helix chain 'SA' and resid 33 through 49 removed outlier: 4.199A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.526A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEUSA 133 " --> pdb=" O ALASA 129 " (cutoff:3.500A) Proline residue: SA 134 - end of helix Processing helix chain 'SA' and resid 135 through 141 removed outlier: 3.635A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.273A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 156 through 161' Processing helix chain 'SA' and resid 163 through 175 Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.782A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.647A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASNSA 198 " --> pdb=" O GLYSA 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 193 through 198' Processing helix chain 'SA' and resid 216 through 222 Processing helix chain 'SA' and resid 236 through 242 Proline residue: SA 242 - end of helix Processing helix chain 'SA' and resid 253 through 263 removed outlier: 3.629A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 Processing helix chain 'SA' and resid 296 through 303 removed outlier: 4.188A pdb=" N ARGSA 300 " --> pdb=" O PROSA 296 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEUSA 302 " --> pdb=" O ILESA 298 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 296 through 303' Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.356A pdb=" N LEUSA 322 " --> pdb=" O PROSA 318 " (cutoff:3.500A) Processing helix chain 'SA' and resid 323 through 329 Processing helix chain 'SA' and resid 330 through 361 removed outlier: 4.484A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SC' and resid 47 through 54 removed outlier: 3.636A pdb=" N GLYSC 53 " --> pdb=" O VALSC 49 " (cutoff:3.500A) Processing helix chain 'SC' and resid 58 through 74 removed outlier: 3.609A pdb=" N LYSSC 70 " --> pdb=" O LYSSC 66 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYRSC 73 " --> pdb=" O TYRSC 69 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.926A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILESC 195 " --> pdb=" O GLNSC 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 190 through 195' Processing helix chain 'SC' and resid 213 through 218 Processing helix chain 'SC' and resid 243 through 262 removed outlier: 3.671A pdb=" N GLNSC 256 " --> pdb=" O ALASC 252 " (cutoff:3.500A) Proline residue: SC 259 - end of helix Processing helix chain 'SC' and resid 266 through 274 removed outlier: 5.206A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.402A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 15 through 79 removed outlier: 3.534A pdb=" N GLNSD 39 " --> pdb=" O LYSSD 35 " (cutoff:3.500A) Processing helix chain 'SD' and resid 102 through 113 Processing helix chain 'SD' and resid 126 through 137 removed outlier: 3.578A pdb=" N METSD 132 " --> pdb=" O ALASD 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VALSD 136 " --> pdb=" O METSD 132 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.115A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.719A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.153A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 238 through 248 removed outlier: 4.526A pdb=" N ARGSD 242 " --> pdb=" O ASPSD 238 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.709A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.643A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 124 Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 164 through 178 removed outlier: 5.026A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEUSE 170 " --> pdb=" O LEUSE 166 " (cutoff:3.500A) Proline residue: SE 171 - end of helix Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.621A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 231 removed outlier: 4.846A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASPSE 228 " --> pdb=" O THRSE 224 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARGSE 229 " --> pdb=" O ASNSE 225 " (cutoff:3.500A) Processing helix chain 'SE' and resid 232 through 237 removed outlier: 4.138A pdb=" N HISSE 236 " --> pdb=" O GLUSE 232 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TRPSE 237 " --> pdb=" O ILESE 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'SE' and resid 232 through 237' Processing helix chain 'SG' and resid 63 through 86 removed outlier: 3.599A pdb=" N ALASG 68 " --> pdb=" O ARGSG 64 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.990A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.866A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.611A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLYSH 69 " --> pdb=" O PHESH 65 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SH' and resid 122 through 127 removed outlier: 5.832A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) Processing helix chain 'SH' and resid 143 through 151 removed outlier: 3.589A pdb=" N LYSSH 147 " --> pdb=" O TYRSH 143 " (cutoff:3.500A) Processing helix chain 'SH' and resid 154 through 180 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.647A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VALSI 83 " --> pdb=" O ARGSI 79 " (cutoff:3.500A) Processing helix chain 'SI' and resid 109 through 120 Processing helix chain 'SI' and resid 133 through 144 Processing helix chain 'SI' and resid 153 through 163 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 3.658A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 3.554A pdb=" N LEUSI 215 " --> pdb=" O ILESI 211 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.035A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARGSI 230 " --> pdb=" O ALASI 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'SI' and resid 225 through 230' Processing helix chain 'SI' and resid 231 through 237 Processing helix chain 'SI' and resid 245 through 255 removed outlier: 4.391A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 664 through 677 Processing helix chain 'SJ' and resid 678 through 689 removed outlier: 4.104A pdb=" N PHESJ 689 " --> pdb=" O ILESJ 685 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 702 through 713 removed outlier: 3.549A pdb=" N GLNSJ 711 " --> pdb=" O GLNSJ 707 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HISSJ 712 " --> pdb=" O GLUSJ 708 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 720 through 731 removed outlier: 3.609A pdb=" N VALSJ 724 " --> pdb=" O GLYSJ 720 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARGSJ 730 " --> pdb=" O HISSJ 726 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 3.844A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 Processing helix chain 'SK' and resid 58 through 63 removed outlier: 3.949A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 88 Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.845A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.462A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SL' and resid 32 through 50 Processing helix chain 'SL' and resid 106 through 122 Processing helix chain 'SL' and resid 131 through 138 Processing helix chain 'SL' and resid 141 through 153 removed outlier: 3.628A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 166 removed outlier: 3.587A pdb=" N ARGSL 162 " --> pdb=" O ASPSL 158 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) Proline residue: SL 166 - end of helix Processing helix chain 'SL' and resid 170 through 177 removed outlier: 3.907A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 Processing helix chain 'SL' and resid 222 through 241 Processing helix chain 'SL' and resid 244 through 249 removed outlier: 6.757A pdb=" N VALSL 248 " --> pdb=" O LYSSL 244 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYSSL 249 " --> pdb=" O TRPSL 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 244 through 249' Processing helix chain 'SM' and resid 19 through 28 Processing helix chain 'SM' and resid 30 through 42 removed outlier: 3.576A pdb=" N LEUSM 40 " --> pdb=" O ARGSM 36 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 77 removed outlier: 4.130A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLUSM 76 " --> pdb=" O PHESM 72 " (cutoff:3.500A) Proline residue: SM 77 - end of helix Processing helix chain 'SM' and resid 78 through 99 removed outlier: 3.614A pdb=" N LYSSM 86 " --> pdb=" O PHESM 82 " (cutoff:3.500A) Processing helix chain 'SM' and resid 100 through 111 Processing helix chain 'SM' and resid 116 through 125 Proline residue: SM 125 - end of helix Processing helix chain 'SM' and resid 126 through 135 removed outlier: 4.886A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) Processing helix chain 'SM' and resid 136 through 148 removed outlier: 3.906A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHESM 147 " --> pdb=" O LEUSM 143 " (cutoff:3.500A) Proline residue: SM 148 - end of helix Processing helix chain 'SM' and resid 154 through 176 Processing helix chain 'SM' and resid 216 through 243 removed outlier: 3.525A pdb=" N METSM 220 " --> pdb=" O ASPSM 216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 3.835A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.690A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.589A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.503A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.629A pdb=" N TYRSM 413 " --> pdb=" O PROSM 409 " (cutoff:3.500A) Processing helix chain 'SM' and resid 436 through 448 Processing helix chain 'SM' and resid 542 through 586 Processing helix chain 'SN' and resid 19 through 30 Processing helix chain 'SN' and resid 49 through 61 Processing helix chain 'SN' and resid 65 through 70 Processing helix chain 'SN' and resid 100 through 127 Proline residue: SN 121 - end of helix Processing helix chain 'SN' and resid 143 through 177 removed outlier: 3.530A pdb=" N ARGSN 171 " --> pdb=" O ALASN 167 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALASN 172 " --> pdb=" O LYSSN 168 " (cutoff:3.500A) Processing helix chain 'SN' and resid 178 through 205 Processing helix chain 'SO' and resid 71 through 86 Proline residue: SO 86 - end of helix Processing helix chain 'SO' and resid 99 through 111 removed outlier: 4.225A pdb=" N ILESO 103 " --> pdb=" O LYSSO 99 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASNSO 104 " --> pdb=" O LEUSO 100 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLUSO 105 " --> pdb=" O PHESO 101 " (cutoff:3.500A) Processing helix chain 'SO' and resid 169 through 176 removed outlier: 4.504A pdb=" N ASPSO 173 " --> pdb=" O ASPSO 169 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLUSO 174 " --> pdb=" O PROSO 170 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEUSO 175 " --> pdb=" O ALASO 171 " (cutoff:3.500A) Proline residue: SO 176 - end of helix No H-bonds generated for 'chain 'SO' and resid 169 through 176' Processing helix chain 'SO' and resid 177 through 190 Processing helix chain 'SO' and resid 261 through 293 removed outlier: 3.786A pdb=" N HISSO 265 " --> pdb=" O SERSO 261 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLUSO 293 " --> pdb=" O LEUSO 289 " (cutoff:3.500A) Processing helix chain 'SO' and resid 328 through 333 removed outlier: 5.779A pdb=" N LYSSO 333 " --> pdb=" O LEUSO 329 " (cutoff:3.500A) Processing helix chain 'SO' and resid 337 through 353 Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.145A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THRSQ 36 " --> pdb=" O LYSSQ 32 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 61 removed outlier: 4.044A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 4.032A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.381A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 149 through 157 Processing helix chain 'SQ' and resid 183 through 194 Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 68 removed outlier: 3.508A pdb=" N LYSSR 50 " --> pdb=" O PHESR 46 " (cutoff:3.500A) Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 120 removed outlier: 3.603A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 145 removed outlier: 3.621A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) Processing helix chain 'SR' and resid 146 through 162 removed outlier: 3.752A pdb=" N LEUSR 161 " --> pdb=" O HISSR 157 " (cutoff:3.500A) Proline residue: SR 162 - end of helix Processing helix chain 'SR' and resid 180 through 189 Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.620A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 229 through 234' Processing helix chain 'SR' and resid 235 through 247 removed outlier: 