Starting phenix.real_space_refine on Thu Feb 22 20:47:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkp_29252/02_2024/8fkp_29252_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkp_29252/02_2024/8fkp_29252.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkp_29252/02_2024/8fkp_29252_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkp_29252/02_2024/8fkp_29252_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkp_29252/02_2024/8fkp_29252_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkp_29252/02_2024/8fkp_29252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkp_29252/02_2024/8fkp_29252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkp_29252/02_2024/8fkp_29252_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkp_29252/02_2024/8fkp_29252_neut_updated.pdb" } resolution = 2.85 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= 0.033 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 2 6.06 5 P 1730 5.49 5 Mg 54 5.21 5 S 273 5.16 5 C 57284 2.51 5 N 18927 2.21 5 O 23178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L6 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L6 GLU 108": "OE1" <-> "OE2" Residue "L7 TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ASP 106": "OD1" <-> "OD2" Residue "L7 GLU 158": "OE1" <-> "OE2" Residue "L7 ASP 190": "OD1" <-> "OD2" Residue "L7 GLU 194": "OE1" <-> "OE2" Residue "L8 PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ASP 32": "OD1" <-> "OD2" Residue "L8 ASP 39": "OD1" <-> "OD2" Residue "L8 ASP 59": "OD1" <-> "OD2" Residue "L8 ASP 81": "OD1" <-> "OD2" Residue "L9 ASP 17": "OD1" <-> "OD2" Residue "L9 GLU 103": "OE1" <-> "OE2" Residue "L9 ASP 124": "OD1" <-> "OD2" Residue "LA GLU 9": "OE1" <-> "OE2" Residue "LA GLU 89": "OE1" <-> "OE2" Residue "LA GLU 152": "OE1" <-> "OE2" Residue "LA GLU 154": "OE1" <-> "OE2" Residue "LB ASP 10": "OD1" <-> "OD2" Residue "LB GLU 17": "OE1" <-> "OE2" Residue "LC GLU 60": "OE1" <-> "OE2" Residue "LC ASP 85": "OD1" <-> "OD2" Residue "LC GLU 96": "OE1" <-> "OE2" Residue "LC GLU 130": "OE1" <-> "OE2" Residue "LE GLU 118": "OE1" <-> "OE2" Residue "LG TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 99": "OE1" <-> "OE2" Residue "LG ASP 127": "OD1" <-> "OD2" Residue "LI ASP 52": "OD1" <-> "OD2" Residue "LI GLU 54": "OE1" <-> "OE2" Residue "LI GLU 83": "OE1" <-> "OE2" Residue "LN PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 199": "OE1" <-> "OE2" Residue "LN TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 279": "OE1" <-> "OE2" Residue "LN TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 383": "OE1" <-> "OE2" Residue "LN GLU 384": "OE1" <-> "OE2" Residue "LN ASP 395": "OD1" <-> "OD2" Residue "LQ TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ ASP 42": "OD1" <-> "OD2" Residue "LQ GLU 84": "OE1" <-> "OE2" Residue "LQ GLU 113": "OE1" <-> "OE2" Residue "LS GLU 15": "OE1" <-> "OE2" Residue "LS GLU 16": "OE1" <-> "OE2" Residue "LS TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 100": "OE1" <-> "OE2" Residue "LT GLU 31": "OE1" <-> "OE2" Residue "LT GLU 40": "OE1" <-> "OE2" Residue "LU GLU 54": "OE1" <-> "OE2" Residue "LU GLU 59": "OE1" <-> "OE2" Residue "NB TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NE GLU 265": "OE1" <-> "OE2" Residue "NE GLU 278": "OE1" <-> "OE2" Residue "NE GLU 297": "OE1" <-> "OE2" Residue "NG ASP 137": "OD1" <-> "OD2" Residue "NG ASP 151": "OD1" <-> "OD2" Residue "NG GLU 159": "OE1" <-> "OE2" Residue "NG ASP 185": "OD1" <-> "OD2" Residue "NG GLU 186": "OE1" <-> "OE2" Residue "NG GLU 190": "OE1" <-> "OE2" Residue "NM ASP 9": "OD1" <-> "OD2" Residue "NM PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NM TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NM TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NM GLU 92": "OE1" <-> "OE2" Residue "NM GLU 142": "OE1" <-> "OE2" Residue "NM GLU 145": "OE1" <-> "OE2" Residue "NN GLU 55": "OE1" <-> "OE2" Residue "NN ASP 72": "OD1" <-> "OD2" Residue "NN ASP 120": "OD1" <-> "OD2" Residue "NO ASP 50": "OD1" <-> "OD2" Residue "NO GLU 184": "OE1" <-> "OE2" Residue "NS GLU 77": "OE1" <-> "OE2" Residue "NS GLU 88": "OE1" <-> "OE2" Residue "NS GLU 121": "OE1" <-> "OE2" Residue "NS ASP 150": "OD1" <-> "OD2" Residue "NS ASP 201": "OD1" <-> "OD2" Residue "NS TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NS GLU 332": "OE1" <-> "OE2" Residue "SA TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 16": "OE1" <-> "OE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 145": "OE1" <-> "OE2" Residue "SA GLU 254": "OE1" <-> "OE2" Residue "SA ASP 352": "OD1" <-> "OD2" Residue "SC TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 81": "OE1" <-> "OE2" Residue "SC TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 229": "OE1" <-> "OE2" Residue "SC GLU 231": "OE1" <-> "OE2" Residue "SC ASP 234": "OD1" <-> "OD2" Residue "SC ASP 254": "OD1" <-> "OD2" Residue "SD GLU 16": "OE1" <-> "OE2" Residue "SD GLU 27": "OE1" <-> "OE2" Residue "SD GLU 188": "OE1" <-> "OE2" Residue "SE ASP 88": "OD1" <-> "OD2" Residue "SE GLU 109": "OE1" <-> "OE2" Residue "SE GLU 165": "OE1" <-> "OE2" Residue "SE GLU 210": "OE1" <-> "OE2" Residue "SE TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE ASP 228": "OD1" <-> "OD2" Residue "SE GLU 232": "OE1" <-> "OE2" Residue "SH ASP 57": "OD1" <-> "OD2" Residue "SH GLU 94": "OE1" <-> "OE2" Residue "SH TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH GLU 163": "OE1" <-> "OE2" Residue "SH ASP 184": "OD1" <-> "OD2" Residue "SI ASP 92": "OD1" <-> "OD2" Residue "SI TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ ASP 697": "OD1" <-> "OD2" Residue "SJ GLU 708": "OE1" <-> "OE2" Residue "SK TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 126": "OE1" <-> "OE2" Residue "SK GLU 127": "OE1" <-> "OE2" Residue "SK PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 168": "OE1" <-> "OE2" Residue "SK GLU 172": "OE1" <-> "OE2" Residue "SK GLU 219": "OE1" <-> "OE2" Residue "SL ASP 41": "OD1" <-> "OD2" Residue "SL TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL ASP 91": "OD1" <-> "OD2" Residue "SL ASP 153": "OD1" <-> "OD2" Residue "SL PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL ASP 196": "OD1" <-> "OD2" Residue "SM TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM GLU 270": "OE1" <-> "OE2" Residue "SM TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN GLU 59": "OE1" <-> "OE2" Residue "SN GLU 68": "OE1" <-> "OE2" Residue "SN ASP 100": "OD1" <-> "OD2" Residue "SN TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN GLU 139": "OE1" <-> "OE2" Residue "SN GLU 165": "OE1" <-> "OE2" Residue "SN TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO GLU 183": "OE1" <-> "OE2" Residue "SO GLU 279": "OE1" <-> "OE2" Residue "SR ASP 369": "OD1" <-> "OD2" Residue "SR GLU 379": "OE1" <-> "OE2" Residue "SR GLU 424": "OE1" <-> "OE2" Residue "SR ASP 427": "OD1" <-> "OD2" Residue "SR GLU 431": "OE1" <-> "OE2" Residue "SR GLU 457": "OE1" <-> "OE2" Residue "SS GLU 129": "OE1" <-> "OE2" Residue "SS TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS ASP 153": "OD1" <-> "OD2" Residue "SS PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST GLU 216": "OE1" <-> "OE2" Residue "ST GLU 237": "OE1" <-> "OE2" Residue "SV PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 72": "OE1" <-> "OE2" Residue "SV GLU 84": "OE1" <-> "OE2" Residue "SV ASP 91": "OD1" <-> "OD2" Residue "SW PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 401": "OE1" <-> "OE2" Residue "SW PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 570": "OE1" <-> "OE2" Residue "SW PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ ASP 44": "OD1" <-> "OD2" Residue "SZ ASP 96": "OD1" <-> "OD2" Residue "SZ GLU 124": "OE1" <-> "OE2" Residue "SZ ASP 129": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 101452 Number of models: 1 Model: "" Number of chains: 57 Chain: "L1" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3234 Classifications: {'RNA': 152} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 11, 'rna3p_pur': 61, 'rna3p_pyr': 66} Link IDs: {'rna2p': 24, 'rna3p': 127} 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: 32319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1507, 32319 Classifications: {'RNA': 1507} Modifications used: {'rna2p_pur': 152, 'rna2p_pyr': 93, 'rna3p_pur': 668, 'rna3p_pyr': 594} Link IDs: {'rna2p': 245, 'rna3p': 1261} Chain breaks: 29 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: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1438 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 162} Chain: "LE" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 702 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 101} 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: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 146 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} 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: "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: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1551 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} 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: "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: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 199, 1650 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Conformer: "B" Number of residues, atoms: 199, 1650 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} bond proxies already assigned to first conformer: 1672 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: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1308 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain breaks: 2 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: "SR" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 642 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain breaks: 1 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Unusual residues: {' MG': 46} Classifications: {'undetermined': 46} Link IDs: {None: 45} 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: "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: "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 56310 SG CYSLW 19 105.511 146.971 147.339 1.00 77.03 S ATOM 56338 SG CYSLW 22 106.119 144.092 149.852 1.00 68.65 S ATOM 56429 SG CYSLW 34 108.100 147.297 150.040 1.00 69.56 S ATOM 56448 SG CYSLW 37 108.714 144.959 147.192 1.00 66.02 S ATOM 59394 SG CYSNM 29 123.100 77.131 191.888 1.00 20.66 S ATOM 59510 SG CYSNM 44 129.017 75.581 190.354 1.00 21.79 S ATOM 59473 SG CYSNM 39 127.586 81.058 193.307 1.00 23.66 S ATOM 59294 SG CYSNM 17 125.728 79.931 186.990 1.00 24.15 S ATOM 95370 SG CYSSV 6 61.365 208.713 252.019 1.00 32.17 S ATOM 95399 SG CYSSV 9 58.234 207.022 251.353 1.00 37.16 S ATOM 95583 SG CYSSV 32 61.417 204.601 251.089 1.00 32.85 S ATOM 95613 SG CYSSV 36 60.624 207.233 248.671 1.00 32.37 S Time building chain proxies: 39.07, per 1000 atoms: 0.39 Number of scatterers: 101452 At special positions: 0 Unit cell: (217.616, 252.992, 321.