4.270A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILESR 241 " --> pdb=" O GLUSR 237 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 Proline residue: SR 277 - end of helix removed outlier: 4.581A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 290 through 295 removed outlier: 3.765A pdb=" N LYSSR 294 " --> pdb=" O LYSSR 290 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARGSR 295 " --> pdb=" O CYSSR 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 290 through 295' Processing helix chain 'SR' and resid 300 through 314 removed outlier: 4.075A pdb=" N ILESR 306 " --> pdb=" O ASPSR 302 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLYSR 314 " --> pdb=" O LEUSR 310 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 345 removed outlier: 3.502A pdb=" N LEUSR 339 " --> pdb=" O ALASR 335 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 417 removed outlier: 4.668A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 417' Processing helix chain 'SR' and resid 421 through 426 removed outlier: 4.187A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N HISSR 426 " --> pdb=" O LEUSR 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 421 through 426' Processing helix chain 'SR' and resid 437 through 442 removed outlier: 4.040A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 442' Processing helix chain 'SR' and resid 445 through 464 removed outlier: 3.709A pdb=" N GLYSR 464 " --> pdb=" O ARGSR 460 " (cutoff:3.500A) Processing helix chain 'SS' and resid 140 through 146 removed outlier: 4.599A pdb=" N TYRSS 144 " --> pdb=" O PROSS 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASPSS 145 " --> pdb=" O LEUSS 141 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASPSS 146 " --> pdb=" O GLUSS 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 140 through 146' Processing helix chain 'SS' and resid 197 through 210 Processing helix chain 'SS' and resid 242 through 248 removed outlier: 3.986A pdb=" N PHESS 246 " --> pdb=" O ASPSS 242 " (cutoff:3.500A) Proline residue: SS 248 - end of helix Processing helix chain 'SS' and resid 249 through 266 removed outlier: 3.593A pdb=" N LYSSS 253 " --> pdb=" O SERSS 249 " (cutoff:3.500A) Processing helix chain 'SS' and resid 317 through 322 removed outlier: 4.005A pdb=" N LEUSS 321 " --> pdb=" O PROSS 317 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LEUSS 322 " --> pdb=" O PROSS 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 317 through 322' Processing helix chain 'SS' and resid 323 through 334 removed outlier: 5.384A pdb=" N GLUSS 334 " --> pdb=" O TRPSS 330 " (cutoff:3.500A) Processing helix chain 'SS' and resid 358 through 372 removed outlier: 3.593A pdb=" N TYRSS 371 " --> pdb=" O CYSSS 367 " (cutoff:3.500A) Processing helix chain 'ST' and resid 214 through 229 removed outlier: 3.595A pdb=" N GLNST 223 " --> pdb=" O GLYST 219 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THRST 229 " --> pdb=" O ALAST 225 " (cutoff:3.500A) Processing helix chain 'SV' and resid 33 through 43 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.382A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.410A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 71' Processing helix chain 'SV' and resid 82 through 136 removed outlier: 3.683A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASPSV 91 " --> pdb=" O ASNSV 87 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYSSV 106 " --> pdb=" O LYSSV 102 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILESV 131 " --> pdb=" O VALSV 127 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILESV 134 " --> pdb=" O ASNSV 130 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALASV 136 " --> pdb=" O HISSV 132 " (cutoff:3.500A) Processing helix chain 'SW' and resid 178 through 184 removed outlier: 4.328A pdb=" N LEUSW 182 " --> pdb=" O SERSW 178 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N CYSSW 183 " --> pdb=" O PHESW 179 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASNSW 184 " --> pdb=" O ALASW 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'SW' and resid 178 through 184' Processing helix chain 'SW' and resid 187 through 198 removed outlier: 3.556A pdb=" N LEUSW 191 " --> pdb=" O ASNSW 187 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYSSW 192 " --> pdb=" O GLUSW 188 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALASW 193 " --> pdb=" O ASNSW 189 " (cutoff:3.500A) Processing helix chain 'SW' and resid 203 through 216 removed outlier: 4.640A pdb=" N ARGSW 211 " --> pdb=" O HISSW 207 " (cutoff:3.500A) Proline residue: SW 212 - end of helix Processing helix chain 'SW' and resid 228 through 245 removed outlier: 3.681A pdb=" N PHESW 233 " --> pdb=" O LYSSW 229 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILESW 235 " --> pdb=" O LEUSW 231 " (cutoff:3.500A) Proline residue: SW 236 - end of helix Processing helix chain 'SW' and resid 260 through 276 removed outlier: 3.791A pdb=" N THRSW 276 " --> pdb=" O LYSSW 272 " (cutoff:3.500A) Processing helix chain 'SW' and resid 290 through 301 removed outlier: 3.584A pdb=" N ASNSW 300 " --> pdb=" O GLNSW 296 " (cutoff:3.500A) Processing helix chain 'SW' and resid 308 through 318 removed outlier: 3.542A pdb=" N LEUSW 312 " --> pdb=" O THRSW 308 " (cutoff:3.500A) Processing helix chain 'SW' and resid 334 through 342 removed outlier: 3.778A pdb=" N GLYSW 342 " --> pdb=" O ILESW 338 " (cutoff:3.500A) Processing helix chain 'SW' and resid 343 through 355 removed outlier: 3.644A pdb=" N GLNSW 349 " --> pdb=" O GLUSW 345 " (cutoff:3.500A) Proline residue: SW 355 - end of helix Processing helix chain 'SW' and resid 368 through 379 Processing helix chain 'SW' and resid 408 through 424 removed outlier: 5.050A pdb=" N PHESW 413 " --> pdb=" O SERSW 409 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEUSW 414 " --> pdb=" O GLUSW 410 " (cutoff:3.500A) Processing helix chain 'SW' and resid 434 through 449 removed outlier: 4.592A pdb=" N ASPSW 449 " --> pdb=" O LEUSW 445 " (cutoff:3.500A) Processing helix chain 'SW' and resid 460 through 475 removed outlier: 5.499A pdb=" N ASPSW 475 " --> pdb=" O PHESW 471 " (cutoff:3.500A) Processing helix chain 'SW' and resid 482 through 488 removed outlier: 5.675A pdb=" N GLYSW 488 " --> pdb=" O VALSW 484 " (cutoff:3.500A) Processing helix chain 'SW' and resid 505 through 516 removed outlier: 3.604A pdb=" N GLYSW 514 " --> pdb=" O ILESW 510 " (cutoff:3.500A) Processing helix chain 'SW' and resid 534 through 545 removed outlier: 4.661A pdb=" N LEUSW 538 " --> pdb=" O GLUSW 534 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARGSW 539 " --> pdb=" O LEUSW 535 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SERSW 544 " --> pdb=" O TYRSW 540 " (cutoff:3.500A) Processing helix chain 'SW' and resid 561 through 573 removed outlier: 4.994A pdb=" N TYRSW 573 " --> pdb=" O ILESW 569 " (cutoff:3.500A) Processing helix chain 'SW' and resid 574 through 593 Processing helix chain 'SW' and resid 595 through 600 Processing helix chain 'SW' and resid 605 through 614 removed outlier: 3.548A pdb=" N LEUSW 611 " --> pdb=" O PROSW 607 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SERSW 612 " --> pdb=" O GLNSW 608 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHESW 613 " --> pdb=" O VALSW 609 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 6 through 12 removed outlier: 3.911A pdb=" N ARGSZ 10 " --> pdb=" O GLYSZ 6 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LYSSZ 12 " --> pdb=" O THRSZ 8 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 18 through 32 Proline residue: SZ 32 - end of helix Processing helix chain 'SZ' and resid 36 through 43 Processing helix chain 'SZ' and resid 48 through 57 Processing helix chain 'SZ' and resid 61 through 67 Proline residue: SZ 67 - end of helix Processing helix chain 'SZ' and resid 90 through 103 removed outlier: 4.532A pdb=" N LEUSZ 94 " --> pdb=" O LYSSZ 90 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 112 through 126 Processing helix chain 'SZ' and resid 129 through 137 removed outlier: 5.690A pdb=" N GLUSZ 137 " --> pdb=" O METSZ 133 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 144 through 159 Processing helix chain 'SZ' and resid 160 through 178 removed outlier: 3.557A pdb=" N GLNSZ 171 " --> pdb=" O LEUSZ 167 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYSSZ 172 " --> pdb=" O ASPSZ 168 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'BA' and resid 11 through 17 removed outlier: 3.988A pdb=" N THRBA 59 " --> pdb=" O VALBA 74 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 3, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 4, first strand: chain 'L8' and resid 11 through 15 removed outlier: 4.401A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEUL8 37 " --> pdb=" O VALL8 28 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.115A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.837A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'LA' and resid 13 through 20 removed outlier: 7.672A pdb=" N LYSLA 13 " --> pdb=" O GLULA 152 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'LB' and resid 118 through 121 removed outlier: 3.609A pdb=" N ALALB 102 " --> pdb=" O LEULB 121 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYSLB 99 " --> pdb=" O LYSLB 78 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.640A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LC' and resid 90 through 99 removed outlier: 4.366A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.945A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LE' and resid 38 through 42 removed outlier: 4.260A pdb=" N ASPLE 38 " --> pdb=" O VALLE 64 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LG' and resid 24 through 27 removed outlier: 5.047A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N METLG 62 " --> pdb=" O ILELG 40 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LG' and resid 87 through 90 removed outlier: 4.045A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.774A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LI' and resid 72 through 75 removed outlier: 3.548A pdb=" N GLNLI 72 " --> pdb=" O TYRLI 81 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.567A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 19, first strand: chain 'LN' and resid 41 through 44 removed outlier: 6.141A pdb=" N GLNLN 184 " --> pdb=" O THRLN 44 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N METLN 84 " --> pdb=" O VALLN 205 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LN' and resid 53 through 58 removed outlier: 6.837A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HISLN 275 " --> pdb=" O THRLN 223 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLYLN 225 " --> pdb=" O GLYLN 273 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLYLN 273 " --> pdb=" O GLYLN 225 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.689A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LN' and resid 77 through 80 Processing sheet with id= 23, first strand: chain 'LN' and resid 88 through 93 Processing sheet with id= 24, first strand: chain 'LN' and resid 215 through 218 removed outlier: 4.385A pdb=" N GLULN 215 " --> pdb=" O ILELN 284 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 26, first strand: chain 'LT' and resid 56 through 60 removed outlier: 5.853A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THRLT 59 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LT' and resid 8 through 12 removed outlier: 5.942A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LT' and resid 6 through 12 removed outlier: 4.554A pdb=" N HISLT 99 " --> pdb=" O PHELT 11 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'NF' and resid 147 through 150 removed outlier: 3.533A pdb=" N ARGNF 148 " --> pdb=" O ARGNF 169 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'NF' and resid 189 through 194 removed outlier: 3.645A pdb=" N ALANF 190 " --> pdb=" O HISNF 185 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASNNF 255 " --> pdb=" O THRNF 245 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TYRNF 241 " --> pdb=" O LEUNF 259 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THRNF 218 " --> pdb=" O VALNF 244 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'NM' and resid 51 through 56 removed outlier: 5.297A pdb=" N CYSNM 61 " --> pdb=" O LEUNM 83 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'NN' and resid 30 through 35 removed outlier: 5.073A pdb=" N VALNN 95 " --> pdb=" O VALNN 112 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THRNN 109 " --> pdb=" O ILENN 284 