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Fe 4 26.01 S 273 16.00 P 1730 15.00 Mg 54 11.99 O 23178 8.00 N 18927 7.00 C 57284 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: 35.85 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4NM 401 " pdb="FE1 SF4NM 401 " - pdb=" SG CYSNM 29 " pdb="FE2 SF4NM 401 " - pdb=" SG CYSNM 44 " pdb="FE3 SF4NM 401 " - pdb=" SG CYSNM 39 " pdb="FE4 SF4NM 401 " - pdb=" SG CYSNM 17 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 12 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15052 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: 293 helices and 69 sheets defined 49.4% alpha, 13.4% beta 562 base pairs and 831 stacking pairs defined. Time for finding SS restraints: 57.55 Creating SS restraints... Processing helix chain 'L6' and resid 27 through 47 removed outlier: 3.550A 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: 4.130A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.800A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.567A pdb=" N GLYL7 30 " --> pdb=" O GLNL7 26 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 56 removed outlier: 3.889A pdb=" N ALAL7 56 " --> pdb=" O LEUL7 52 " (cutoff:3.500A) Processing helix chain 'L7' and resid 75 through 89 removed outlier: 3.609A pdb=" N LEUL7 88 " --> pdb=" O VALL7 84 " (cutoff:3.500A) Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 3.588A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.839A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.433A 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: 3.537A pdb=" N THRL7 153 " --> pdb=" O TYRL7 149 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLUL7 186 " --> pdb=" O GLUL7 182 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILEL7 189 " --> pdb=" O VALL7 185 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.809A pdb=" N HISL7 199 " --> pdb=" O VALL7 195 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLYL7 200 " --> pdb=" O LEUL7 196 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.977A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.328A 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: 3.614A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.513A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 4.030A 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: 4.206A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 4.767A 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: 3.773A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.659A 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: 6.467A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.986A 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: 3.544A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 3.924A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 3.936A 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: 3.908A pdb=" N LEULA 112 " --> pdb=" O ASPLA 108 " (cutoff:3.500A) removed outlier: 5.560A 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: 4.146A pdb=" N VALLA 164 " --> pdb=" O PROLA 160 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALALA 165 " --> pdb=" O GLULA 161 " (cutoff:3.500A) Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.090A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.719A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.542A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 Processing helix chain 'LB' and resid 146 through 152 removed outlier: 4.267A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) Processing helix chain 'LB' and resid 7 through 12 removed outlier: 3.635A pdb=" N ASPLB 10 " --> pdb=" O HISLB 7 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARGLB 11 " --> pdb=" O ASNLB 8 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYSLB 12 " --> pdb=" O LYSLB 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 7 through 12' 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: 3.505A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.212A 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 133 through 138 removed outlier: 5.955A pdb=" N ARGLC 138 " --> pdb=" O ALALC 134 " (cutoff:3.500A) Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.323A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 4.881A 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: 3.743A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.283A 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: 3.584A pdb=" N SERLE 104 " --> pdb=" O LYSLE 100 " (cutoff:3.500A) removed outlier: 4.038A 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: 3.762A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLYLG 137 " --> pdb=" O ALALG 133 " (cutoff:3.500A) 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: 3.771A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.436A 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: 4.169A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.704A 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: 3.858A pdb=" N LYSLK 10 " --> pdb=" O ARGLK 6 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARGLK 12 " --> pdb=" O THRLK 8 " (cutoff:3.500A) Processing helix chain 'LK' and resid 60 through 67 removed outlier: 3.580A pdb=" N ASNLK 66 " --> pdb=" O HISLK 62 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLNLK 67 " --> pdb=" O LEULK 63 " (cutoff:3.500A) Processing helix chain 'LK' and resid 74 through 83 removed outlier: 4.635A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 93 Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.605A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 Processing helix chain 'LN' and resid 111 through 120 removed outlier: 4.354A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 3.879A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.454A 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: 3.881A 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 removed outlier: 3.538A pdb=" N ARGLN 200 " --> pdb=" O TRPLN 196 " (cutoff:3.500A) Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.986A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 244 through 251 removed outlier: 3.617A pdb=" N LYSLN 250 " --> pdb=" O ARGLN 246 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VALLN 251 " --> pdb=" O GLYLN 247 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 4.509A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.263A 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: 3.524A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 24 through 29' Processing helix chain 'LQ' and resid 43 through 48 Processing helix chain 'LQ' and resid 81 through 89 removed outlier: 3.891A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.708A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.544A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 removed outlier: 4.214A pdb=" N GLYLS 38 " --> pdb=" O ALALS 34 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.947A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (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: 5.579A 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: 3.745A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.480A 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: 4.158A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.230A 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: 3.589A pdb=" N GLYLU 49 " --> pdb=" O ARGLU 45 " (cutoff:3.500A) Processing helix chain 'LU' and resid 51 through 64 removed outlier: 3.710A pdb=" N VALLU 63 " --> pdb=" O GLULU 59 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SERLU 64 " --> pdb=" O LEULU 60 " (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 Processing helix chain 'LW' and resid 64 through 77 removed outlier: 3.928A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLYLW 77 " --> pdb=" O ARGLW 73 " (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 removed outlier: 3.624A pdb=" N LYSNE 269 " --> pdb=" O GLUNE 265 " (cutoff:3.500A) Processing helix chain 'NE' and resid 285 through 348 removed outlier: 3.721A pdb=" N LYSNE 309 " --> pdb=" O ARGNE 305 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARGNE 310 " --> pdb=" O ARGNE 306 " (cutoff:3.500A) Processing helix chain 'NE' and resid 351 through 357 Processing helix chain 'NG' and resid 127 through 145 removed outlier: 4.411A pdb=" N METNG 144 " --> pdb=" O LEUNG 140 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N METNG 145 " --> pdb=" O GLUNG 141 " (cutoff:3.500A) Processing helix chain 'NG' and resid 151 through 192 removed outlier: 5.501A pdb=" N GLUNG 157 " --> pdb=" O VALNG 153 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THRNG 158 " --> pdb=" O GLNNG 154 " (cutoff:3.500A) Processing helix chain 'NG' and resid 194 through 206 removed outlier: 3.557A pdb=" N VALNG 205 " --> pdb=" O LEUNG 201 " (cutoff:3.500A) removed outlier: 5.557A 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: 5.314A pdb=" N SERNM 49 " --> pdb=" O PRONM 45 " (cutoff:3.500A) Processing helix chain 'NM' and resid 67 through 72 removed outlier: 3.756A pdb=" N ALANM 71 " --> pdb=" O VALNM 67 " (cutoff:3.500A) removed outlier: 4.808A 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 removed outlier: 3.640A pdb=" N ILENM 99 " --> pdb=" O ASPNM 95 " (cutoff:3.500A) Processing helix chain 'NM' and resid 102 through 129 Processing helix chain 'NM' and resid 138 through 173 removed outlier: 6.142A pdb=" N LEUNM 158 " --> pdb=" O ILENM 154 " (cutoff:3.500A) removed outlier: 8.720A 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: 3.661A 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 removed outlier: 3.603A pdb=" N GLUNN 55 " --> pdb=" O ARGNN 51 " (cutoff:3.500A) Processing helix chain 'NN' and resid 69 through 81 removed outlier: 3.718A pdb=" N CYSNN 73 " --> pdb=" O SERNN 69 " (cutoff:3.500A) removed outlier: 3.736A 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: 5.024A pdb=" N ARGNN 126 " --> pdb=" O VALNN 122 " (cutoff:3.500A) Processing helix chain 'NN' and resid 131 through 137 removed outlier: 4.190A pdb=" N PHENN 135 " --> pdb=" O HISNN 131 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALANN 136 " --> pdb=" O GLUNN 132 " (cutoff:3.500A) removed outlier: 4.231A 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: 3.758A pdb=" N LYSNN 154 " --> pdb=" O GLYNN 150 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHENN 164 " --> pdb=" O PHENN 160 " (cutoff:3.500A) Proline residue: NN 165 - end of helix Processing helix chain 'NN' and resid 173 through 178 removed outlier: 3.985A pdb=" N ILENN 177 " --> pdb=" O ASNNN 173 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYSNN 178 " --> pdb=" O LEUNN 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'NN' and resid 173 through 178' Processing helix chain 'NN' and resid 246 through 251 removed outlier: 4.073A pdb=" N ILENN 250 " --> pdb=" O GLYNN 246 " (cutoff:3.500A) removed outlier: 5.018A 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 'NO' and resid 8 through 19 Processing helix chain 'NO' and resid 21 through 43 removed outlier: 3.605A pdb=" N ARGNO 42 " --> pdb=" O ALANO 38 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ALANO 43 " --> pdb=" O ARGNO 39 " (cutoff:3.500A) Processing helix chain 'NO' and resid 48 through 66 Processing helix chain 'NO' and resid 68 through 86 removed outlier: 3.765A pdb=" N GLUNO 74 " --> pdb=" O LEUNO 70 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VALNO 83 " --> pdb=" O ILENO 79 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N HISNO 84 " --> pdb=" O SERNO 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALANO 85 " --> pdb=" O GLNNO 81 " (cutoff:3.500A) removed outlier: 3.722A 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: 4.188A pdb=" N ASPNO 116 " --> pdb=" O ARGNO 112 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYSNO 117 " --> pdb=" O LEUNO 113 " (cutoff:3.500A) removed outlier: 3.868A 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: 4.703A pdb=" N LEUNO 174 " --> pdb=" O ILENO 170 " (cutoff:3.500A) removed outlier: 4.685A 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 Processing helix chain 'NO' and resid 206 through 244 removed outlier: 3.591A pdb=" N PHENO 218 " --> pdb=" O THRNO 214 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLUNO 219 " --> pdb=" O ARGNO 215 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRNO 220 " --> pdb=" O GLYNO 216 " (cutoff:3.500A) Proline residue: NO 226 - end of helix removed outlier: 3.531A pdb=" N LEUNO 232 " --> pdb=" O ALANO 228 " (cutoff:3.500A) Processing helix chain 'NO' and resid 299 through 313 removed outlier: 3.770A pdb=" N ARGNO 313 " --> pdb=" O GLUNO 309 " (cutoff:3.500A) Processing helix chain 'NO' and resid 317 through 337 removed outlier: 3.529A pdb=" N LYSNO 326 " --> pdb=" O LYSNO 322 " (cutoff:3.500A) Processing helix chain 'NO' and resid 345 through 353 removed outlier: 3.551A pdb=" N ARGNO 351 " --> pdb=" O LYSNO 347 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEUNO 352 " --> pdb=" O ALANO 348 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEUNO 353 " --> pdb=" O CYSNO 349 " (cutoff:3.500A) Processing helix chain 'NQ' and resid 1 through 9 removed outlier: 3.651A pdb=" N ARGNQ 7 " --> pdb=" O ALANQ 3 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRPNQ 8 " --> pdb=" O ALANQ 4 " (cutoff:3.500A) Processing helix chain 'NS' and resid 59 through 93 Processing helix chain 'NS' and resid 104 through 109 Processing helix chain 'NS' and resid 120 through 130 Processing helix chain 'NS' and resid 132 through 138 removed outlier: 3.509A 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: 5.234A pdb=" N LYSNS 233 " --> pdb=" O ARGNS 229 " (cutoff:3.500A) Processing helix chain 'NS' and resid 253 through 268 removed outlier: 3.803A pdb=" N LEUNS 266 " --> pdb=" O METNS 262 " (cutoff:3.500A) removed outlier: 4.040A 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: 4.465A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.078A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.507A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.811A 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: 3.661A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 155 through 161 removed outlier: 4.693A pdb=" N GLUSA 159 " --> pdb=" O GLUSA 155 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 155 through 161' Processing helix chain 'SA' and resid 163 through 175 Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.896A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.542A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.717A 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: 3.714A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 removed outlier: 3.516A pdb=" N ILESA 292 " --> pdb=" O ASPSA 288 " (cutoff:3.500A) Processing helix chain 'SA' and resid 296 through 303 removed outlier: 3.963A pdb=" N ARGSA 300 " --> pdb=" O PROSA 296 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.595A 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: 4.489A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SC' and resid 47 through 54 removed outlier: 3.526A pdb=" N VALSC 51 " --> pdb=" O ASNSC 47 " (cutoff:3.500A) Processing helix chain 'SC' and resid 58 through 74 removed outlier: 3.680A pdb=" N TYRSC 63 " --> pdb=" O ARGSC 59 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYSSC 70 " --> pdb=" O LYSSC 66 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYRSC 73 " --> pdb=" O TYRSC 69 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.891A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.442A 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: 3.769A 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: 5.233A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.413A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 15 through 79 removed outlier: 3.605A pdb=" N ILESD 30 " --> pdb=" O ALASD 26 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEUSD 33 " --> pdb=" O LYSSD 29 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARGSD 34 " --> pdb=" O ILESD 30 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYSSD 35 " --> pdb=" O LYSSD 31 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) Processing helix chain 'SD' and resid 102 through 113 Processing helix chain 'SD' and resid 126 through 137 removed outlier: 3.577A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.956A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.814A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.194A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 238 through 248 removed outlier: 4.720A pdb=" N ARGSD 242 " --> pdb=" O ASPSD 238 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.677A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.612A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.875A 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: 4.983A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.829A 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: 3.612A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 231 removed outlier: 4.953A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASNSE 227 " --> pdb=" O ARGSE 223 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASPSE 228 " --> pdb=" O THRSE 224 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARGSE 229 " --> pdb=" O ASNSE 225 " (cutoff:3.500A) Processing helix chain 'SE' and resid 232 through 237 removed outlier: 3.909A pdb=" N HISSE 236 " --> pdb=" O GLUSE 232 " (cutoff:3.500A) removed outlier: 5.413A 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 'SH' and resid 57 through 69 removed outlier: 3.719A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.599A 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: 5.912A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) Processing helix chain 'SH' and resid 143 through 151 removed outlier: 3.519A 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: 3.766A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.172A 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 164 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 3.519A 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: 5.092A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 3.974A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 4.905A 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: 4.446A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 664 through 677 Processing helix chain 'SJ' and resid 678 through 690 removed outlier: 3.635A pdb=" N PHESJ 689 " --> pdb=" O ILESJ 685 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASNSJ 690 " --> pdb=" O ASPSJ 686 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 702 through 713 removed outlier: 3.517A pdb=" N GLUSJ 709 " --> pdb=" O PHESJ 705 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLNSJ 711 " --> pdb=" O GLNSJ 707 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 720 through 731 Processing helix chain 'SK' and resid 12 through 17 removed outlier: 4.026A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.528A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLUSK 41 " --> pdb=" O VALSK 37 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 4.010A 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 134 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: 4.079A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.232A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SL' and resid 32 through 50 removed outlier: 3.553A pdb=" N ARGSL 50 " --> pdb=" O HISSL 46 " (cutoff:3.500A) 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: 3.760A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 166 removed outlier: 3.541A pdb=" N ARGSL 162 " --> pdb=" O ASPSL 158 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.572A 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: 4.025A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 removed outlier: 3.638A pdb=" N GLUSL 193 " --> pdb=" O ASNSL 189 " (cutoff:3.500A) Processing helix chain 'SL' and resid 222 through 241 removed outlier: 3.502A pdb=" N GLUSL 239 " --> pdb=" O LYSSL 235 " (cutoff:3.500A) Processing helix chain 'SL' and resid 244 through 249 removed outlier: 6.674A pdb=" N VALSL 248 " --> pdb=" O LYSSL 244 " (cutoff:3.500A) removed outlier: 6.369A 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: 3.532A pdb=" N LEUSM 40 " --> pdb=" O ARGSM 36 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 77 removed outlier: 3.994A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 4.009A 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: 3.620A 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: 3.629A pdb=" N ASPSM 133 " --> pdb=" O ASPSM 129 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) Processing helix chain 'SM' and resid 136 through 148 removed outlier: 4.100A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 3.948A 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: 3.560A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 3.793A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.638A pdb=" N LYSSM 315 " --> pdb=" O GLUSM 311 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.569A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLYSM 351 " --> pdb=" O ILESM 347 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.339A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.723A 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 541 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: 3.585A pdb=" N ALASN 167 " --> pdb=" O ARGSN 163 " (cutoff:3.500A) Processing helix chain 'SN' and resid 239 through 249 removed outlier: 3.678A pdb=" N TYRSN 243 " --> pdb=" O ALASN 239 " (cutoff:3.500A) Processing helix chain 'SN' and resid 261 through 267 removed outlier: 3.591A pdb=" N ASPSN 266 " --> pdb=" O ARGSN 262 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASPSN 267 " --> pdb=" O GLUSN 263 " (cutoff:3.500A) 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: 4.174A pdb=" N ILESO 103 " --> pdb=" O LYSSO 99 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASNSO 104 " --> pdb=" O LEUSO 100 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLUSO 105 " --> pdb=" O PHESO 101 " (cutoff:3.500A) Processing helix chain 'SO' and resid 169 through 176 removed outlier: 4.446A pdb=" N ASPSO 173 " --> pdb=" O ASPSO 169 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLUSO 174 " --> pdb=" O PROSO 170 " (cutoff:3.500A) removed outlier: 3.658A 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: 3.646A pdb=" N HISSO 265 " --> pdb=" O SERSO 261 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLUSO 293 " --> pdb=" O LEUSO 289 " (cutoff:3.500A) Processing helix chain 'SO' and resid 303 through 309 removed outlier: 4.950A pdb=" N PHESO 307 " --> pdb=" O THRSO 303 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VALSO 308 " --> pdb=" O ALASO 304 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N THRSO 309 " --> pdb=" O ASPSO 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'SO' and resid 303 through 309' Processing helix chain 'SO' and resid 328 through 333 removed outlier: 5.595A pdb=" N LYSSO 333 " --> pdb=" O LEUSO 329 " (cutoff:3.500A) Processing helix chain 'SO' and resid 337 through 353 removed outlier: 3.597A pdb=" N METSO 343 " --> pdb=" O ARGSO 339 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 418 removed outlier: 3.896A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASPSR 418 " --> pdb=" O GLNSR 414 " (cutoff:3.500A) Processing helix chain 'SR' and resid 437 through 442 removed outlier: 3.941A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.754A 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 Processing helix chain 'SS' and resid 140 through 146 removed outlier: 4.688A pdb=" N TYRSS 144 " --> pdb=" O PROSS 140 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASPSS 145 " --> pdb=" O LEUSS 141 " (cutoff:3.500A) removed outlier: 4.698A 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: 3.999A pdb=" N PHESS 246 " --> pdb=" O ASPSS 242 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILESS 247 " --> pdb=" O LYSSS 243 " (cutoff:3.500A) Proline residue: SS 248 - end of helix No H-bonds generated for 'chain 'SS' and resid 242 through 248' Processing helix chain 'SS' and resid 249 through 266 removed outlier: 3.585A pdb=" N LYSSS 253 " --> pdb=" O SERSS 249 " (cutoff:3.500A) Processing helix chain 'SS' and resid 317 through 322 removed outlier: 4.105A pdb=" N LEUSS 321 " --> pdb=" O PROSS 317 " (cutoff:3.500A) removed outlier: 5.701A 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: 5.414A pdb=" N GLUSS 334 " --> pdb=" O TRPSS 330 " (cutoff:3.500A) Processing helix chain 'SS' and resid 358 through 372 removed outlier: 3.950A pdb=" N TYRSS 371 " --> pdb=" O CYSSS 367 " (cutoff:3.500A) Processing helix chain 'ST' and resid 214 through 229 removed outlier: 3.620A pdb=" N VALST 227 " --> pdb=" O GLNST 223 " (cutoff:3.500A) removed outlier: 4.195A 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: 5.327A 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: 4.142A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.388A 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 135 removed outlier: 3.614A pdb=" N ARGSV 111 " --> pdb=" O PHESV 107 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.328A 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: 3.974A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILESV 131 " --> pdb=" O VALSV 127 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) Processing helix chain 'SW' and resid 178 through 184 removed outlier: 4.447A pdb=" N LEUSW 182 " --> pdb=" O SERSW 178 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYSSW 183 " --> pdb=" O PHESW 179 " (cutoff:3.500A) removed outlier: 5.134A 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: 3.515A pdb=" N LYSSW 192 " --> pdb=" O GLUSW 188 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALASW 193 " --> pdb=" O ASNSW 189 " (cutoff:3.500A) Processing helix chain 'SW' and resid 203 through 216 removed outlier: 4.695A 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: 3.598A pdb=" N PHESW 233 " --> pdb=" O LYSSW 229 " (cutoff:3.500A) Proline residue: SW 236 - end of helix Processing helix chain 'SW' and resid 260 through 276 removed outlier: 3.782A pdb=" N THRSW 276 " --> pdb=" O LYSSW 272 " (cutoff:3.500A) Processing helix chain 'SW' and resid 290 through 301 Processing helix chain 'SW' and resid 308 through 318 removed outlier: 3.546A pdb=" N LEUSW 312 " --> pdb=" O THRSW 308 " (cutoff:3.500A) Processing helix chain 'SW' and resid 334 through 342 removed outlier: 3.796A pdb=" N GLYSW 342 " --> pdb=" O ILESW 338 " (cutoff:3.500A) Processing helix chain 'SW' and resid 343 through 355 removed outlier: 3.531A 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: 5.140A pdb=" N PHESW 413 " --> pdb=" O SERSW 409 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEUSW 414 " --> pdb=" O GLUSW 410 " (cutoff:3.500A) Processing helix chain 'SW' and resid 434 through 449 removed outlier: 4.562A pdb=" N ASPSW 449 " --> pdb=" O LEUSW 445 " (cutoff:3.500A) Processing helix chain 'SW' and resid 460 through 475 removed outlier: 3.561A pdb=" N ASNSW 473 " --> pdb=" O PHESW 469 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASPSW 475 " --> pdb=" O PHESW 471 " (cutoff:3.500A) Processing helix chain 'SW' and resid 482 through 487 Processing helix chain 'SW' and resid 505 through 516 removed outlier: 3.555A pdb=" N GLYSW 514 " --> pdb=" O ILESW 510 " (cutoff:3.500A) Processing helix chain 'SW' and resid 534 through 545 removed outlier: 4.659A pdb=" N LEUSW 538 " --> pdb=" O GLUSW 534 