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THRNN 280 " --> pdb=" O LYSNN 113 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEUNN 283 " --> pdb=" O GLNNN 190 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N GLNNN 190 " --> pdb=" O LEUNN 283 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLUNN 191 " --> pdb=" O ASNNN 186 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'NN' and resid 106 through 109 removed outlier: 3.701A pdb=" N LYSNN 285 " --> pdb=" O THRNN 109 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'NN' and resid 197 through 203 No H-bonds generated for sheet with id= 34 Processing sheet with id= 35, first strand: chain 'NQ' and resid 28 through 34 removed outlier: 4.519A pdb=" N ILENQ 19 " --> pdb=" O THRNQ 15 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N HISNQ 10 " --> pdb=" O SERNQ 320 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYSNQ 316 " --> pdb=" O GLYNQ 14 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'NQ' and resid 46 through 51 removed outlier: 4.018A pdb=" N ALANQ 47 " --> pdb=" O GLYNQ 61 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLNNQ 57 " --> pdb=" O GLYNQ 51 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THRNQ 66 " --> pdb=" O CYSNQ 62 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ARGNQ 65 " --> pdb=" O CYSNQ 83 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLYNQ 79 " --> pdb=" O HISNQ 69 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'NQ' and resid 92 through 95 removed outlier: 3.933A pdb=" N GLYNQ 92 " --> pdb=" O CYSNQ 103 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLYNQ 107 " --> pdb=" O VALNQ 129 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'NQ' and resid 134 through 139 removed outlier: 5.737A pdb=" N VALNQ 145 " --> pdb=" O ASPNQ 139 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N HISNQ 144 " --> pdb=" O LEUNQ 160 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEUNQ 155 " --> pdb=" O ALANQ 170 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHENQ 168 " --> pdb=" O ILENQ 157 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'NQ' and resid 188 through 192 removed outlier: 3.795A pdb=" N ASPNQ 188 " --> pdb=" O CYSNQ 201 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LYSNQ 197 " --> pdb=" O LEUNQ 192 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N HISNQ 205 " --> pdb=" O TYRNQ 225 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'NQ' and resid 232 through 236 removed outlier: 5.650A pdb=" N SERNQ 241 " --> pdb=" O THRNQ 236 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASNNQ 240 " --> pdb=" O LEUNQ 256 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLUNQ 253 " --> pdb=" O LEUNQ 262 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'NQ' and resid 273 through 278 removed outlier: 5.384A pdb=" N LEUNQ 283 " --> pdb=" O HISNQ 278 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLYNQ 288 " --> pdb=" O VALNQ 292 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VALNQ 292 " --> pdb=" O GLYNQ 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HISNQ 306 " --> pdb=" O ILENQ 295 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'NS' and resid 169 through 173 removed outlier: 4.892A pdb=" N THRNS 148 " --> pdb=" O TYRNS 173 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLUNS 200 " --> pdb=" O SERNS 149 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASNNS 206 " --> pdb=" O METNS 223 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HISNS 220 " --> pdb=" O ARGNS 317 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHENS 312 " --> pdb=" O PHENS 290 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'SA' and resid 6 through 9 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.414A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'SC' and resid 147 through 153 removed outlier: 4.270A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 47, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.297A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'SD' and resid 158 through 161 removed outlier: 6.708A pdb=" N GLYSD 158 " --> pdb=" O LEUSD 169 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 50, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.819A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 52, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.422A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.510A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SG' and resid 88 through 92 Processing sheet with id= 55, first strand: chain 'SH' and resid 72 through 77 removed outlier: 3.689A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYRSH 88 " --> pdb=" O SERSH 77 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SI' and resid 147 through 151 removed outlier: 3.534A pdb=" N GLYSI 150 " --> pdb=" O PHESI 98 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARGSI 101 " --> pdb=" O SERSI 126 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SK' and resid 2 through 5 removed outlier: 3.545A pdb=" N CYSSK 206 " --> pdb=" O VALSK 3 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 59, first strand: chain 'SK' and resid 69 through 72 Processing sheet with id= 60, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 61, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 62, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.197A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEUSL 78 " --> pdb=" O ILESL 205 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SL' and resid 127 through 130 Processing sheet with id= 64, first strand: chain 'SL' and resid 210 through 216 removed outlier: 6.109A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEUSL 251 " --> pdb=" O ILESL 263 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SM' and resid 179 through 184 Processing sheet with id= 66, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 67, first strand: chain 'SO' and resid 87 through 91 removed outlier: 3.505A pdb=" N ILESO 62 " --> pdb=" O HISSO 87 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASPSO 91 " --> pdb=" O ILESO 64 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SERSO 66 " --> pdb=" O ASPSO 91 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALASO 120 " --> pdb=" O SERSO 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASPSO 125 " --> pdb=" O LYSSO 121 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEUSO 126 " --> pdb=" O VALSO 143 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYSSO 140 " --> pdb=" O ILESO 241 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALASO 228 " --> pdb=" O ILESO 223 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASNSO 219 " --> pdb=" O ILESO 232 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHESO 217 " --> pdb=" O PROSO 234 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHESO 236 " --> pdb=" O ILESO 215 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILESO 215 " --> pdb=" O PHESO 236 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASPSO 203 " --> pdb=" O ILESO 222 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SO' and resid 137 through 140 removed outlier: 3.554A pdb=" N LYSSO 242 " --> pdb=" O LYSSO 140 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 5.094A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.852A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 72, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.560A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.445A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'SR' and resid 204 through 211 removed outlier: 7.686A pdb=" N SERSR 204 " --> pdb=" O PROSR 223 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SS' and resid 183 through 188 removed outlier: 6.390A pdb=" N ARGSS 183 " --> pdb=" O LEUSS 196 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARGSS 192 " --> pdb=" O ASPSS 187 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SV' and resid 3 through 6 removed outlier: 4.452A pdb=" N GLYSV 11 " --> pdb=" O CYSSV 6 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'SV' and resid 18 through 23 removed outlier: 3.928A pdb=" N LYSSV 27 " --> pdb=" O ARGSV 23 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'SW' and resid 281 through 285 removed outlier: 3.895A pdb=" N LEUSW 219 " --> pdb=" O THRSW 360 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALASW 221 " --> pdb=" O LEUSW 362 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALASW 223 " --> pdb=" O SERSW 364 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VALSW 388 " --> pdb=" O ALASW 222 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'SW' and resid 452 through 455 removed outlier: 3.707A pdb=" N GLYSW 477 " --> pdb=" O LYSSW 426 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILESW 529 " --> pdb=" O GLNSW 499 " (cutoff:3.500A) 3488 hydrogen bonds defined for protein. 10394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1673 hydrogen bonds 2930 hydrogen bond angles 0 basepair planarities 630 basepair parallelities 970 stacking parallelities Total time for adding SS restraints: 88.26 Time building geometry restraints manager: 43.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 48382 1.41 - 1.63: 73741 1.63 - 1.86: 506 1.86 - 2.09: 0 2.09 - 2.31: 12 Bond restraints: 122641 Sorted by residual: bond pdb=" N7 GDPSR1001 " pdb=" C5 GDPSR1001 " ideal model delta sigma weight residual 1.350 1.517 -0.167 2.00e-02 2.50e+03 7.00e+01 bond pdb=" C6 GDPSR1001 " pdb=" O6 GDPSR1001 " ideal model delta sigma weight residual 1.250 1.398 -0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" C2 GDPSR1001 " pdb=" N2 GDPSR1001 " ideal model delta sigma weight residual 1.355 1.450 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" N1 GDPSR1001 " pdb=" C2 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.406 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1' GDPSR1001 " pdb=" N9 GDPSR1001 " ideal model delta sigma weight residual 1.485 1.425 0.060 2.00e-02 2.50e+03 9.06e+00 ... (remaining 122636 not shown) Histogram of bond angle deviations from ideal: 71.62 - 85.16: 12 85.16 - 98.70: 2 98.70 - 112.24: 76090 112.24 - 125.79: 91356 125.79 - 139.33: 7503 Bond angle restraints: 174963 Sorted by residual: angle pdb=" N ILENN 275 " pdb=" CA ILENN 275 " pdb=" C ILENN 275 " ideal model delta sigma weight residual 112.96 107.83 5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" N VALLE 80 " pdb=" CA VALLE 80 " pdb=" C VALLE 80 " ideal model delta sigma weight residual 110.21 105.06 5.15 1.13e+00 7.83e-01 2.08e+01 angle pdb=" C8 GDPSR1001 " pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 108.00 120.91 -12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" C GLUNN 55 " pdb=" N PRONN 56 " pdb=" CA PRONN 56 " ideal model delta sigma weight residual 127.00 135.28 -8.28 2.40e+00 1.74e-01 1.19e+01 angle pdb=" CB METSD 71 " pdb=" CG METSD 71 " pdb=" SD METSD 71 " ideal model delta sigma weight residual 112.70 121.68 -8.98 3.00e+00 1.11e-01 8.97e+00 ... (remaining 174958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 72296 35.67 - 71.34: 5011 71.34 - 107.02: 710 107.02 - 142.69: 8 142.69 - 178.36: 12 Dihedral angle restraints: 78037 sinusoidal: 51527 harmonic: 26510 Sorted by residual: dihedral pdb=" O4' CL33869 " pdb=" C1' CL33869 " pdb=" N1 CL33869 " pdb=" C2 CL33869 " ideal model delta sinusoidal sigma weight residual -160.00 14.45 -174.45 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' UL31381 " pdb=" C1' UL31381 " pdb=" N1 UL31381 " pdb=" C2 UL31381 " ideal model delta sinusoidal sigma weight residual 200.00 26.53 173.47 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' CL35008 " pdb=" C1' CL35008 " pdb=" N1 CL35008 " pdb=" C2 CL35008 " ideal model delta sinusoidal sigma weight residual -160.00 9.82 -169.82 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 78034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 19246 0.059 - 0.119: 1469 0.119 - 0.178: 209 0.178 - 0.237: 3 0.237 - 0.296: 2 Chirality restraints: 20929 Sorted by residual: chirality pdb=" CB ILELE 154 " pdb=" CA ILELE 154 " pdb=" CG1 ILELE 154 " pdb=" CG2 ILELE 154 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb="FE1 SF4NM 401 " pdb=" S2 SF4NM 401 " pdb=" S3 SF4NM 401 " pdb=" S4 SF4NM 401 " both_signs ideal model delta sigma weight residual False -10.55 -10.28 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C1' GL3 448 " pdb=" O4' GL3 448 " pdb=" C2' GL3 448 " pdb=" N9 GL3 448 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 20926 not shown) Planarity restraints: 14854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GL1 39 " -0.050 2.00e-02 2.50e+03 2.05e-02 1.26e+01 pdb=" N9 GL1 39 " 0.045 2.00e-02 2.50e+03 pdb=" C8 GL1 39 " 0.010 2.00e-02 2.50e+03 pdb=" N7 GL1 39 " -0.000 2.00e-02 2.50e+03 pdb=" C5 GL1 39 " 0.000 2.00e-02 2.50e+03 pdb=" C6 GL1 39 " -0.007 2.00e-02 2.50e+03 pdb=" O6 GL1 39 " -0.014 2.00e-02 2.50e+03 pdb=" N1 GL1 39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GL1 39 " 0.003 2.00e-02 2.50e+03 pdb=" N2 GL1 39 " 0.003 2.00e-02 2.50e+03 pdb=" N3 GL1 39 " 0.008 2.00e-02 2.50e+03 pdb=" C4 GL1 39 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CL1 21 " 0.036 2.00e-02 2.50e+03 1.84e-02 7.63e+00 pdb=" N1 CL1 21 " -0.038 2.00e-02 2.50e+03 pdb=" C2 CL1 21 " -0.002 2.00e-02 2.50e+03 pdb=" O2 CL1 21 " -0.005 2.00e-02 2.50e+03 pdb=" N3 CL1 21 " 0.002 2.00e-02 2.50e+03 pdb=" C4 CL1 21 " 0.005 2.00e-02 2.50e+03 pdb=" N4 CL1 21 " 0.011 2.00e-02 2.50e+03 pdb=" C5 CL1 21 " -0.002 2.00e-02 2.50e+03 pdb=" C6 CL1 21 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GL31961 " -0.038 2.00e-02 2.50e+03 1.59e-02 7.62e+00 pdb=" N9 GL31961 " 0.037 2.00e-02 2.50e+03 pdb=" C8 GL31961 " 0.004 2.00e-02 2.50e+03 pdb=" N7 GL31961 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GL31961 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GL31961 " -0.005 2.00e-02 2.50e+03 pdb=" O6 GL31961 " -0.010 2.00e-02 2.50e+03 pdb=" N1 GL31961 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GL31961 " 0.001 2.00e-02 2.50e+03 pdb=" N2 GL31961 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GL31961 " 0.006 2.00e-02 2.50e+03 pdb=" C4 GL31961 " 0.008 2.00e-02 2.50e+03 ... (remaining 14851 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 664 2.58 - 3.22: 102997 3.22 - 3.86: 241394 3.86 - 4.50: 340842 4.50 - 5.14: 487718 Nonbonded interactions: 1173615 Sorted by model distance: nonbonded pdb=" O6 GL3 356 " pdb="MG MGL36010 " model vdw 1.940 2.170 nonbonded pdb=" OG1 THRSS 197 " pdb=" OE1 GLNSS 200 " model vdw 1.940 2.440 nonbonded pdb=" OP2 AL31917 " pdb="MG MGL36030 " model vdw 1.999 2.170 nonbonded pdb=" OP1 AL3 306 " pdb=" OH TYRLU 53 " model vdw 2.008 2.440 nonbonded pdb=" O2' UL3 184 " pdb=" OP2 GL3 189 " model vdw 2.013 2.440 ... (remaining 1173610 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: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 24.390 Check model and map are aligned: 1.300 Set scattering table: 0.790 Process input model: 361.710 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.280 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: 0.010 Load rotamer database and sin/cos tables:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 410.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.003 0.167 122641 Z= 0.207 Angle : 0.552 12.908 174963 Z= 0.287 Chirality : 0.035 0.296 20929 Planarity : 0.004 0.109 14854 Dihedral : 20.108 178.359 60827 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.01 % Allowed : 0.09 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 8932 helix: 2.23 (0.08), residues: 3757 sheet: 0.64 (0.14), residues: 1306 loop : 0.29 (0.09), residues: 3869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPSV 86 HIS 0.014 0.001 HISSR 436 PHE 0.022 0.001 PHENO 95 TYR 0.024 0.001 TYRNM 119 ARG 0.018 0.001 ARGL8 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 953 time to evaluate : 7.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LI 43 ASN cc_start: 0.7794 (t0) cc_final: 0.7394 (t0) REVERT: LI 114 ASP cc_start: 0.7897 (m-30) cc_final: 0.7691 (m-30) REVERT: LN 119 TYR cc_start: 0.6798 (m-80) cc_final: 0.6573 (m-80) REVERT: LS 65 GLN cc_start: 0.7925 (tt0) cc_final: 0.7570 (tm-30) REVERT: NE 228 LEU cc_start: 0.7252 (pp) cc_final: 0.6906 (mp) REVERT: NO 300 TYR cc_start: 0.7848 (m-80) cc_final: 0.7558 (m-80) REVERT: NQ 1 MET cc_start: 0.3141 (ttt) cc_final: 0.2840 (tmm) REVERT: SI 196 ASP cc_start: 0.8352 (m-30) cc_final: 0.8136 (m-30) REVERT: SK 1 MET cc_start: 0.5968 (tmm) cc_final: 0.5747 (tmm) REVERT: SO 94 MET cc_start: 0.7799 (ttm) cc_final: 0.7558 (ttm) REVERT: SQ 214 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7706 (tpp80) REVERT: SS 182 TRP cc_start: 0.7099 (p-90) cc_final: 0.6763 (p-90) REVERT: ST 232 VAL cc_start: 0.8610 (t) cc_final: 0.8329 (p) REVERT: SW 202 MET cc_start: 0.7057 (mtt) cc_final: 0.6851 (mtp) REVERT: SZ 171 GLN cc_start: 0.7501 (tp40) cc_final: 0.7079 (mm-40) outliers start: 1 outliers final: 5 residues processed: 954 average time/residue: 1.7716 time to fit residues: 2376.6779 Evaluate side-chains 734 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 729 time to evaluate : 7.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LG residue 100 ASP Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain SH residue 101 ILE Chi-restraints excluded: chain SQ residue 83 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 915 optimal weight: 2.9990 chunk 821 optimal weight: 1.9990 chunk 455 optimal weight: 30.0000 chunk 280 optimal weight: 5.9990 chunk 554 optimal weight: 5.9990 chunk 438 optimal weight: 3.9990 chunk 849 optimal weight: 8.9990 chunk 328 optimal weight: 0.0470 chunk 516 optimal weight: 5.9990 chunk 632 optimal weight: 5.9990 chunk 984 optimal weight: 20.0000 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 70 GLN BA 111 ASN BA 142 ASN L6 104 ASN L7 143 HIS L7 184 ASN LA 40 HIS LA 93 HIS LC 50 GLN LG 77 HIS LI 96 HIS LN 109 HIS LN 121 ASN LN 302 ASN LU 26 HIS NF 33 HIS NF 247 ASN NG 161 ASN NG 172 GLN NN 131 HIS NO 127 ASN NO 305 ASN NQ 69 HIS NQ 313 GLN NS 277 GLN SA 231 ASN SA 245 HIS SC 190 HIS SC 211 HIS SC 227 HIS SC 250 GLN SC 266 GLN SD 63 GLN SD 151 ASN SD 163 ASN SE 149 ASN SG 98 HIS SG 106 GLN SG 140 GLN SH 51 HIS SH 67 GLN SI 66 HIS SI 71 GLN SI 113 GLN SI 171 ASN SJ 716 GLN SK 68 HIS SK 82 GLN SK 83 HIS SK 86 ASN SK 93 GLN SL 46 HIS ** SL 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 218 HIS SM 211 HIS SO 113 ASN SQ 25 ASN SQ 152 GLN SQ 186 GLN SR 3 HIS SR 37 HIS SR 59 HIS SR 64 GLN SR 157 HIS SR 209 HIS ** SR 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 421 ASN ST 213 GLN SV 17 HIS ** SW 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 593 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 122641 Z= 0.285 Angle : 0.573 11.116 174963 Z= 0.297 Chirality : 0.038 0.235 20929 Planarity : 0.004 0.060 14854 Dihedral : 21.743 178.769 41714 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.68 % Allowed : 6.45 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 8932 helix: 2.27 (0.08), residues: 3840 sheet: 0.56 (0.14), residues: 1296 loop : 0.24 (0.10), residues: 3796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPNQ 112 HIS 0.012 0.001 HISLA 25 PHE 0.021 0.002 PHENO 95 TYR 0.034 0.002 TYRNM 119 ARG 0.010 0.001 ARGSA 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 778 time to evaluate : 7.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 114 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7666 (ttm-80) REVERT: LC 113 MET cc_start: 0.7577 (mmm) cc_final: 0.7213 (mmm) REVERT: LE 118 GLU cc_start: 0.6503 (tm-30) cc_final: 0.6225 (tt0) REVERT: LG 71 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: LI 30 MET cc_start: 0.9026 (mtp) cc_final: 0.8790 (mtp) REVERT: LI 114 ASP cc_start: 0.7920 (m-30) cc_final: 0.7676 (m-30) REVERT: LN 97 ARG cc_start: 0.6985 (tmm160) cc_final: 0.6343 (ttt180) REVERT: LN 332 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7518 (ttp) REVERT: NF 196 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7849 (pt) REVERT: NG 141 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6837 (mt-10) REVERT: NS 129 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8481 (p) REVERT: NS 287 TYR cc_start: 0.8779 (m-80) cc_final: 0.8388 (m-10) REVERT: SA 57 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8106 (pt) REVERT: SD 220 MET cc_start: 0.8060 (ttp) cc_final: 0.7062 (ttm) REVERT: SE 63 LEU cc_start: 0.8572 (tt) cc_final: 0.8312 (mp) REVERT: SG 128 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8670 (mmm) REVERT: SJ 713 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7068 (mtp85) REVERT: SL 30 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6362 (mp10) REVERT: SN 100 ASP cc_start: 0.5713 (t0) cc_final: 0.5430 (t0) REVERT: SN 119 VAL cc_start: 0.8307 (t) cc_final: 0.8060 (m) REVERT: SO 94 MET cc_start: 0.7795 (ttm) cc_final: 0.7470 (ttm) REVERT: SQ 214 ARG cc_start: 0.7942 (mmm-85) cc_final: 0.7686 (mmm-85) REVERT: ST 232 VAL cc_start: 0.8567 (t) cc_final: 0.8308 (p) REVERT: SW 265 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7482 (mtm) outliers start: 131 outliers final: 48 residues processed: 832 average time/residue: 1.8244 time to fit residues: 2121.9109 Evaluate side-chains 749 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 692 time to evaluate : 7.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain BA residue 135 THR Chi-restraints excluded: chain L7 residue 183 LYS Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L9 residue 142 ILE Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LE residue 143 THR Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 71 GLU Chi-restraints excluded: chain LG residue 100 ASP Chi-restraints excluded: chain LN residue 250 LYS Chi-restraints excluded: chain LN residue 332 MET Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LS residue 64 THR Chi-restraints excluded: chain LT residue 31 GLU Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 174 MET Chi-restraints excluded: chain NF residue 196 ILE Chi-restraints excluded: chain NF residue 260 VAL Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NQ residue 324 ASN Chi-restraints excluded: chain NS residue 129 THR Chi-restraints excluded: chain NS residue 307 GLU Chi-restraints excluded: chain NS residue 349 LEU Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SC residue 62 MET Chi-restraints excluded: chain SC residue 238 GLU Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SG residue 128 MET Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SH residue 189 ILE Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SJ residue 713 ARG Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SL residue 30 GLN Chi-restraints excluded: chain SL residue 54 TYR Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SN residue 65 GLU Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SR residue 257 LEU Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SV residue 85 LEU Chi-restraints excluded: chain SW residue 265 MET Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 109 ASN Chi-restraints excluded: chain SZ residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 547 optimal weight: 9.9990 chunk 305 optimal weight: 0.5980 chunk 819 optimal weight: 2.9990 chunk 670 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 986 optimal weight: 8.9990 chunk 1065 optimal weight: 9.9990 chunk 878 optimal weight: 9.9990 chunk 977 optimal weight: 0.8980 chunk 336 optimal weight: 10.0000 chunk 791 optimal weight: 6.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 142 ASN ** BA 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L7 180 GLN L7 184 ASN LA 40 HIS LC 50 GLN LI 61 HIS LK 62 HIS LN 109 HIS LQ 134 ASN NF 108 GLN NG 161 ASN NG 172 GLN NG 178 GLN NN 10 GLN NN 68 ASN NN 137 HIS NO 6 GLN ** NO 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NO 305 ASN NQ 10 HIS NS 59 ASN SC 250 GLN SD 63 GLN SD 163 ASN SD 206 ASN SE 85 GLN SG 140 GLN SJ 716 GLN SK 93 GLN SL 61 ASN SL 189 ASN SM 102 ASN SM 253 GLN SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 3 HIS SR 64 GLN SW 402 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 122641 Z= 0.339 Angle : 0.583 10.079 174963 Z= 0.301 Chirality : 0.039 0.250 20929 Planarity : 0.005 0.056 14854 Dihedral : 21.701 179.552 41710 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.76 % Allowed : 9.11 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.09), residues: 8932 helix: 2.16 (0.08), residues: 3823 sheet: 0.40 (0.14), residues: 1294 loop : 0.03 (0.09), residues: 3815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPSD 209 HIS 0.010 0.001 HISLW 66 PHE 0.023 0.002 PHESR 279 TYR 0.028 0.002 TYRNM 119 ARG 0.009 0.001 ARGBA 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 723 time to evaluate : 7.