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARGSW 539 " --> pdb=" O LEUSW 535 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SERSW 544 " --> pdb=" O TYRSW 540 " (cutoff:3.500A) Processing helix chain 'SW' and resid 561 through 573 removed outlier: 5.116A pdb=" N TYRSW 573 " --> pdb=" O ILESW 569 " (cutoff:3.500A) Processing helix chain 'SW' and resid 574 through 593 removed outlier: 3.598A pdb=" N HISSW 593 " --> pdb=" O ALASW 589 " (cutoff:3.500A) Processing helix chain 'SW' and resid 595 through 600 Processing helix chain 'SW' and resid 605 through 614 removed outlier: 3.753A pdb=" N LEUSW 611 " --> pdb=" O PROSW 607 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SERSW 612 " --> pdb=" O GLNSW 608 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHESW 613 " --> pdb=" O VALSW 609 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 6 through 12 removed outlier: 3.648A pdb=" N ARGSZ 10 " --> pdb=" O GLYSZ 6 " (cutoff:3.500A) removed outlier: 5.488A 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 104 removed outlier: 4.581A pdb=" N LEUSZ 94 " --> pdb=" O LYSSZ 90 " (cutoff:3.500A) Proline residue: SZ 104 - end of helix Processing helix chain 'SZ' and resid 112 through 126 Processing helix chain 'SZ' and resid 129 through 136 removed outlier: 3.511A pdb=" N ARGSZ 135 " --> pdb=" O LYSSZ 131 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 144 through 159 Processing helix chain 'SZ' and resid 160 through 178 Processing sheet with id= 1, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 2, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 3, first strand: chain 'L8' and resid 11 through 15 removed outlier: 4.559A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEUL8 37 " --> pdb=" O VALL8 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.158A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.821A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'LA' and resid 13 through 20 removed outlier: 7.529A pdb=" N LYSLA 13 " --> pdb=" O GLULA 152 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'LB' and resid 118 through 121 removed outlier: 3.596A pdb=" N ALALB 102 " --> pdb=" O LEULB 121 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYSLB 99 " --> pdb=" O LYSLB 78 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.516A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LC' and resid 89 through 98 removed outlier: 4.632A pdb=" N GLYLC 89 " --> pdb=" O SERLC 86 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.863A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LE' and resid 38 through 43 removed outlier: 4.092A pdb=" N ASPLE 38 " --> pdb=" O VALLE 64 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LG' and resid 36 through 39 removed outlier: 5.083A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASNLG 101 " --> pdb=" O VALLG 25 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILELG 105 " --> pdb=" O ALALG 29 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASPLG 59 " --> pdb=" O VALLG 81 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LG' and resid 87 through 90 removed outlier: 3.955A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LG' and resid 82 through 85 removed outlier: 3.516A pdb=" N ARGLG 83 " --> pdb=" O ALALG 102 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.683A 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 Processing sheet with id= 17, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.648A 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: 6.510A pdb=" N GLNLN 184 " --> pdb=" O THRLN 44 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.840A 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: 6.799A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HISLN 275 " --> pdb=" O THRLN 223 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.814A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (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: 4.328A 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: 5.860A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.350A 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: 6.063A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LT' and resid 6 through 10 Processing sheet with id= 29, first strand: chain 'LW' and resid 15 through 18 removed outlier: 8.505A pdb=" N THRLW 15 " --> pdb=" O HISLW 28 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HISLW 28 " --> pdb=" O THRLW 15 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THRLW 17 " --> pdb=" O ALALW 26 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'NM' and resid 19 through 23 removed outlier: 7.262A pdb=" N PHENM 19 " --> pdb=" O ARGNM 30 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THRNM 23 " --> pdb=" O GLNNM 26 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLNNM 26 " --> pdb=" O THRNM 23 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'NM' and resid 51 through 57 Processing sheet with id= 32, first strand: chain 'NN' and resid 30 through 36 removed outlier: 4.788A pdb=" N LYSNN 90 " --> pdb=" O ARGNN 36 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VALNN 95 " --> pdb=" O VALNN 112 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THRNN 109 " --> pdb=" O ILENN 284 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THRNN 280 " --> pdb=" O LYSNN 113 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEUNN 283 " --> pdb=" O GLNNN 190 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N GLNNN 190 " --> pdb=" O LEUNN 283 " (cutoff:3.500A) removed outlier: 3.809A 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: 3.626A pdb=" N LYSNN 285 " --> pdb=" O THRNN 109 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'NN' and resid 196 through 203 removed outlier: 7.171A pdb=" N HISNN 196 " --> pdb=" O ILENN 275 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'NQ' and resid 28 through 34 removed outlier: 7.428A pdb=" N HISNQ 10 " --> pdb=" O SERNQ 320 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.975A pdb=" N ALANQ 47 " --> pdb=" O GLYNQ 61 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLNNQ 57 " --> pdb=" O GLYNQ 51 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N THRNQ 56 " --> pdb=" O THRNQ 72 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THRNQ 66 " --> pdb=" O CYSNQ 62 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HISNQ 69 " --> pdb=" O GLNNQ 78 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILENQ 76 " --> pdb=" O SERNQ 71 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'NQ' and resid 92 through 95 removed outlier: 4.019A pdb=" N GLYNQ 92 " --> pdb=" O CYSNQ 103 " (cutoff:3.500A) removed outlier: 6.856A 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: 5.703A pdb=" N VALNQ 145 " --> pdb=" O ASPNQ 139 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N HISNQ 144 " --> pdb=" O LEUNQ 160 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'NQ' and resid 188 through 192 removed outlier: 3.792A pdb=" N ASPNQ 188 " --> pdb=" O CYSNQ 201 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYSNQ 197 " --> pdb=" O LEUNQ 192 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HISNQ 205 " --> pdb=" O TYRNQ 225 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYRNQ 225 " --> pdb=" O HISNQ 205 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'NQ' and resid 232 through 236 removed outlier: 5.654A pdb=" N SERNQ 241 " --> pdb=" O THRNQ 236 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEUNQ 251 " --> pdb=" O LEUNQ 265 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYNQ 263 " --> pdb=" O GLUNQ 253 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'NQ' and resid 273 through 278 removed outlier: 5.393A pdb=" N LEUNQ 283 " --> pdb=" O HISNQ 278 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLYNQ 288 " --> pdb=" O VALNQ 292 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VALNQ 292 " --> pdb=" O GLYNQ 288 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'NQ' and resid 65 through 69 removed outlier: 5.707A pdb=" N ARGNQ 65 " --> pdb=" O CYSNQ 83 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLYNQ 79 " --> pdb=" O HISNQ 69 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'NS' and resid 169 through 173 removed outlier: 4.805A pdb=" N THRNS 148 " --> pdb=" O TYRNS 173 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLUNS 200 " --> pdb=" O SERNS 149 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLYNS 207 " --> pdb=" O ASNNS 199 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASNNS 206 " --> pdb=" O METNS 223 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N METNS 223 " --> pdb=" O ASNNS 206 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HISNS 220 " --> pdb=" O ARGNS 317 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHENS 312 " --> pdb=" O PHENS 290 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'SA' and resid 6 through 10 removed outlier: 4.854A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.541A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SC' and resid 147 through 153 removed outlier: 4.468A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLYSC 177 " --> pdb=" O PROSC 185 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.288A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEUSD 213 " --> pdb=" O PHESD 118 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'SD' and resid 158 through 161 removed outlier: 6.424A 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 'SH' and resid 72 through 76 removed outlier: 3.684A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SI' and resid 147 through 151 removed outlier: 4.204A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 52, 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= 53, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 54, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 55, first strand: chain 'SK' and resid 114 through 117 removed outlier: 3.521A pdb=" N PHESK 138 " --> pdb=" O ALASK 115 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VALSK 117 " --> pdb=" O PHESK 138 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 57, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.290A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEUSL 78 " --> pdb=" O ILESL 205 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SL' and resid 127 through 130 Processing sheet with id= 59, first strand: chain 'SL' and resid 210 through 216 removed outlier: 6.127A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEUSL 251 " --> pdb=" O ILESL 263 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'SM' and resid 179 through 184 Processing sheet with id= 61, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 62, first strand: chain 'SO' and resid 87 through 91 removed outlier: 4.194A pdb=" N ASPSO 91 " --> pdb=" O ILESO 64 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SERSO 66 " --> pdb=" O ASPSO 91 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALASO 120 " --> pdb=" O SERSO 67 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEUSO 126 " --> pdb=" O VALSO 143 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYSSO 140 " --> pdb=" O ILESO 241 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALASO 228 " --> pdb=" O ILESO 223 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASNSO 219 " --> pdb=" O ILESO 232 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHESO 217 " --> pdb=" O PROSO 234 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHESO 236 " --> pdb=" O ILESO 215 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILESO 215 " --> pdb=" O PHESO 236 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASPSO 203 " --> pdb=" O ILESO 222 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SO' and resid 137 through 140 Processing sheet with id= 64, first strand: chain 'SS' and resid 183 through 188 removed outlier: 6.348A pdb=" N ARGSS 183 " --> pdb=" O LEUSS 196 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARGSS 192 " --> pdb=" O ASPSS 187 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SV' and resid 3 through 6 removed outlier: 3.640A pdb=" N GLUSV 4 " --> pdb=" O ILESV 13 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLYSV 11 " --> pdb=" O CYSSV 6 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'SV' and resid 18 through 23 removed outlier: 4.117A pdb=" N LYSSV 27 " --> pdb=" O ARGSV 23 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SW' and resid 281 through 285 removed outlier: 3.769A pdb=" N LEUSW 219 " --> pdb=" O THRSW 360 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALASW 223 " --> pdb=" O SERSW 364 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VALSW 388 " --> pdb=" O ALASW 222 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SW' and resid 427 through 432 Processing sheet with id= 69, first strand: chain 'SW' and resid 452 through 455 2999 hydrogen bonds defined for protein. 