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 87 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6396 (mtm) REVERT: LC 9 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5904 (tm-30) REVERT: LC 31 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6107 (ptm160) REVERT: LC 113 MET cc_start: 0.7726 (mmm) cc_final: 0.7326 (mmm) REVERT: LI 114 ASP cc_start: 0.7973 (m-30) cc_final: 0.7731 (m-30) REVERT: LN 97 ARG cc_start: 0.7165 (tmm160) cc_final: 0.6812 (ttt180) REVERT: LQ 11 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7576 (pmmt) REVERT: LQ 90 MET cc_start: 0.8619 (mmm) cc_final: 0.8307 (mmm) REVERT: LS 7 ARG cc_start: 0.6478 (mpp80) cc_final: 0.6113 (mpt-90) REVERT: LS 65 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7589 (tm-30) REVERT: NB 370 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6829 (tt0) REVERT: NF 68 HIS cc_start: 0.7120 (t-90) cc_final: 0.6864 (t70) REVERT: NF 243 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7451 (tm-30) REVERT: NQ 1 MET cc_start: 0.3850 (OUTLIER) cc_final: 0.3117 (tmm) REVERT: SA 57 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8313 (pt) REVERT: SC 68 MET cc_start: 0.7218 (mmm) cc_final: 0.7001 (tpp) REVERT: SD 64 MET cc_start: 0.7529 (mtp) cc_final: 0.7267 (mtp) REVERT: SD 220 MET cc_start: 0.7931 (ttp) cc_final: 0.7496 (ttp) REVERT: SE 63 LEU cc_start: 0.8752 (tt) cc_final: 0.8434 (mp) REVERT: SG 128 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.7643 (mpm) REVERT: SI 104 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7028 (mtm-85) REVERT: SL 30 GLN cc_start: 0.6464 (OUTLIER) cc_final: 0.6156 (mp10) REVERT: SO 57 LYS cc_start: 0.7890 (tptt) cc_final: 0.7625 (tptm) REVERT: SQ 214 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7690 (mmm-85) REVERT: SS 361 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: ST 213 GLN cc_start: 0.7984 (mt0) cc_final: 0.7501 (mm110) REVERT: ST 232 VAL cc_start: 0.8672 (t) cc_final: 0.8463 (p) outliers start: 137 outliers final: 73 residues processed: 795 average time/residue: 1.8062 time to fit residues: 2005.3080 Evaluate side-chains 753 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 669 time to evaluate : 7.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain BA residue 135 THR Chi-restraints excluded: chain L7 residue 87 MET Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 182 HIS Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 1 MET Chi-restraints excluded: chain LC residue 9 GLU Chi-restraints excluded: chain LC residue 31 ARG Chi-restraints excluded: chain LC residue 75 VAL Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LE residue 112 ASN Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 100 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 68 SER Chi-restraints excluded: chain LN residue 189 THR Chi-restraints excluded: chain LQ residue 11 LYS Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 41 ILE Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LS residue 64 THR Chi-restraints excluded: chain LS residue 100 GLU Chi-restraints excluded: chain LT residue 31 GLU Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain NB residue 370 GLN Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 203 VAL Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 72 ASN Chi-restraints excluded: chain NF residue 174 MET Chi-restraints excluded: chain NF residue 191 THR Chi-restraints excluded: chain NF residue 215 THR Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NN residue 180 CYS Chi-restraints excluded: chain NO residue 338 ILE Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NQ residue 324 ASN Chi-restraints excluded: chain NS residue 307 GLU Chi-restraints excluded: chain NS residue 349 LEU Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SC residue 62 MET Chi-restraints excluded: chain SC residue 238 GLU Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SG residue 128 MET Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 176 LEU Chi-restraints excluded: chain SH residue 189 ILE Chi-restraints excluded: chain SI residue 104 ARG Chi-restraints excluded: chain SI residue 153 ASN Chi-restraints excluded: chain SJ residue 673 VAL Chi-restraints excluded: chain SL residue 30 GLN Chi-restraints excluded: chain SL residue 53 ASN Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SN residue 65 GLU Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SN residue 156 THR Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 113 ASN Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SQ residue 207 MET Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 257 LEU Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SS residue 209 SER Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain SS residue 361 GLN Chi-restraints excluded: chain SV residue 52 THR Chi-restraints excluded: chain SV residue 85 LEU Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 109 ASN Chi-restraints excluded: chain SZ residue 144 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 974 optimal weight: 9.9990 chunk 741 optimal weight: 2.9990 chunk 511 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 470 optimal weight: 9.9990 chunk 662 optimal weight: 5.9990 chunk 989 optimal weight: 7.9990 chunk 1047 optimal weight: 3.9990 chunk 517 optimal weight: 2.9990 chunk 937 optimal weight: 0.8980 chunk 282 optimal weight: 0.0470 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 142 ASN ** BA 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L7 184 ASN LA 40 HIS LC 50 GLN LN 109 HIS LQ 80 HIS NF 247 ASN NG 161 ASN NG 178 GLN NN 68 ASN NO 156 HIS NO 305 ASN NQ 313 GLN SA 50 GLN SA 231 ASN SD 63 GLN SD 163 ASN SE 149 ASN SJ 711 GLN SJ 716 GLN ** SK 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 37 HIS ** SR 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 129 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 122641 Z= 0.208 Angle : 0.514 10.059 174963 Z= 0.265 Chirality : 0.036 0.231 20929 Planarity : 0.004 0.054 14854 Dihedral : 21.660 178.403 41710 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.69 % Allowed : 10.58 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.09), residues: 8932 helix: 2.30 (0.08), residues: 3825 sheet: 0.40 (0.14), residues: 1278 loop : 0.05 (0.09), residues: 3829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPL9 120 HIS 0.010 0.001 HISLW 66 PHE 0.019 0.001 PHESN 60 TYR 0.027 0.001 TYRSN 109 ARG 0.009 0.000 ARGSA 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 710 time to evaluate : 7.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 87 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6308 (mtm) REVERT: LA 3 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.5668 (ttm170) REVERT: LC 113 MET cc_start: 0.7746 (mmm) cc_final: 0.7417 (mmm) REVERT: LN 97 ARG cc_start: 0.7123 (tmm160) cc_final: 0.6829 (ttt180) REVERT: LQ 90 MET cc_start: 0.8572 (mmm) cc_final: 0.8316 (mmm) REVERT: LS 65 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7549 (tm-30) REVERT: NF 68 HIS cc_start: 0.7083 (t-90) cc_final: 0.6819 (t70) REVERT: NF 243 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7400 (tm-30) REVERT: NQ 1 MET cc_start: 0.3702 (OUTLIER) cc_final: 0.3095 (tmm) REVERT: NS 129 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8226 (p) REVERT: SA 57 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8342 (pt) REVERT: SA 284 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8369 (ttp) REVERT: SE 63 LEU cc_start: 0.8742 (tt) cc_final: 0.8443 (mp) REVERT: SG 128 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.7565 (mpm) REVERT: SI 196 ASP cc_start: 0.8268 (m-30) cc_final: 0.7996 (m-30) REVERT: SO 57 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7619 (tptm) REVERT: SQ 214 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7622 (mmm-85) REVERT: ST 213 GLN cc_start: 0.7839 (mt0) cc_final: 0.7464 (mm110) REVERT: ST 232 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8478 (p) outliers start: 132 outliers final: 66 residues processed: 777 average time/residue: 1.8516 time to fit residues: 2013.4925 Evaluate side-chains 746 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 671 time to evaluate : 7.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L7 residue 87 MET Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L9 residue 182 HIS Chi-restraints excluded: chain LA residue 3 ARG Chi-restraints excluded: chain LA residue 45 THR Chi-restraints excluded: chain LB residue 151 HIS Chi-restraints excluded: chain LC residue 1 MET Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 68 SER Chi-restraints excluded: chain LN residue 189 THR Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 41 ILE Chi-restraints excluded: chain LQ residue 69 MET Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LS residue 64 THR Chi-restraints excluded: chain LT residue 31 GLU Chi-restraints excluded: chain LU residue 89 GLU Chi-restraints excluded: chain NE residue 224 VAL Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 174 MET Chi-restraints excluded: chain NG residue 137 ASP Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NN residue 180 CYS Chi-restraints excluded: chain NN residue 294 LYS Chi-restraints excluded: chain NO residue 65 MET Chi-restraints excluded: chain NO residue 338 ILE Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 324 ASN Chi-restraints excluded: chain NS residue 129 THR Chi-restraints excluded: chain NS residue 307 GLU Chi-restraints excluded: chain NS residue 349 LEU Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SC residue 62 MET Chi-restraints excluded: chain SC residue 238 GLU Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SG residue 128 MET Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 176 LEU Chi-restraints excluded: chain SH residue 189 ILE Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SM residue 155 VAL Chi-restraints excluded: chain SN residue 65 GLU Chi-restraints excluded: chain SO residue 57 LYS Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 113 ASN Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SQ residue 207 MET Chi-restraints excluded: chain SR residue 257 LEU Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SS residue 209 SER Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 332 GLN Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 222 MET Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 68 SER Chi-restraints excluded: chain SZ residue 109 ASN Chi-restraints excluded: chain SZ residue 144 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 872 optimal weight: 7.9990 chunk 594 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 780 optimal weight: 10.0000 chunk 432 optimal weight: 0.2980 chunk 894 optimal weight: 10.0000 chunk 724 optimal weight: 0.0670 chunk 1 optimal weight: 9.9990 chunk 535 optimal weight: 10.0000 chunk 940 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 overall best weight: 2.6724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 142 ASN BA 147 HIS LA 40 HIS LC 50 GLN LE 112 ASN LN 109 HIS LQ 134 ASN LS 20 GLN NG 161 ASN NG 175 ASN NG 178 GLN NN 42 ASN NN 131 HIS NO 127 ASN NO 305 ASN SD 63 GLN SD 163 ASN SE 149 ASN SJ 711 GLN SJ 716 GLN ** SK 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 24 GLN SR 5 ASN ** SR 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 24 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 122641 Z= 0.246 Angle : 0.526 10.721 174963 Z= 0.271 Chirality : 0.036 0.202 20929 Planarity : 0.004 0.055 14854 Dihedral : 21.619 178.612 41706 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.87 % Allowed : 11.51 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.09), residues: 8932 helix: 2.28 (0.08), residues: 3820 sheet: 0.35 (0.14), residues: 1284 loop : -0.01 (0.09), residues: 3828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPL9 120 HIS 0.011 0.001 HISLW 66 PHE 0.019 0.001 PHESR 279 TYR 0.028 0.002 TYRSN 109 ARG 0.010 0.000 ARGSA 311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 703 time to evaluate : 7.