8930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1499 hydrogen bonds 2636 hydrogen bond angles 0 basepair planarities 562 basepair parallelities 831 stacking parallelities Total time for adding SS restraints: 69.52 Time building geometry restraints manager: 39.01 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: 42126 1.41 - 1.63: 64412 1.63 - 1.86: 429 1.86 - 2.08: 0 2.08 - 2.31: 12 Bond restraints: 106979 Sorted by residual: bond pdb=" N CYSSV 32 " pdb=" CA CYSSV 32 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 8.85e+00 bond pdb=" N PHESV 31 " pdb=" CA PHESV 31 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.24e-02 6.50e+03 8.59e+00 bond pdb=" CB PROSW 320 " pdb=" CG PROSW 320 " ideal model delta sigma weight residual 1.492 1.623 -0.131 5.00e-02 4.00e+02 6.86e+00 bond pdb=" CE1 HICLN 245 " pdb=" NE2 HICLN 245 " ideal model delta sigma weight residual 1.347 1.398 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" N ARGNE 349 " pdb=" CA ARGNE 349 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.25e-02 6.40e+03 5.28e+00 ... (remaining 106974 not shown) Histogram of bond angle deviations from ideal: 71.47 - 84.01: 12 84.01 - 96.56: 0 96.56 - 109.10: 25508 109.10 - 121.64: 103036 121.64 - 134.18: 24006 Bond angle restraints: 152562 Sorted by residual: angle pdb=" CA GLNLS 30 " pdb=" CB GLNLS 30 " pdb=" CG GLNLS 30 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" N ILESK 58 " pdb=" CA ILESK 58 " pdb=" C ILESK 58 " ideal model delta sigma weight residual 106.21 110.40 -4.19 1.07e+00 8.73e-01 1.53e+01 angle pdb=" CA PROSW 320 " pdb=" N PROSW 320 " pdb=" CD PROSW 320 " ideal model delta sigma weight residual 112.00 117.41 -5.41 1.40e+00 5.10e-01 1.49e+01 angle pdb=" N CYSSV 32 " pdb=" CA CYSSV 32 " pdb=" C CYSSV 32 " ideal model delta sigma weight residual 111.36 115.42 -4.06 1.09e+00 8.42e-01 1.39e+01 angle pdb=" CA TRPSR 417 " pdb=" CB TRPSR 417 " pdb=" CG TRPSR 417 " ideal model delta sigma weight residual 113.60 120.62 -7.02 1.90e+00 2.77e-01 1.36e+01 ... (remaining 152557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 63151 35.93 - 71.86: 4380 71.86 - 107.79: 606 107.79 - 143.72: 5 143.72 - 179.65: 11 Dihedral angle restraints: 68153 sinusoidal: 44969 harmonic: 23184 Sorted by residual: dihedral pdb=" O4' UL3 45 " pdb=" C1' UL3 45 " pdb=" N1 UL3 45 " pdb=" C2 UL3 45 " ideal model delta sinusoidal sigma weight residual 200.00 20.35 179.65 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' UL31381 " pdb=" C1' UL31381 " pdb=" N1 UL31381 " pdb=" C2 UL31381 " ideal model delta sinusoidal sigma weight residual 200.00 20.41 179.59 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' CL35008 " pdb=" C1' CL35008 " pdb=" N1 CL35008 " pdb=" C2 CL35008 " ideal model delta sinusoidal sigma weight residual -160.00 13.40 -173.40 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 68150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 17108 0.073 - 0.147: 1057 0.147 - 0.220: 35 0.220 - 0.294: 1 0.294 - 0.367: 2 Chirality restraints: 18203 Sorted by residual: 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 -10.19 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA THRLC 174 " pdb=" N THRLC 174 " pdb=" C THRLC 174 " pdb=" CB THRLC 174 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb="FE2 SF4NM 401 " pdb=" S1 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 1.86e+00 ... (remaining 18200 not shown) Planarity restraints: 12999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRPSR 417 " 0.043 2.00e-02 2.50e+03 3.06e-02 2.34e+01 pdb=" CG TRPSR 417 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TRPSR 417 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRPSR 417 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRPSR 417 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRPSR 417 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRPSR 417 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRPSR 417 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRPSR 417 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRPSR 417 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GL1 39 " -0.050 2.00e-02 2.50e+03 2.06e-02 1.27e+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 " 0.001 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 " -0.015 2.00e-02 2.50e+03 pdb=" N1 GL1 39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GL1 39 " 0.002 2.00e-02 2.50e+03 pdb=" N2 GL1 39 " 0.004 2.00e-02 2.50e+03 pdb=" N3 GL1 39 " 0.010 2.00e-02 2.50e+03 pdb=" C4 GL1 39 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GL33895 " -0.044 2.00e-02 2.50e+03 1.82e-02 9.92e+00 pdb=" N9 GL33895 " 0.038 2.00e-02 2.50e+03 pdb=" C8 GL33895 " 0.012 2.00e-02 2.50e+03 pdb=" N7 GL33895 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GL33895 " 0.009 2.00e-02 2.50e+03 pdb=" C6 GL33895 " -0.007 2.00e-02 2.50e+03 pdb=" O6 GL33895 " -0.014 2.00e-02 2.50e+03 pdb=" N1 GL33895 " -0.006 2.00e-02 2.50e+03 pdb=" C2 GL33895 " 0.001 2.00e-02 2.50e+03 pdb=" N2 GL33895 " 0.004 2.00e-02 2.50e+03 pdb=" N3 GL33895 " 0.007 2.00e-02 2.50e+03 pdb=" C4 GL33895 " 0.003 2.00e-02 2.50e+03 ... (remaining 12996 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 22 2.14 - 2.83: 28324 2.83 - 3.52: 133466 3.52 - 4.21: 274713 4.21 - 4.90: 422258 Nonbonded interactions: 858783 Sorted by model distance: nonbonded pdb=" OXT AMENM 1 " pdb=" CA GLNNM 2 " model vdw 1.446 2.776 nonbonded pdb=" O6 GL3 356 " pdb="MG MGL35113 " model vdw 1.920 2.170 nonbonded pdb=" OG SERSA 295 " pdb=" OE1 GLUSA 297 " model vdw 1.958 2.440 nonbonded pdb=" OP1 AL32279 " pdb="MG MGL35120 " model vdw 2.031 2.170 nonbonded pdb=" OP1 AL3 306 " pdb=" OH TYRLU 53 " model vdw 2.037 2.440 ... (remaining 858778 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: 6.280 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: 0.080 Extract box with map and model: 24.490 Check model and map are aligned: 1.210 Set scattering table: 0.680 Process input model: 306.680 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 353.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 : 0.005 0.131 106979 Z= 0.298 Angle : 0.606 7.990 152562 Z= 0.320 Chirality : 0.038 0.367 18203 Planarity : 0.005 0.090 12999 Dihedral : 20.184 179.655 53101 Min Nonbonded Distance : 1.446 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 1.46 (0.09), residues: 7811 helix: 1.94 (0.09), residues: 3276 sheet: 0.44 (0.15), residues: 1097 loop : 0.31 (0.10), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRPSR 417 HIS 0.011 0.002 HISSK 118 PHE 0.023 0.002 PHESO 65 TYR 0.044 0.002 TYRLC 84 ARG 0.020 0.001 ARGLC 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 954 time to evaluate : 6.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 180 GLN cc_start: 0.8078 (tp40) cc_final: 0.7868 (mm-40) REVERT: L8 39 ASP cc_start: 0.7989 (t0) cc_final: 0.7734 (t0) REVERT: L8 48 GLN cc_start: 0.8254 (pt0) cc_final: 0.7685 (pt0) REVERT: LA 163 GLU cc_start: 0.5972 (tt0) cc_final: 0.5664 (tt0) REVERT: LG 135 ASN cc_start: 0.7547 (m-40) cc_final: 0.7219 (m110) REVERT: LH 25 LYS cc_start: 0.8823 (tttp) cc_final: 0.8570 (ttmt) REVERT: LS 73 TYR cc_start: 0.7968 (m-80) cc_final: 0.7594 (m-80) REVERT: NE 328 ASN cc_start: 0.7875 (m110) cc_final: 0.7614 (m110) REVERT: NG 141 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6495 (mt-10) REVERT: SC 249 ASP cc_start: 0.7755 (m-30) cc_final: 0.7554 (m-30) REVERT: SM 218 ARG cc_start: 0.7562 (mtt180) cc_final: 0.7328 (mtt180) REVERT: SO 300 HIS cc_start: 0.7963 (t70) cc_final: 0.7718 (t-90) REVERT: SR 450 LEU cc_start: 0.8378 (tp) cc_final: 0.7927 (tm) REVERT: SV 93 MET cc_start: 0.8494 (ttp) cc_final: 0.8227 (ttm) REVERT: SZ 10 ARG cc_start: 0.6513 (mtt180) cc_final: 0.6152 (mtt-85) outliers start: 0 outliers final: 4 residues processed: 954 average time/residue: 1.8077 time to fit residues: 2354.0608 Evaluate side-chains 740 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 736 time to evaluate : 6.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LG residue 30 ASP Chi-restraints excluded: chain LH residue 22 LEU Chi-restraints excluded: chain LT residue 110 ILE Chi-restraints excluded: chain SV residue 19 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 946 random chunks: chunk 798 optimal weight: 4.9990 chunk 717 optimal weight: 5.9990 chunk 397 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 483 optimal weight: 4.9990 chunk 383 optimal weight: 2.9990 chunk 741 optimal weight: 0.0870 chunk 286 optimal weight: 4.9990 chunk 450 optimal weight: 4.9990 chunk 551 optimal weight: 8.9990 chunk 859 optimal weight: 0.9980 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 90 HIS L7 143 HIS L8 66 HIS L8 83 ASN ** LB 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 96 HIS LK 62 HIS LS 68 ASN LU 26 HIS NE 235 ASN NM 160 ASN NM 172 GLN ** NN 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NS 171 HIS NS 257 HIS NS 277 GLN NS 335 HIS SA 21 ASN SA 60 HIS SA 245 HIS SC 190 HIS SC 211 HIS SC 227 HIS SC 250 GLN SC 266 GLN SC 268 GLN SE 64 GLN SE 85 GLN SE 236 HIS SI 71 GLN ** SI 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 219 HIS SI 249 GLN SJ 687 ASN SJ 711 GLN SJ 712 HIS SJ 716 GLN SJ 726 HIS SK 83 HIS SL 30 GLN SL 46 HIS SL 112 GLN SL 218 HIS SM 170 HIS SM 243 ASN SM 375 HIS SS 333 GLN ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 525 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 106979 Z= 0.311 Angle : 0.581 14.560 152562 Z= 0.302 Chirality : 0.039 0.251 18203 Planarity : 0.005 0.059 12999 Dihedral : 21.768 179.788 36391 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.83 % Allowed : 7.21 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 1.57 (0.09), residues: 7811 helix: 2.18 (0.09), residues: 3345 sheet: 0.29 (0.15), residues: 1098 loop : 0.23 (0.10), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRPSR 417 HIS 0.009 0.001 HISSE 195 PHE 0.026 0.002 PHESW 233 TYR 0.023 0.002 TYRLG 38 ARG 0.009 0.001 ARGNE 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 781 time to evaluate : 6.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L8 48 GLN cc_start: 0.8173 (pt0) cc_final: 0.7815 (pt0) REVERT: LC 99 ASP cc_start: 0.6876 (m-30) cc_final: 0.5950 (m-30) REVERT: LC 108 GLN cc_start: 0.7802 (mt0) cc_final: 0.7540 (mt0) REVERT: LE 106 LEU cc_start: 0.6830 (mt) cc_final: 0.6626 (mm) REVERT: LE 152 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7424 (mm-30) REVERT: LS 73 TYR cc_start: 0.7876 (m-80) cc_final: 0.7631 (m-80) REVERT: LW 80 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6801 (mt-10) REVERT: NE 251 ASP cc_start: 0.7623 (m-30) cc_final: 0.7329 (m-30) REVERT: NE 328 ASN cc_start: 0.7763 (m110) cc_final: 0.7467 (m110) REVERT: SC 250 GLN cc_start: 0.8314 (tp40) cc_final: 0.8063 (tp-100) REVERT: SC 254 ASP cc_start: 0.7075 (m-30) cc_final: 0.6584 (m-30) REVERT: SD 71 MET cc_start: 0.8098 (mmp) cc_final: 0.7700 (mmp) REVERT: SD 220 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.6263 (mtp) REVERT: SJ 726 HIS cc_start: 0.8121 (OUTLIER) cc_final: 0.7561 (t-170) REVERT: SL 101 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: SL 244 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7617 (mttm) REVERT: SM 218 ARG cc_start: 0.7282 (mtt180) cc_final: 0.7049 (mtt180) REVERT: SN 100 ASP cc_start: 0.6312 (t0) cc_final: 0.6099 (t0) REVERT: SN 101 ASP cc_start: 0.7125 (p0) cc_final: 0.6910 (p0) REVERT: SN 147 MET cc_start: 0.8578 (mmm) cc_final: 0.8356 (mmm) REVERT: SO 300 HIS cc_start: 0.8080 (t70) cc_final: 0.7816 (t-90) REVERT: SS 184 THR cc_start: 0.8180 (m) cc_final: 0.7961 (m) REVERT: SV 111 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7272 (ttp-110) outliers start: 125 outliers final: 51 residues processed: 835 average time/residue: 1.8508 time to fit residues: 2113.4765 Evaluate side-chains 763 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 708 time to evaluate : 6.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 193 THR Chi-restraints excluded: chain L8 residue 69 HIS Chi-restraints excluded: chain L8 residue 75 GLN Chi-restraints excluded: chain L9 residue 189 ARG Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 109 VAL Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LC residue 87 ARG Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LE residue 143 THR Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LG residue 111 GLU Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 107 THR Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 258 HIS Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LS residue 23 ASP Chi-restraints excluded: chain LU residue 9 VAL Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 228 LEU Chi-restraints excluded: chain NE residue 311 THR Chi-restraints excluded: chain NG residue 159 GLU Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NS residue 85 LEU Chi-restraints excluded: chain NS residue 274 ILE Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 189 MET Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SD residue 14 VAL Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SJ residue 714 ILE Chi-restraints excluded: chain SJ residue 726 HIS Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 46 ILE Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SN residue 263 GLU Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 242 ASP Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SZ residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 946 random chunks: chunk 477 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 714 optimal weight: 2.9990 chunk 584 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 860 optimal weight: 0.7980 chunk 929 optimal weight: 3.9990 chunk 766 optimal weight: 1.9990 chunk 853 optimal weight: 8.9990 chunk 293 optimal weight: 1.9990 chunk 690 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L8 83 ASN L9 145 ASN ** LB 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 68 ASN NG 175 ASN NM 160 ASN NM 172 GLN NN 68 ASN NN 134 GLN NQ 10 HIS NS 59 ASN NS 220 HIS SE 64 GLN SH 60 GLN SI 71 GLN SI 249 GLN SJ 687 ASN SJ 726 HIS SL 30 GLN SL 61 ASN SL 112 GLN SL 189 ASN ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SS 333 GLN ST 213 GLN ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 171 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 106979 Z= 0.176 Angle : 0.496 13.964 152562 Z= 0.257 Chirality : 0.035 0.232 18203 Planarity : 0.004 0.049 12999 Dihedral : 21.682 179.263 36382 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.81 % Allowed : 8.97 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 1.72 (0.09), residues: 7811 helix: 2.38 (0.09), residues: 3360 sheet: 0.22 (0.15), residues: 1106 loop : 0.26 (0.10), residues: 3345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRPSR 417 HIS 0.011 0.001 HISSJ 726 PHE 0.026 0.001 PHEL8 17 TYR 0.022 0.001 TYRSW 324 ARG 0.007 0.000 ARGNG 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 762 time to evaluate : 6.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 87 MET cc_start: 0.8624 (mtt) cc_final: 0.8410 (mtt) REVERT: L7 96 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7700 (mm-40) REVERT: LC 99 ASP cc_start: 0.6988 (m-30) cc_final: 0.5598 (m-30) REVERT: LC 126 ILE cc_start: 0.8666 (pt) cc_final: 0.8453 (pt) REVERT: LE 102 ARG cc_start: 0.7503 (mmm160) cc_final: 0.7261 (mtp85) REVERT: LS 73 TYR cc_start: 0.7871 (m-80) cc_final: 0.7618 (m-80) REVERT: LU 46 GLU cc_start: 0.7360 (tt0) cc_final: 0.7094 (tt0) REVERT: LW 80 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6919 (mt-10) REVERT: NE 251 ASP cc_start: 0.7556 (m-30) cc_final: 0.7314 (m-30) REVERT: NE 328 ASN cc_start: 0.7823 (m110) cc_final: 0.7496 (m110) REVERT: NM 4 ASP cc_start: 0.6800 (m-30) cc_final: 0.6598 (m-30) REVERT: NM 27 SER cc_start: 0.8211 (p) cc_final: 0.7997 (p) REVERT: NS 72 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6668 (mp10) REVERT: SC 250 GLN cc_start: 0.8239 (tp40) cc_final: 0.7861 (tp-100) REVERT: SC 254 ASP cc_start: 0.7165 (m-30) cc_final: 0.6702 (m-30) REVERT: SD 43 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6686 (ptp-170) REVERT: SL 101 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: SL 244 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7471 (mttm) REVERT: SN 165 GLU cc_start: 0.8325 (tp30) cc_final: 0.7877 (tp30) REVERT: SN 265 TYR cc_start: 0.8180 (t80) cc_final: 0.7946 (t80) REVERT: SR 421 ASN cc_start: 0.7987 (m-40) cc_final: 0.7736 (m-40) REVERT: SS 141 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7317 (tt) REVERT: SS 184 THR cc_start: 0.7802 (m) cc_final: 0.7569 (m) REVERT: SS 298 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.5040 (pmm) REVERT: SW 202 MET cc_start: 0.7277 (ptp) cc_final: 0.6879 (ptp) REVERT: SW 213 LEU cc_start: 0.8155 (mp) cc_final: 0.7918 (mp) outliers start: 124 outliers final: 57 residues processed: 825 average time/residue: 1.8753 time to fit residues: 2107.8322 Evaluate side-chains 775 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 712 time to evaluate : 6.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L7 residue 39 GLU Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 185 VAL Chi-restraints excluded: chain L8 residue 69 HIS Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 109 VAL Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LG residue 28 CYS Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LG residue 111 GLU Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LN residue 258 HIS Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LU residue 9 VAL Chi-restraints excluded: chain NE residue 228 LEU Chi-restraints excluded: chain NE residue 250 LEU Chi-restraints excluded: chain NE residue 260 LYS Chi-restraints excluded: chain NE residue 350 ILE Chi-restraints excluded: chain NN residue 53 VAL Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 272 LEU Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NS residue 72 GLN Chi-restraints excluded: chain NS residue 85 LEU Chi-restraints excluded: chain NS residue 246 ILE Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SA residue 189 MET Chi-restraints excluded: chain SD residue 14 VAL Chi-restraints excluded: chain SD residue 43 ARG Chi-restraints excluded: chain SE residue 106 THR Chi-restraints excluded: chain SE residue 210 GLU Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SJ residue 673 VAL Chi-restraints excluded: chain SJ residue 707 GLN Chi-restraints excluded: chain SJ residue 714 ILE Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 102 SER Chi-restraints excluded: chain SL residue 80 VAL Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SN residue 267 ASP Chi-restraints excluded: chain SR residue 449 LYS Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 242 ASP Chi-restraints excluded: chain SS residue 298 MET Chi-restraints excluded: chain SV residue 19 MET Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 946 random chunks: chunk 850 optimal weight: 6.9990 chunk 647 optimal weight: 2.9990 chunk 446 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 410 optimal weight: 10.0000 chunk 577 optimal weight: 7.9990 chunk 863 optimal weight: 7.9990 chunk 914 optimal weight: 5.9990 chunk 451 optimal weight: 5.9990 chunk 818 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L8 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 83 ASN L8 125 ASN ** LA 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 36 ASN NG 175 ASN NM 160 ASN NN 134 GLN NN 298 HIS SA 21 ASN SA 119 GLN SE 64 GLN SI 71 GLN SI 249 GLN SJ 687 ASN SJ 726 HIS SL 30 GLN SL 61 ASN SR 436 HIS ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ST 213 GLN SV 24 ASN ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 189 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 106979 Z= 0.344 Angle : 0.571 13.869 152562 Z= 0.294 Chirality : 0.039 0.253 18203 Planarity : 0.005 0.052 12999 Dihedral : 21.639 179.773 36382 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.37 % Allowed : 10.50 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 1.49 (0.09), residues: 7811 helix: 2.23 (0.09), residues: 3352 sheet: 0.12 (0.15), residues: 1098 loop : 0.10 (0.10), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPSR 417 HIS 0.010 0.001 HISSH 51 PHE 0.028 0.002 PHEL8 17 TYR 0.024 0.002 TYRSW 324 ARG 0.007 0.001 ARGSO 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 737 time to evaluate : 6.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LC 28 TYR cc_start: 0.8115 (m-80) cc_final: 0.7723 (m-80) REVERT: LC 99 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6515 (m-30) REVERT: LC 126 ILE cc_start: 0.8612 (pt) cc_final: 0.8366 (pt) REVERT: LE 102 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7474 (mtp85) REVERT: LN 153 MET cc_start: 0.8516 (mtp) cc_final: 0.8301 (mtp) REVERT: LQ 133 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: LS 72 PHE cc_start: 0.8518 (t80) cc_final: 0.8156 (t80) REVERT: LS 78 TYR cc_start: 0.6557 (OUTLIER) cc_final: 0.5640 (t80) REVERT: LW 80 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6861 (mt-10) REVERT: NG 209 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6340 (m-30) REVERT: NS 72 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: SC 250 GLN cc_start: 0.8259 (tp40) cc_final: 0.7903 (tp-100) REVERT: SC 254 ASP cc_start: 0.7140 (m-30) cc_final: 0.6730 (m-30) REVERT: SD 71 MET cc_start: 0.8044 (mmp) cc_final: 0.7690 (mmp) REVERT: SJ 700 GLU cc_start: 0.7469 (tt0) cc_final: 0.7230 (tt0) REVERT: SJ 708 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: SL 101 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: SN 100 ASP cc_start: 0.6147 (t0) cc_final: 0.5569 (t0) REVERT: SN 101 ASP cc_start: 0.7287 (p0) cc_final: 0.7049 (p0) REVERT: SN 140 MET cc_start: 0.6100 (mmm) cc_final: 0.5470 (mmm) REVERT: SN 165 GLU cc_start: 0.8353 (tp30) cc_final: 0.7914 (tp30) REVERT: SR 421 ASN cc_start: 0.7947 (m-40) cc_final: 0.7731 (m-40) REVERT: SS 141 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7552 (tm) REVERT: SS 184 THR cc_start: 0.7794 (m) cc_final: 0.7568 (m) REVERT: SS 298 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.5065 (pmm) REVERT: SW 202 MET cc_start: 0.7322 (ptp) cc_final: 0.6968 (ptp) outliers start: 162 outliers final: 91 residues processed: 821 average time/residue: 1.8258 time to fit residues: 2052.1073 Evaluate side-chains 808 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 708 time to evaluate : 6.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 39 GLU Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 185 VAL Chi-restraints excluded: chain L7 residue 193 THR Chi-restraints excluded: chain L8 residue 69 HIS Chi-restraints excluded: chain L8 residue 75 GLN Chi-restraints excluded: chain L8 residue 104 MET Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 109 VAL Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 30 MET Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LC residue 87 ARG Chi-restraints excluded: chain LC residue 99 ASP Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LE residue 143 THR Chi-restraints excluded: chain LG residue 28 CYS Chi-restraints excluded: chain LG residue 59 ASP Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LG residue 111 GLU Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 107 THR Chi-restraints excluded: chain LN residue 160 ILE Chi-restraints excluded: chain LN residue 258 HIS Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 78 TYR Chi-restraints excluded: chain LS residue 88 THR Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LU residue 9 VAL Chi-restraints excluded: chain NE residue 228 LEU Chi-restraints excluded: chain NE residue 260 LYS Chi-restraints excluded: chain NE residue 311 THR Chi-restraints excluded: chain NG residue 144 MET Chi-restraints excluded: chain NG residue 209 ASP Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NN residue 19 LEU Chi-restraints excluded: chain NN residue 53 VAL Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 199 ILE Chi-restraints excluded: chain NN residue 288 GLU Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NQ residue 52 THR Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NS residue 72 GLN Chi-restraints excluded: chain NS residue 85 LEU Chi-restraints excluded: chain NS residue 246 ILE Chi-restraints excluded: chain NS residue 262 MET Chi-restraints excluded: chain NS residue 334 VAL Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SC residue 235 THR Chi-restraints excluded: chain SD residue 14 VAL Chi-restraints excluded: chain SD residue 43 ARG Chi-restraints excluded: chain SE residue 91 THR Chi-restraints excluded: chain SE residue 106 THR Chi-restraints excluded: chain SH residue 154 THR Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SJ residue 707 GLN Chi-restraints excluded: chain SJ residue 708 GLU Chi-restraints excluded: chain SJ residue 714 ILE Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 102 SER Chi-restraints excluded: chain SK residue 117 VAL Chi-restraints excluded: chain SK residue 137 VAL Chi-restraints excluded: chain SK residue 177 LEU Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 80 VAL Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SM residue 388 ILE Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SO residue 289 LEU Chi-restraints excluded: chain SR residue 450 LEU Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 242 ASP Chi-restraints excluded: chain SS residue 298 MET Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SV residue 19 MET Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 946 random chunks: chunk 761 optimal weight: 2.9990 chunk 519 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 680 optimal weight: 0.6980 chunk 377 optimal weight: 5.9990 chunk 780 optimal weight: 4.9990 chunk 632 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 466 optimal weight: 4.9990 chunk 820 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L8 48 GLN L8 83 ASN ** LA 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 117 HIS LI 14 ASN NG 175 ASN NM 160 ASN NM 172 GLN NQ 113 HIS SI 71 GLN SI 249 GLN SJ 687 ASN SJ 726 HIS ** SK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 157 GLN SL 30 GLN SL 61 ASN SL 112 GLN ** SS 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 333 GLN ST 213 GLN ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 402 GLN SZ 11 GLN SZ 171 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 106979 Z= 0.346 Angle : 0.573 13.798 152562 Z= 0.295 Chirality : 0.039 0.255 18203 Planarity : 0.005 0.052 12999 Dihedral : 21.652 179.725 36382 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.74 % Allowed : 11.32 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 1.31 (0.09), residues: 7811 helix: 2.13 (0.09), residues: 3342 sheet: -0.03 (0.15), residues: 1091 loop : -0.03 (0.10), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRPSR 417 HIS 0.013 0.001 HISSH 51 PHE 0.031 0.002 PHEL8 17 TYR 0.031 0.002 TYRLC 84 ARG 0.009 0.001 ARGLA 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 731 time to evaluate : 6.