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 87 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6326 (mtm) REVERT: LA 3 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.5726 (ttm170) REVERT: LC 113 MET cc_start: 0.7752 (mmm) cc_final: 0.7445 (mmm) REVERT: LN 97 ARG cc_start: 0.7132 (tmm160) cc_final: 0.6848 (ttt180) REVERT: LN 332 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7428 (ttp) REVERT: LQ 90 MET cc_start: 0.8577 (mmm) cc_final: 0.8340 (mmm) REVERT: LS 7 ARG cc_start: 0.6756 (mpp80) cc_final: 0.6506 (mpt-90) REVERT: LS 22 ASP cc_start: 0.5880 (m-30) cc_final: 0.5465 (m-30) REVERT: LS 65 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7472 (tm-30) REVERT: NF 68 HIS cc_start: 0.7125 (t-90) cc_final: 0.6846 (t70) REVERT: NF 243 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7394 (tm-30) REVERT: NO 300 TYR cc_start: 0.7268 (m-80) cc_final: 0.6827 (m-80) REVERT: NQ 1 MET cc_start: 0.4240 (OUTLIER) cc_final: 0.3473 (tmm) REVERT: NS 129 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8233 (p) REVERT: SA 57 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8439 (pt) REVERT: SA 284 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8119 (mtm) REVERT: SE 63 LEU cc_start: 0.8759 (tt) cc_final: 0.8452 (mp) REVERT: SG 128 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.7594 (mpm) REVERT: SI 196 ASP cc_start: 0.8353 (m-30) cc_final: 0.8109 (m-30) REVERT: SO 57 LYS cc_start: 0.7873 (tptt) cc_final: 0.7613 (tptm) REVERT: SS 361 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6858 (mp10) REVERT: ST 223 GLN cc_start: 0.7464 (mp10) cc_final: 0.7238 (mp10) outliers start: 146 outliers final: 92 residues processed: 786 average time/residue: 1.8113 time to fit residues: 2001.0283 Evaluate side-chains 774 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 673 time to evaluate : 7.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 18 THR Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L7 residue 87 MET Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 106 ASP Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 182 HIS Chi-restraints excluded: chain LA residue 3 ARG Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 151 HIS Chi-restraints excluded: chain LC residue 1 MET Chi-restraints excluded: chain LC residue 75 VAL Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LE residue 112 ASN Chi-restraints excluded: chain LE residue 143 THR Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 68 SER Chi-restraints excluded: chain LN residue 189 THR Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 332 MET Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 69 MET Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LS residue 64 THR Chi-restraints excluded: chain LS residue 100 GLU Chi-restraints excluded: chain LT residue 31 GLU Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LU residue 89 GLU Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 224 VAL Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 174 MET Chi-restraints excluded: chain NF residue 191 THR Chi-restraints excluded: chain NF residue 260 VAL Chi-restraints excluded: chain NG residue 165 ILE Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NN residue 38 CYS Chi-restraints excluded: chain NN residue 159 MET Chi-restraints excluded: chain NN residue 284 ILE Chi-restraints excluded: chain NN residue 294 LYS Chi-restraints excluded: chain NO residue 338 ILE Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NQ residue 324 ASN Chi-restraints excluded: chain NS residue 129 THR Chi-restraints excluded: chain NS residue 307 GLU Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SC residue 62 MET Chi-restraints excluded: chain SC residue 238 GLU Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SE residue 91 THR Chi-restraints excluded: chain SG residue 128 MET Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 176 LEU Chi-restraints excluded: chain SH residue 189 ILE Chi-restraints excluded: chain SI residue 153 ASN Chi-restraints excluded: chain SJ residue 722 LYS Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SL residue 53 ASN Chi-restraints excluded: chain SL residue 83 THR Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SM residue 155 VAL Chi-restraints excluded: chain SN residue 65 GLU Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 113 ASN Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 244 LEU Chi-restraints excluded: chain SR residue 257 LEU Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain SS residue 361 GLN Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 222 MET Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SW residue 230 THR Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 109 ASN Chi-restraints excluded: chain SZ residue 144 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 352 optimal weight: 5.9990 chunk 943 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 615 optimal weight: 4.9990 chunk 258 optimal weight: 0.7980 chunk 1048 optimal weight: 0.7980 chunk 870 optimal weight: 9.9990 chunk 485 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 346 optimal weight: 6.9990 chunk 550 optimal weight: 0.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 142 ASN BA 147 HIS LA 40 HIS LC 50 GLN LE 112 ASN LN 109 HIS NF 247 ASN NG 161 ASN NO 127 ASN NO 305 ASN SD 63 GLN SD 163 ASN SE 149 ASN SJ 711 GLN SJ 716 GLN SK 86 ASN SL 30 GLN ** SL 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 209 HIS SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 340 GLN SQ 47 ASN ** SR 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 186 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 122641 Z= 0.246 Angle : 0.526 12.831 174963 Z= 0.271 Chirality : 0.036 0.239 20929 Planarity : 0.004 0.062 14854 Dihedral : 21.597 178.739 41706 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.10 % Allowed : 12.10 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 8932 helix: 2.29 (0.08), residues: 3821 sheet: 0.26 (0.14), residues: 1303 loop : -0.01 (0.10), residues: 3808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL9 120 HIS 0.010 0.001 HISLW 66 PHE 0.020 0.001 PHESR 279 TYR 0.028 0.001 TYRSN 109 ARG 0.011 0.000 ARGSA 311 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 698 time to evaluate : 6.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 87 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6360 (mtm) REVERT: L8 126 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7572 (pp20) REVERT: LA 3 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.5647 (ttm170) REVERT: LC 113 MET cc_start: 0.7704 (mmm) cc_final: 0.7458 (mmm) REVERT: LN 97 ARG cc_start: 0.7185 (tmm160) cc_final: 0.6901 (ttt180) REVERT: LN 332 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7426 (ttm) REVERT: LQ 90 MET cc_start: 0.8572 (mmm) cc_final: 0.8248 (mmm) REVERT: LS 7 ARG cc_start: 0.6764 (mpp80) cc_final: 0.6550 (mpt-90) REVERT: LS 22 ASP cc_start: 0.5953 (m-30) cc_final: 0.5543 (m-30) REVERT: LS 65 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7425 (tm-30) REVERT: NE 351 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6108 (mt) REVERT: NF 68 HIS cc_start: 0.7176 (t-90) cc_final: 0.6893 (t70) REVERT: NF 243 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7364 (tm-30) REVERT: NO 300 TYR cc_start: 0.7333 (m-80) cc_final: 0.6924 (m-80) REVERT: NQ 1 MET cc_start: 0.4300 (OUTLIER) cc_final: 0.3487 (tmm) REVERT: NS 129 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8218 (p) REVERT: SA 57 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8468 (pt) REVERT: SA 284 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8082 (mtm) REVERT: SD 220 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7554 (ttm) REVERT: SE 63 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8449 (mp) REVERT: SE 232 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6273 (tm-30) REVERT: SG 128 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.7572 (mpm) REVERT: SI 196 ASP cc_start: 0.8351 (m-30) cc_final: 0.8099 (m-30) REVERT: SL 94 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7226 (m-30) REVERT: SO 57 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7633 (tptm) REVERT: SR 459 LEU cc_start: 0.7947 (pp) cc_final: 0.7643 (pt) REVERT: SS 361 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6862 (mp10) REVERT: SW 202 MET cc_start: 0.6921 (mtp) cc_final: 0.6533 (ptp) outliers start: 164 outliers final: 101 residues processed: 792 average time/residue: 1.7944 time to fit residues: 1995.5981 Evaluate side-chains 784 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 668 time to evaluate : 7.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 12 VAL Chi-restraints excluded: chain BA residue 18 THR Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain BA residue 135 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 87 MET Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 106 ASP Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 182 HIS Chi-restraints excluded: chain LA residue 3 ARG Chi-restraints excluded: chain LA residue 45 THR Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 151 HIS Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LE residue 112 ASN Chi-restraints excluded: chain LE residue 143 THR Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 100 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 68 SER Chi-restraints excluded: chain LN residue 189 THR Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 332 MET Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 69 MET Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LS residue 64 THR Chi-restraints excluded: chain LS residue 73 TYR Chi-restraints excluded: chain LS residue 100 GLU Chi-restraints excluded: chain LT residue 31 GLU Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LU residue 89 GLU Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NE residue 351 LEU Chi-restraints excluded: chain NF residue 191 THR Chi-restraints excluded: chain NF residue 215 THR Chi-restraints excluded: chain NG residue 165 ILE Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NN residue 38 CYS Chi-restraints excluded: chain NN residue 159 MET Chi-restraints excluded: chain NN residue 182 LEU Chi-restraints excluded: chain NN residue 284 ILE Chi-restraints excluded: chain NN residue 294 LYS Chi-restraints excluded: chain NO residue 338 ILE Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 324 ASN Chi-restraints excluded: chain NS residue 129 THR Chi-restraints excluded: chain NS residue 307 GLU Chi-restraints excluded: chain NS residue 349 LEU Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SC residue 62 MET Chi-restraints excluded: chain SC residue 238 GLU Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SD residue 224 THR Chi-restraints excluded: chain SE residue 63 LEU Chi-restraints excluded: chain SE residue 91 THR Chi-restraints excluded: chain SE residue 232 GLU Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 128 MET Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 176 LEU Chi-restraints excluded: chain SH residue 189 ILE Chi-restraints excluded: chain SI residue 153 ASN Chi-restraints excluded: chain SJ residue 697 ASP Chi-restraints excluded: chain SJ residue 722 LYS Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SL residue 58 LEU Chi-restraints excluded: chain SL residue 83 THR Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SM residue 155 VAL Chi-restraints excluded: chain SN residue 65 GLU Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SO residue 57 LYS Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 113 ASN Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 244 LEU Chi-restraints excluded: chain SR residue 257 LEU Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain SS residue 361 GLN Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 85 LEU Chi-restraints excluded: chain SW residue 230 THR Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 109 ASN Chi-restraints excluded: chain SZ residue 144 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 1011 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 597 optimal weight: 0.7980 chunk 765 optimal weight: 2.9990 chunk 593 optimal weight: 3.9990 chunk 882 optimal weight: 5.9990 chunk 585 optimal weight: 0.9980 chunk 1044 optimal weight: 4.9990 chunk 653 optimal weight: 0.9990 chunk 636 optimal weight: 1.9990 chunk 482 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 142 ASN BA 147 HIS LA 40 HIS LC 50 GLN LN 109 HIS NF 247 ASN NG 161 ASN NO 127 ASN NO 305 ASN SD 63 GLN SD 163 ASN SE 149 ASN SJ 711 GLN SJ 716 GLN SL 30 GLN ** SL 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 225 HIS SM 209 HIS SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 47 ASN ** SR 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 186 GLN SZ 95 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 122641 Z= 0.164 Angle : 0.495 10.627 174963 Z= 0.255 Chirality : 0.034 0.214 20929 Planarity : 0.004 0.054 14854 Dihedral : 21.568 178.270 41706 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.71 % Allowed : 12.79 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.09), residues: 8932 helix: 2.40 (0.08), residues: 3822 sheet: 0.30 (0.14), residues: 1283 loop : 0.03 (0.10), residues: 3827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL9 120 HIS 0.011 0.001 HISLW 66 PHE 0.020 0.001 PHESR 279 TYR 0.053 0.001 TYRLS 73 ARG 0.012 0.000 ARGSA 311 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 702 time to evaluate : 7.