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LA 40 HIS cc_start: 0.6423 (t70) cc_final: 0.5751 (t70) REVERT: LC 28 TYR cc_start: 0.8094 (m-80) cc_final: 0.7785 (m-80) REVERT: LC 99 ASP cc_start: 0.7145 (m-30) cc_final: 0.6889 (m-30) REVERT: LE 102 ARG cc_start: 0.7842 (mmm160) cc_final: 0.7636 (mtp85) REVERT: LG 26 ILE cc_start: 0.8413 (pp) cc_final: 0.8161 (pt) REVERT: LK 65 ARG cc_start: 0.7633 (mmt180) cc_final: 0.7325 (mmt180) REVERT: LQ 133 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: LS 72 PHE cc_start: 0.8520 (t80) cc_final: 0.8150 (t80) REVERT: LS 78 TYR cc_start: 0.6434 (OUTLIER) cc_final: 0.5575 (t80) REVERT: LT 31 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: LW 80 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6902 (mt-10) REVERT: NS 72 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: SC 250 GLN cc_start: 0.8241 (tp40) cc_final: 0.7854 (tp-100) REVERT: SC 254 ASP cc_start: 0.7116 (m-30) cc_final: 0.6676 (m-30) REVERT: SD 43 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6600 (ptp-170) REVERT: SI 93 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7324 (tppt) REVERT: SJ 708 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: SL 101 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: SN 140 MET cc_start: 0.6513 (mmm) cc_final: 0.6052 (mmm) REVERT: SN 165 GLU cc_start: 0.8378 (tp30) cc_final: 0.7951 (tp30) REVERT: SS 141 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7650 (tm) REVERT: SS 184 THR cc_start: 0.7884 (m) cc_final: 0.7670 (m) REVERT: ST 223 GLN cc_start: 0.8311 (tp40) cc_final: 0.8022 (mm-40) REVERT: SV 19 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6374 (tpp) REVERT: SV 25 ASP cc_start: 0.6432 (p0) cc_final: 0.6189 (p0) REVERT: SW 202 MET cc_start: 0.7301 (ptp) cc_final: 0.6936 (ptp) REVERT: SW 363 PHE cc_start: 0.6585 (m-10) cc_final: 0.6351 (m-10) outliers start: 187 outliers final: 110 residues processed: 836 average time/residue: 1.8389 time to fit residues: 2108.7559 Evaluate side-chains 821 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 701 time to evaluate : 6.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 39 GLU Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 126 VAL Chi-restraints excluded: chain L7 residue 152 VAL Chi-restraints excluded: chain L7 residue 185 VAL Chi-restraints excluded: chain L8 residue 69 HIS Chi-restraints excluded: chain L8 residue 75 GLN Chi-restraints excluded: chain L8 residue 104 MET Chi-restraints excluded: chain L8 residue 108 ASP Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 109 VAL Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LE residue 143 THR Chi-restraints excluded: chain LG residue 28 CYS Chi-restraints excluded: chain LG residue 59 ASP Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 111 GLU Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 107 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LN residue 160 ILE Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 258 HIS Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 92 ASN Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 78 TYR Chi-restraints excluded: chain LS residue 88 THR Chi-restraints excluded: chain LT residue 31 GLU Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LU residue 9 VAL Chi-restraints excluded: chain LU residue 66 ASP Chi-restraints excluded: chain NB residue 354 THR Chi-restraints excluded: chain NE residue 201 ASN Chi-restraints excluded: chain NE residue 228 LEU Chi-restraints excluded: chain NE residue 250 LEU Chi-restraints excluded: chain NE residue 251 ASP Chi-restraints excluded: chain NE residue 260 LYS Chi-restraints excluded: chain NE residue 311 THR Chi-restraints excluded: chain NE residue 332 LYS Chi-restraints excluded: chain NG residue 144 MET Chi-restraints excluded: chain NG residue 157 GLU Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NN residue 19 LEU Chi-restraints excluded: chain NN residue 53 VAL Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 156 MET Chi-restraints excluded: chain NN residue 275 ILE Chi-restraints excluded: chain NN residue 288 GLU Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NQ residue 52 THR Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NS residue 72 GLN Chi-restraints excluded: chain NS residue 75 ARG Chi-restraints excluded: chain NS residue 85 LEU Chi-restraints excluded: chain NS residue 262 MET Chi-restraints excluded: chain NS residue 334 VAL Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SA residue 150 LEU Chi-restraints excluded: chain SC residue 232 ILE Chi-restraints excluded: chain SD residue 14 VAL Chi-restraints excluded: chain SD residue 43 ARG Chi-restraints excluded: chain SE residue 106 THR Chi-restraints excluded: chain SE residue 210 GLU Chi-restraints excluded: chain SI residue 93 LYS Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SJ residue 673 VAL Chi-restraints excluded: chain SJ residue 707 GLN Chi-restraints excluded: chain SJ residue 708 GLU Chi-restraints excluded: chain SJ residue 714 ILE Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 102 SER Chi-restraints excluded: chain SK residue 137 VAL Chi-restraints excluded: chain SK residue 177 LEU Chi-restraints excluded: chain SK residue 181 LEU Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 80 VAL Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 146 LEU Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SO residue 289 LEU Chi-restraints excluded: chain SR residue 362 LEU Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 242 ASP Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SV residue 19 MET Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SZ residue 17 VAL Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 946 random chunks: chunk 307 optimal weight: 1.9990 chunk 823 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 536 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 915 optimal weight: 7.9990 chunk 759 optimal weight: 4.9990 chunk 423 optimal weight: 0.8980 chunk 76 optimal weight: 30.0000 chunk 302 optimal weight: 0.0470 chunk 480 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 167 HIS ** L8 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 83 ASN L8 125 ASN LA 116 HIS ** LB 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 14 ASN LN 236 HIS LN 289 GLN LS 107 GLN NG 175 ASN NG 181 GLN NM 160 ASN NM 172 GLN SD 63 GLN SD 110 GLN SE 64 GLN SI 71 GLN SI 249 GLN SJ 687 ASN SJ 726 HIS ** SK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 30 GLN SL 61 ASN SL 112 GLN SM 209 HIS SR 421 ASN ** SS 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 333 GLN ST 213 GLN ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 11 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 106979 Z= 0.158 Angle : 0.496 16.267 152562 Z= 0.256 Chirality : 0.035 0.348 18203 Planarity : 0.004 0.050 12999 Dihedral : 21.628 179.476 36382 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.00 % Allowed : 12.61 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 1.55 (0.09), residues: 7811 helix: 2.36 (0.09), residues: 3359 sheet: 0.08 (0.15), residues: 1071 loop : 0.05 (0.10), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPSR 417 HIS 0.004 0.001 HISNQ 205 PHE 0.030 0.001 PHEL8 17 TYR 0.027 0.001 TYRLC 84 ARG 0.008 0.000 ARGSH 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 748 time to evaluate : 6.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 52 LEU cc_start: 0.5505 (pp) cc_final: 0.5020 (mt) REVERT: L7 87 MET cc_start: 0.8669 (mtt) cc_final: 0.8422 (mtt) REVERT: LA 140 MET cc_start: 0.4940 (OUTLIER) cc_final: 0.4089 (tmt) REVERT: LC 54 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6855 (mtm) REVERT: LK 65 ARG cc_start: 0.7542 (mmt180) cc_final: 0.7187 (mmt180) REVERT: LQ 133 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: LS 72 PHE cc_start: 0.8507 (t80) cc_final: 0.8166 (t80) REVERT: LS 78 TYR cc_start: 0.6496 (OUTLIER) cc_final: 0.5517 (t80) REVERT: LW 80 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6798 (mt-10) REVERT: NS 72 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6719 (mp10) REVERT: SC 250 GLN cc_start: 0.8238 (tp40) cc_final: 0.7866 (tp-100) REVERT: SC 254 ASP cc_start: 0.7282 (m-30) cc_final: 0.6842 (m-30) REVERT: SD 43 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6643 (ptp-170) REVERT: SD 71 MET cc_start: 0.7961 (mmp) cc_final: 0.7645 (mmp) REVERT: SE 226 TYR cc_start: 0.8551 (t80) cc_final: 0.8298 (t80) REVERT: SJ 708 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: SJ 726 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7551 (t-90) REVERT: SK 95 ARG cc_start: 0.6576 (tpt-90) cc_final: 0.6319 (tpp-160) REVERT: SL 101 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: SL 244 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7372 (mttp) REVERT: SN 140 MET cc_start: 0.6331 (mmm) cc_final: 0.5926 (mmm) REVERT: SN 165 GLU cc_start: 0.8369 (tp30) cc_final: 0.7939 (tp30) REVERT: SS 141 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7457 (tt) REVERT: ST 213 GLN cc_start: 0.7603 (mt0) cc_final: 0.7352 (mm-40) REVERT: ST 223 GLN cc_start: 0.8355 (tp40) cc_final: 0.8008 (mm-40) REVERT: SV 19 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6352 (tpp) REVERT: SW 202 MET cc_start: 0.7279 (ptp) cc_final: 0.6911 (ptp) REVERT: SW 363 PHE cc_start: 0.6619 (m-10) cc_final: 0.6391 (m-10) REVERT: SZ 61 ASP cc_start: 0.7373 (t0) cc_final: 0.7081 (t0) outliers start: 137 outliers final: 71 residues processed: 826 average time/residue: 1.9021 time to fit residues: 2160.6374 Evaluate side-chains 793 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 710 time to evaluate : 6.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L7 residue 39 GLU Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 185 VAL Chi-restraints excluded: chain L7 residue 193 THR Chi-restraints excluded: chain L8 residue 69 HIS Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 109 VAL Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LA residue 140 MET Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 54 MET Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LC residue 87 ARG Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LE residue 150 LEU Chi-restraints excluded: chain LG residue 28 CYS Chi-restraints excluded: chain LG residue 59 ASP Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 258 HIS Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LQ residue 8 VAL Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 78 TYR Chi-restraints excluded: chain LS residue 88 THR Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LU residue 9 VAL Chi-restraints excluded: chain NB residue 354 THR Chi-restraints excluded: chain NE residue 228 LEU Chi-restraints excluded: chain NE residue 260 LYS Chi-restraints excluded: chain NE residue 311 THR Chi-restraints excluded: chain NE residue 332 LYS Chi-restraints excluded: chain NG residue 144 MET Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 288 GLU Chi-restraints excluded: chain NO residue 89 THR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NS residue 72 GLN Chi-restraints excluded: chain NS residue 85 LEU Chi-restraints excluded: chain NS residue 246 ILE Chi-restraints excluded: chain NS residue 334 VAL Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 14 VAL Chi-restraints excluded: chain SD residue 43 ARG Chi-restraints excluded: chain SE residue 210 GLU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SJ residue 707 GLN Chi-restraints excluded: chain SJ residue 708 GLU Chi-restraints excluded: chain SJ residue 714 ILE Chi-restraints