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 87 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6648 (mtt) REVERT: LA 3 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.5732 (ttm170) REVERT: LC 113 MET cc_start: 0.7690 (mmm) cc_final: 0.7477 (mmm) REVERT: LE 118 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6281 (tm-30) REVERT: LN 97 ARG cc_start: 0.7163 (tmm160) cc_final: 0.6886 (ttt180) REVERT: LN 272 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7154 (mtmm) REVERT: LQ 90 MET cc_start: 0.8555 (mmm) cc_final: 0.8353 (mmm) REVERT: LS 22 ASP cc_start: 0.6040 (m-30) cc_final: 0.5612 (m-30) REVERT: LS 65 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7450 (tm-30) REVERT: NE 351 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6115 (mt) REVERT: NF 68 HIS cc_start: 0.7151 (t-90) cc_final: 0.6835 (t70) REVERT: NF 243 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7354 (tm-30) REVERT: NO 300 TYR cc_start: 0.7330 (m-80) cc_final: 0.6976 (m-80) REVERT: NQ 1 MET cc_start: 0.4221 (OUTLIER) cc_final: 0.3705 (ptt) REVERT: NS 129 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8165 (p) REVERT: SE 232 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6063 (tm-30) REVERT: SI 196 ASP cc_start: 0.8336 (m-30) cc_final: 0.8089 (m-30) REVERT: SL 94 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: SN 119 VAL cc_start: 0.8281 (t) cc_final: 0.7922 (m) REVERT: SO 57 LYS cc_start: 0.7884 (tptt) cc_final: 0.7634 (tptm) REVERT: SR 459 LEU cc_start: 0.7843 (pp) cc_final: 0.7565 (pt) REVERT: SW 202 MET cc_start: 0.6978 (mtp) cc_final: 0.6605 (ptp) outliers start: 133 outliers final: 84 residues processed: 782 average time/residue: 1.8412 time to fit residues: 2029.9075 Evaluate side-chains 759 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 667 time to evaluate : 7.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 12 VAL Chi-restraints excluded: chain BA residue 18 THR Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 87 MET Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 106 ASP Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 182 HIS Chi-restraints excluded: chain LA residue 3 ARG Chi-restraints excluded: chain LA residue 45 THR Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 151 HIS Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LE residue 112 ASN Chi-restraints excluded: chain LE residue 143 THR Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 100 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 68 SER Chi-restraints excluded: chain LN residue 189 THR Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 272 LYS Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 69 MET Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LS residue 100 GLU Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 351 LEU Chi-restraints excluded: chain NF residue 191 THR Chi-restraints excluded: chain NG residue 158 THR Chi-restraints excluded: chain NG residue 165 ILE Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NO residue 89 THR Chi-restraints excluded: chain NO residue 338 ILE Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NS residue 129 THR Chi-restraints excluded: chain NS residue 307 GLU Chi-restraints excluded: chain NS residue 334 VAL Chi-restraints excluded: chain NS residue 349 LEU Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SC residue 62 MET Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SD residue 224 THR Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 232 GLU Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SH residue 189 ILE Chi-restraints excluded: chain SI residue 153 ASN Chi-restraints excluded: chain SJ residue 697 ASP Chi-restraints excluded: chain SJ residue 722 LYS Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SL residue 58 LEU Chi-restraints excluded: chain SL residue 83 THR Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SM residue 155 VAL Chi-restraints excluded: chain SN residue 65 GLU Chi-restraints excluded: chain SO residue 101 PHE Chi-restraints excluded: chain SO residue 173 ASP Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 244 LEU Chi-restraints excluded: chain SR residue 257 LEU Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 216 GLU Chi-restraints excluded: chain SV residue 52 THR Chi-restraints excluded: chain SV residue 85 LEU Chi-restraints excluded: chain SW residue 230 THR Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 144 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 646 optimal weight: 0.7980 chunk 417 optimal weight: 8.9990 chunk 624 optimal weight: 20.0000 chunk 314 optimal weight: 2.9990 chunk 205 optimal weight: 8.9990 chunk 202 optimal weight: 20.0000 chunk 664 optimal weight: 0.5980 chunk 711 optimal weight: 2.9990 chunk 516 optimal weight: 0.0270 chunk 97 optimal weight: 10.0000 chunk 821 optimal weight: 2.9990 overall best weight: 1.4842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN BA 142 ASN BA 147 HIS LA 40 HIS LC 50 GLN LE 112 ASN LN 109 HIS ** LN 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 20 GLN NG 161 ASN NO 127 ASN NO 305 ASN NQ 113 HIS SD 63 GLN SD 99 ASN SD 163 ASN SJ 711 GLN SJ 716 GLN SL 30 GLN ** SL 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 209 HIS SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 47 ASN ** SR 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 122641 Z= 0.163 Angle : 0.493 12.314 174963 Z= 0.253 Chirality : 0.034 0.247 20929 Planarity : 0.004 0.057 14854 Dihedral : 21.527 178.780 41706 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.81 % Allowed : 12.99 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.09), residues: 8932 helix: 2.42 (0.08), residues: 3828 sheet: 0.30 (0.14), residues: 1293 loop : 0.05 (0.10), residues: 3811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL9 120 HIS 0.011 0.001 HISLW 66 PHE 0.028 0.001 PHELC 176 TYR 0.029 0.001 TYRSN 109 ARG 0.013 0.000 ARGSA 311 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 692 time to evaluate : 7.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 87 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6558 (mtt) REVERT: LC 113 MET cc_start: 0.7686 (mmm) cc_final: 0.7469 (mmm) REVERT: LE 118 GLU cc_start: 0.6660 (tm-30) cc_final: 0.6279 (tm-30) REVERT: LN 97 ARG cc_start: 0.7102 (tmm160) cc_final: 0.6554 (ttp-170) REVERT: LN 272 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7130 (mtmm) REVERT: LN 332 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7391 (ttm) REVERT: LS 22 ASP cc_start: 0.6088 (m-30) cc_final: 0.5657 (m-30) REVERT: NF 68 HIS cc_start: 0.7084 (t-90) cc_final: 0.6781 (t70) REVERT: NF 243 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7382 (tm-30) REVERT: NG 137 ASP cc_start: 0.7465 (t0) cc_final: 0.7174 (t0) REVERT: NN 177 ILE cc_start: 0.8608 (mt) cc_final: 0.8399 (mm) REVERT: NO 300 TYR cc_start: 0.7359 (m-80) cc_final: 0.6955 (m-80) REVERT: NQ 1 MET cc_start: 0.4275 (OUTLIER) cc_final: 0.3685 (ptt) REVERT: NS 129 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8176 (p) REVERT: SA 284 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8127 (mtm) REVERT: SE 232 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6019 (tm-30) REVERT: SI 196 ASP cc_start: 0.8336 (m-30) cc_final: 0.8071 (m-30) REVERT: SI 237 MET cc_start: 0.8396 (mmm) cc_final: 0.8194 (mpt) REVERT: SK 1 MET cc_start: 0.7041 (tpp) cc_final: 0.6430 (mmm) REVERT: SL 94 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: SN 119 VAL cc_start: 0.8267 (t) cc_final: 0.7907 (m) REVERT: SO 57 LYS cc_start: 0.7890 (tptt) cc_final: 0.7648 (tptm) REVERT: SR 459 LEU cc_start: 0.7772 (pp) cc_final: 0.7507 (pt) REVERT: SW 202 MET cc_start: 0.6912 (mtp) cc_final: 0.6542 (ptp) outliers start: 141 outliers final: 91 residues processed: 773 average time/residue: 1.7914 time to fit residues: 1952.3810 Evaluate side-chains 773 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 674 time to evaluate : 7.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 12 VAL Chi-restraints excluded: chain BA residue 18 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 87 MET Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 55 MET Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 182 HIS Chi-restraints excluded: chain LA residue 45 THR Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 151 HIS Chi-restraints excluded: chain LC residue 48 VAL Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LE residue 143 THR Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 100 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 68 SER Chi-restraints excluded: chain LN residue 189 THR Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 272 LYS Chi-restraints excluded: chain LN residue 332 MET Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 69 MET Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LS residue 100 GLU Chi-restraints excluded: chain LT residue 31 GLU Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LU residue 89 GLU Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NF residue 191 THR Chi-restraints excluded: chain NG residue 158 THR Chi-restraints excluded: chain NG residue 165 ILE Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NN residue 38 CYS Chi-restraints excluded: chain NO residue 89 THR Chi-restraints excluded: chain NO residue 338 ILE Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 324 ASN Chi-restraints excluded: chain NS residue 129 THR Chi-restraints excluded: chain NS residue 307 GLU Chi-restraints excluded: chain NS residue 334 VAL Chi-restraints excluded: chain NS residue 349 LEU Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SC residue 62 MET Chi-restraints excluded: chain SC residue 237 LYS Chi-restraints excluded: chain SC residue 238 GLU Chi-restraints excluded: chain SC residue 281 ILE Chi-restraints excluded: chain SD residue 224 THR Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 232 GLU Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SH residue 189 ILE Chi-restraints excluded: chain SI residue 153 ASN Chi-restraints excluded: chain SJ residue 722 LYS Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SL residue 58 LEU Chi-restraints excluded: chain SL residue 83 THR Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SM residue 155 VAL Chi-restraints excluded: chain SN residue 65 GLU Chi-restraints excluded: chain SO residue 101 PHE Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 113 ASN Chi-restraints excluded: chain SO residue 173 ASP Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 257 LEU Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SV residue 85 LEU Chi-restraints excluded: chain SW residue 230 THR Chi-restraints excluded: chain SZ residue 144 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 950 optimal weight: 8.9990 chunk 1000 optimal weight: 0.0570 chunk 913 optimal weight: 0.9980 chunk 973 optimal weight: 10.0000 chunk 586 optimal weight: 10.0000 chunk 424 optimal weight: 2.9990 chunk 764 optimal weight: 0.7980 chunk 298 optimal weight: 4.9990 chunk 879 optimal weight: 9.9990 chunk 920 optimal weight: 2.9990 chunk 970 optimal weight: 0.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 142 ASN BA 147 HIS LA 40 HIS LC 50 GLN LE 112 ASN LN 109 HIS ** LN 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NF 247 ASN NG 161 ASN NO 22 GLN NO 66 GLN NO 127 ASN NO 305 ASN SD 63 GLN SD 163 ASN SG 188 GLN SJ 711 GLN SJ 716 GLN SL 30 GLN ** SL 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 47 ASN SZ 95 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 122641 Z= 0.144 Angle : 0.485 11.472 174963 Z= 0.249 Chirality : 0.034 0.256 20929 Planarity : 0.004 0.065 14854 Dihedral : 21.486 179.446 41706 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.49 % Allowed : 13.50 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.09), residues: 8932 helix: 2.47 (0.08), residues: 3829 sheet: 0.29 (0.14), residues: 1282 loop : 0.09 (0.10), residues: 3821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPNG 142 HIS 0.012 0.001 HISLW 66 PHE 0.028 0.001 PHELC 176 TYR 0.029 0.001 TYRSN 109 ARG 0.013 0.000 ARGSA 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 698 time to evaluate : 7.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 87 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6674 (mtt) REVERT: LC 113 MET cc_start: 0.7677 (mmm) cc_final: 0.7460 (mmm) REVERT: LE 114 GLN cc_start: 0.6645 (tm-30) cc_final: 0.6273 (tm-30) REVERT: LE 117 LYS cc_start: 0.7039 (pmtt) cc_final: 0.6215 (mmtm) REVERT: LE 118 GLU cc_start: 0.6797 (tm-30) cc_final: 0.6562 (tm-30) REVERT: LN 97 ARG cc_start: 0.7140 (tmm160) cc_final: 0.6595 (ttp-170) REVERT: LN 272 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7105 (mtmm) REVERT: LS 22 ASP cc_start: 0.5953 (m-30) cc_final: 0.5554 (m-30) REVERT: NF 68 HIS cc_start: 0.7043 (t-90) cc_final: 0.6740 (t70) REVERT: NF 243 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7348 (tm-30) REVERT: NO 300 TYR cc_start: 0.7403 (m-80) cc_final: 0.7050 (m-80) REVERT: NQ 1 MET cc_start: 0.4327 (OUTLIER) cc_final: 0.3736 (ptt) REVERT: NQ 228 TYR cc_start: 0.8841 (m-80) cc_final: 0.8502 (m-80) REVERT: NQ 317 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8878 (pt) REVERT: NS 129 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8172 (p) REVERT: SE 232 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.5981 (tm-30) REVERT: SI 196 ASP cc_start: 0.8331 (m-30) cc_final: 0.8069 (m-30) REVERT: SJ 697 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7124 (t0) REVERT: SK 1 MET cc_start: 0.7075 (tpp) cc_final: 0.6531 (mmm) REVERT: SK 197 MET cc_start: 0.8008 (tmm) cc_final: 0.7703 (ttp) REVERT: SL 94 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7230 (m-30) REVERT: SN 72 VAL cc_start: 0.8150 (p) cc_final: 0.7886 (p) REVERT: SN 119 VAL cc_start: 0.8215 (t) cc_final: 0.7873 (m) REVERT: SO 57 LYS cc_start: 0.7877 (tptt) cc_final: 0.7675 (tptm) REVERT: SR 459 LEU cc_start: 0.7773 (pp) cc_final: 0.7507 (pt) REVERT: SW 202 MET cc_start: 0.6895 (mtp) cc_final: 0.6529 (ptp) outliers start: 116 outliers final: 84 residues processed: 767 average time/residue: 1.7898 time to fit residues: 1933.8955 Evaluate side-chains 763 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 671 time to evaluate : 7.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 12 VAL Chi-restraints excluded: chain BA residue 18 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 87 MET Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 55 MET Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 182 HIS Chi-restraints excluded: chain LA residue 45 THR Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LB residue 151 HIS Chi-restraints excluded: chain LC residue 1 MET Chi-restraints excluded: chain LC residue 75 VAL Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 100 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LN residue 189 THR Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 272 LYS Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 69 MET Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LS residue 100 GLU Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LU residue 89 GLU Chi-restraints excluded: chain NF residue 191 THR Chi-restraints excluded: chain NG residue 137 ASP Chi-restraints excluded: chain NG residue 158 THR Chi-restraints excluded: chain NG residue 165 ILE Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NN residue 38 CYS Chi-restraints excluded: chain NO residue 89 THR Chi-restraints excluded: chain NO residue 338 ILE Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 317 LEU Chi-restraints excluded: chain NQ residue 324 ASN Chi-restraints excluded: chain NS residue 129 THR Chi-restraints excluded: chain NS residue 307 GLU Chi-restraints excluded: chain NS residue 334 VAL Chi-restraints excluded: chain NS residue 349 LEU Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SC residue 62 MET Chi-restraints excluded: chain SC residue 237 LYS Chi-restraints excluded: chain SC residue 238 GLU Chi-restraints excluded: chain SC residue 281 ILE Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 232 GLU Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SH residue 189 ILE Chi-restraints excluded: chain SI residue 153 ASN Chi-restraints excluded: chain SJ residue 697 ASP Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SL residue 58 LEU Chi-restraints excluded: chain SL residue 83 THR Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SN residue 65 GLU Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SO residue 101 PHE Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 173 ASP Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 257 LEU Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SW residue 230 THR Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 639 optimal weight: 5.9990 chunk 1029 optimal weight: 7.9990 chunk 628 optimal weight: 6.9990 chunk 488 optimal weight: 8.9990 chunk 715 optimal weight: 4.9990 chunk 1079 optimal weight: 8.9990 chunk 993 optimal weight: 0.0970 chunk 859 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 664 optimal weight: 3.9990 chunk 527 optimal weight: 5.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 142 ASN BA 147 HIS L8 125 ASN L9 8 GLN LA 40 HIS LC 50 GLN LE 112 ASN LN 109 HIS ** LN 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LW 66 HIS NG 161 ASN NN 42 ASN NO 22 GLN NO 66 GLN NO 127 ASN NO 305 ASN SD 63 GLN SD 163 ASN ** SJ 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 716 GLN SL 30 GLN SL 61 ASN SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 47 ASN SQ 155 GLN ** SR 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 213 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 122641 Z= 0.360 Angle : 0.594 12.093 174963 Z= 0.303 Chirality : 0.039 0.259 20929 Planarity : 0.005 0.057 14854 Dihedral : 21.493 178.199 41706 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.58 % Allowed : 13.77 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.09), residues: 8932 helix: 2.20 (0.08), residues: 3826 sheet: 0.14 (0.14), residues: 1312 loop : -0.07 (0.10), residues: 3794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPNG 142 HIS 0.013 0.001 HISBA 147 PHE 0.033 0.002 PHESI 189 TYR 0.048 0.002 TYRSA 331 ARG 0.027 0.001 ARGNG 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17864 Ramachandran restraints generated. 8932 Oldfield, 0 Emsley, 8932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 700 time to evaluate : 7.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 87 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6448 (mtm) REVERT: LC 113 MET cc_start: 0.7816 (mmm) cc_final: 0.7460 (mmm) REVERT: LE 118 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6743 (tm-30) REVERT: LN 97 ARG cc_start: 0.7188 (tmm160) cc_final: 0.6658 (ttp-170) REVERT: LN 272 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7312 (mtmm) REVERT: LN 389 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8037 (mtm) REVERT: LS 22 ASP cc_start: 0.6079 (m-30) cc_final: 0.5693 (m-30) REVERT: NF 42 MET cc_start: 0.7317 (ttp) cc_final: 0.6647 (ptm) REVERT: NF 68 HIS cc_start: 0.7222 (t-90) cc_final: 0.6911 (t70) REVERT: NF 243 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7432 (tm-30) REVERT: NO 300 TYR cc_start: 0.7500 (m-80) cc_final: 0.7154 (m-80) REVERT: NQ 1 MET cc_start: 0.4301 (OUTLIER) cc_final: 0.3701 (ptt) REVERT: NQ 317 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9043 (pt) REVERT: NS 129 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8188 (p) REVERT: SH 133 ASP cc_start: 0.7838 (m-30) cc_final: 0.7599 (OUTLIER) REVERT: SI 196 ASP cc_start: 0.8367 (m-30) cc_final: 0.8090 (m-30) REVERT: SK 1 MET cc_start: 0.7072 (tpp) cc_final: 0.6547 (mmt) REVERT: SN 72 VAL cc_start: 0.8146 (p) cc_final: 0.7892 (p) REVERT: SN 106 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6347 (mmt) REVERT: SR 459 LEU cc_start: 0.7732 (pp) cc_final: 0.7471 (pt) REVERT: SW 202 MET cc_start: 0.6923 (mtp) cc_final: 0.6551 (ptp) REVERT: SW 275 MET cc_start: 0.8015 (mmt) cc_final: 0.7675 (mmm) outliers start: 123 outliers final: 92 residues processed: 770 average time/residue: 1.8454 time to fit residues: 1991.4476 Evaluate side-chains 771 residues out of total 8015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 673 time to evaluate : 7.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 12 VAL Chi-restraints excluded: chain BA residue 18 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 87 MET Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 55 MET Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 182 HIS Chi-restraints excluded: chain LA residue 45 THR Chi-restraints excluded: chain LA residue 94 MET Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 75 VAL Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 100 ASP Chi-restraints excluded: chain LG residue 125 CYS Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LN residue 189 THR Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 272 LYS Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 69 MET Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LS residue 100 GLU Chi-restraints excluded: chain LT residue 31 GLU Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LU residue 89 GLU Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 314 VAL Chi-restraints excluded: chain NF residue 191 THR Chi-restraints excluded: chain NF residue 215 THR Chi-restraints excluded: chain NG residue 158 THR Chi-restraints excluded: chain NG residue 165 ILE Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NN residue 38 CYS Chi-restraints excluded: chain NN residue 83 THR Chi-restraints excluded: chain NO residue 89 THR Chi-restraints excluded: chain NO residue 338 ILE Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 317 LEU Chi-restraints excluded: chain NQ residue 324 ASN Chi-restraints excluded: chain NS residue 129 THR Chi-restraints excluded: chain NS residue 307 GLU Chi-restraints excluded: chain NS residue 349 LEU Chi-restraints excluded: chain SA residue 115 VAL Chi-restraints excluded: chain SC residue 62 MET Chi-restraints excluded: chain SC residue 237 LYS Chi-restraints excluded: chain SC residue 238 GLU Chi-restraints excluded: chain SC residue 281 ILE Chi-restraints excluded: chain SD residue 224 THR Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 144 LEU Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 176 LEU Chi-restraints excluded: chain SH residue 189 ILE Chi-restraints excluded: chain SI residue 153 ASN Chi-restraints excluded: chain SJ residue 724 VAL Chi-restraints excluded: chain SL residue 58 LEU Chi-restraints excluded: chain SL residue 83 THR Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SN residue 65 GLU Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SN residue 106 MET Chi-restraints excluded: chain SO residue 113 ASN Chi-restraints excluded: chain SO residue 173 ASP Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SQ residue 172 ASP Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 257 LEU Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SW residue 230 THR Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 683 optimal weight: 0.9990 chunk 916 optimal weight: 7.9990 chunk 263 optimal weight: 2.9990 chunk 792 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 238 optimal weight: 10.0000 chunk 861 optimal weight: 0.8980 chunk 360 optimal weight: 10.0000 chunk 884 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 142 ASN BA 147 HIS L7 90 HIS L8 125 ASN LA 40 HIS LC 50 GLN LN 109 HIS ** LN 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NF 247 ASN NG 161 ASN NO 127 ASN NO 305 ASN SD 63 GLN SD 163 ASN SJ 711 GLN SJ 716 GLN SL 30 GLN SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 47 ASN SQ 155 GLN ** SR 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 208 HIS ** ST 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.088241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.065778 restraints weight = 382569.329| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.91 r_work: 0.3126 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 122641 Z= 0.280 Angle : 0.558 13.125 174963 Z= 0.286 Chirality : 0.037 0.240 20929 Planarity : 0.004 0.057 14854 Dihedral : 21.512 178.926 41706 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.52 % Allowed : 13.97 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 8932 helix: 2.19 (0.08), residues: 3830 sheet: 0.15 (0.14), residues: 1306 loop : -0.10 (0.10), residues: 3796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPSR 217 HIS 0.012 0.001 HISBA 147 PHE 0.029 0.002 PHELC 176 TYR 0.040 0.002 TYRSA 331 ARG 0.013 0.000 ARGSA 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34454.03 seconds wall clock time: 599 minutes 6.73 seconds (35946.73 seconds total)