excluded: chain SJ residue 726 HIS Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 102 SER Chi-restraints excluded: chain SK residue 179 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SK residue 199 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SM residue 169 MET Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SO residue 289 LEU Chi-restraints excluded: chain SR residue 443 ASP Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SV residue 19 MET Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 946 random chunks: chunk 882 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 521 optimal weight: 10.0000 chunk 668 optimal weight: 5.9990 chunk 517 optimal weight: 6.9990 chunk 770 optimal weight: 5.9990 chunk 511 optimal weight: 5.9990 chunk 911 optimal weight: 4.9990 chunk 570 optimal weight: 8.9990 chunk 555 optimal weight: 0.7980 chunk 420 optimal weight: 0.8980 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L8 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 83 ASN L8 125 ASN LA 64 ASN ** LB 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 67 GLN LN 302 ASN LQ 80 HIS LS 107 GLN ** LW 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NG 181 GLN NM 160 ASN NM 172 GLN NN 134 GLN NO 6 GLN NO 211 ASN SD 110 GLN SD 248 ASN SE 64 GLN SI 71 GLN SJ 687 ASN SJ 726 HIS ** SK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 30 GLN SL 112 GLN SM 235 ASN SR 421 ASN ** SS 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 11 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 106979 Z= 0.293 Angle : 0.544 13.187 152562 Z= 0.279 Chirality : 0.038 0.258 18203 Planarity : 0.004 0.051 12999 Dihedral : 21.573 179.425 36382 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.17 % Allowed : 13.33 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 1.44 (0.09), residues: 7811 helix: 2.28 (0.09), residues: 3357 sheet: 0.00 (0.15), residues: 1074 loop : -0.01 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPSR 417 HIS 0.018 0.001 HISSJ 726 PHE 0.029 0.002 PHEL8 17 TYR 0.026 0.002 TYRLC 84 ARG 0.008 0.000 ARGL9 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 703 time to evaluate : 6.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 52 LEU cc_start: 0.5691 (pp) cc_final: 0.5225 (mt) REVERT: L7 87 MET cc_start: 0.8780 (mtt) cc_final: 0.8550 (mtt) REVERT: LA 40 HIS cc_start: 0.6374 (t70) cc_final: 0.5728 (t70) REVERT: LC 28 TYR cc_start: 0.8136 (m-80) cc_final: 0.7797 (m-10) REVERT: LC 54 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6998 (mtm) REVERT: LC 99 ASP cc_start: 0.7389 (m-30) cc_final: 0.7179 (m-30) REVERT: LC 108 GLN cc_start: 0.8044 (mt0) cc_final: 0.7775 (pt0) REVERT: LG 26 ILE cc_start: 0.8391 (pp) cc_final: 0.8098 (pt) REVERT: LK 65 ARG cc_start: 0.7708 (mmt180) cc_final: 0.7360 (mmt180) REVERT: LQ 133 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: LS 72 PHE cc_start: 0.8447 (t80) cc_final: 0.8123 (t80) REVERT: LS 78 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.5547 (t80) REVERT: LW 80 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6967 (mt-10) REVERT: NE 328 ASN cc_start: 0.8032 (t0) cc_final: 0.7566 (m110) REVERT: NS 72 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6813 (mp10) REVERT: SC 250 GLN cc_start: 0.8239 (tp40) cc_final: 0.7849 (tp-100) REVERT: SC 254 ASP cc_start: 0.7281 (m-30) cc_final: 0.6855 (m-30) REVERT: SD 43 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6587 (ptp-170) REVERT: SI 93 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7320 (tppt) REVERT: SJ 708 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7345 (mt-10) REVERT: SL 101 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: SL 222 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: SL 244 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7412 (mttp) REVERT: SN 165 GLU cc_start: 0.8371 (tp30) cc_final: 0.7942 (tp30) REVERT: SS 141 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7701 (tm) REVERT: ST 213 GLN cc_start: 0.7719 (mt0) cc_final: 0.7404 (mm-40) REVERT: SV 19 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6457 (mmm) REVERT: SW 202 MET cc_start: 0.7376 (ptp) cc_final: 0.7020 (ptp) REVERT: SW 343 PHE cc_start: 0.6939 (m-10) cc_final: 0.6707 (m-10) REVERT: SW 363 PHE cc_start: 0.6551 (m-10) cc_final: 0.6311 (m-10) REVERT: SZ 61 ASP cc_start: 0.7397 (t0) cc_final: 0.7110 (t0) outliers start: 148 outliers final: 100 residues processed: 794 average time/residue: 1.8363 time to fit residues: 1994.1688 Evaluate side-chains 802 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 690 time to evaluate : 6.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 39 GLU Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 185 VAL Chi-restraints excluded: chain L7 residue 193 THR Chi-restraints excluded: chain L8 residue 69 HIS Chi-restraints excluded: chain L8 residue 75 GLN Chi-restraints excluded: chain L8 residue 108 ASP Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 109 VAL Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 54 MET Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LC residue 87 ARG Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LE residue 150 LEU Chi-restraints excluded: chain LG residue 28 CYS Chi-restraints excluded: chain LG residue 59 ASP Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LG residue 132 ILE Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 107 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 258 HIS Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LQ residue 8 VAL Chi-restraints excluded: chain LQ residue 92 ASN Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 78 TYR Chi-restraints excluded: chain LS residue 88 THR Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LU residue 9 VAL Chi-restraints excluded: chain NB residue 354 THR Chi-restraints excluded: chain NE residue 228 LEU Chi-restraints excluded: chain NE residue 250 LEU Chi-restraints excluded: chain NE residue 251 ASP Chi-restraints excluded: chain NE residue 260 LYS Chi-restraints excluded: chain NE residue 311 THR Chi-restraints excluded: chain NE residue 332 LYS Chi-restraints excluded: chain NG residue 144 MET Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 156 MET Chi-restraints excluded: chain NN residue 199 ILE Chi-restraints excluded: chain NN residue 275 ILE Chi-restraints excluded: chain NN residue 288 GLU Chi-restraints excluded: chain NO residue 89 THR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NQ residue 199 VAL Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NS residue 72 GLN Chi-restraints excluded: chain NS residue 85 LEU Chi-restraints excluded: chain NS residue 246 ILE Chi-restraints excluded: chain NS residue 334 VAL Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SD residue 14 VAL Chi-restraints excluded: chain SD residue 30 ILE Chi-restraints excluded: chain SD residue 43 ARG Chi-restraints excluded: chain SE residue 91 THR Chi-restraints excluded: chain SE residue 106 THR Chi-restraints excluded: chain SE residue 210 GLU Chi-restraints excluded: chain SH residue 154 THR Chi-restraints excluded: chain SI residue 93 LYS Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SJ residue 673 VAL Chi-restraints excluded: chain SJ residue 707 GLN Chi-restraints excluded: chain SJ residue 708 GLU Chi-restraints excluded: chain SJ residue 714 ILE Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 137 VAL Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 197 MET Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SK residue 199 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 80 VAL Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 222 GLN Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SO residue 289 LEU Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 242 ASP Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SV residue 19 MET Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SV residue 99 ILE Chi-restraints excluded: chain SZ residue 17 VAL Chi-restraints excluded: chain SZ residue 110 THR Chi-restraints excluded: chain SZ residue 129 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 946 random chunks: chunk 564 optimal weight: 9.9990 chunk 364 optimal weight: 4.9990 chunk 544 optimal weight: 6.9990 chunk 274 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 579 optimal weight: 0.9980 chunk 621 optimal weight: 0.0270 chunk 450 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 716 optimal weight: 2.9990 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L8 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 83 ASN L8 125 ASN ** LB 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 37 HIS LK 67 GLN LS 107 GLN ** LW 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NE 328 ASN NG 181 GLN NM 160 ASN NM 172 GLN NO 6 GLN SC 268 GLN SD 63 GLN SD 110 GLN SE 64 GLN SI 71 GLN SJ 687 ASN SJ 726 HIS SL 30 GLN SL 112 GLN SR 421 ASN ** SS 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 333 GLN ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 278 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 106979 Z= 0.160 Angle : 0.497 15.031 152562 Z= 0.255 Chirality : 0.034 0.242 18203 Planarity : 0.004 0.050 12999 Dihedral : 21.569 179.717 36382 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.78 % Allowed : 13.85 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 1.60 (0.09), residues: 7811 helix: 2.44 (0.09), residues: 3349 sheet: 0.04 (0.15), residues: 1075 loop : 0.06 (0.10), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRPSR 417 HIS 0.017 0.001 HISSJ 726 PHE 0.029 0.001 PHEL8 17 TYR 0.027 0.001 TYRLC 84 ARG 0.012 0.000 ARGSK 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 708 time to evaluate : 6.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 52 LEU cc_start: 0.5749 (pp) cc_final: 0.5375 (mt) REVERT: L7 87 MET cc_start: 0.8632 (mtt) cc_final: 0.8377 (mtt) REVERT: L8 126 GLU cc_start: 0.7353 (tp30) cc_final: 0.7103 (tm-30) REVERT: LA 40 HIS cc_start: 0.6226 (t70) cc_final: 0.5632 (t70) REVERT: LC 54 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6902 (mtm) REVERT: LG 100 ASP cc_start: 0.7256 (p0) cc_final: 0.6986 (p0) REVERT: LK 65 ARG cc_start: 0.7673 (mmt180) cc_final: 0.7285 (mmt180) REVERT: LQ 133 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: LW 80 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: NE 314 VAL cc_start: 0.8211 (t) cc_final: 0.7989 (t) REVERT: NE 328 ASN cc_start: 0.7967 (t0) cc_final: 0.7490 (m110) REVERT: NS 72 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6727 (mp10) REVERT: SC 250 GLN cc_start: 0.8230 (tp40) cc_final: 0.7847 (tp-100) REVERT: SC 254 ASP cc_start: 0.7299 (m-30) cc_final: 0.6862 (m-30) REVERT: SD 43 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6536 (ptp-170) REVERT: SE 226 TYR cc_start: 0.8526 (t80) cc_final: 0.8275 (t80) REVERT: SJ 708 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: SJ 726 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7475 (t-170) REVERT: SL 101 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: SL 222 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: SL 244 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7506 (mttm) REVERT: SN 165 GLU cc_start: 0.8337 (tp30) cc_final: 0.7916 (tp30) REVERT: SN 241 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7773 (tpt170) REVERT: SS 141 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7669 (tm) REVERT: ST 213 GLN cc_start: 0.7668 (mt0) cc_final: 0.7385 (mm110) REVERT: SW 202 MET cc_start: 0.7370 (ptp) cc_final: 0.7011 (ptp) REVERT: SW 363 PHE cc_start: 0.6448 (m-10) cc_final: 0.6209 (m-10) REVERT: SZ 10 ARG cc_start: 0.7214 (mpp-170) cc_final: 0.6735 (mtm-85) REVERT: SZ 61 ASP cc_start: 0.7367 (t0) cc_final: 0.7076 (t0) outliers start: 122 outliers final: 86 residues processed: 783 average time/residue: 1.8433 time to fit residues: 1971.8625 Evaluate side-chains 790 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 692 time to evaluate : 6.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 39 GLU Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 185 VAL Chi-restraints excluded: chain L8 residue 69 HIS Chi-restraints excluded: chain L8 residue 75 GLN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 109 VAL Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 54 MET Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LG residue 28 CYS Chi-restraints excluded: chain LG residue 59 ASP Chi-restraints excluded: chain LG residue 80 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 258 HIS Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LQ residue 8 VAL Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 88 THR Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LU residue 9 VAL Chi-restraints excluded: chain LU residue 66 ASP Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain NB residue 354 THR Chi-restraints excluded: chain NE residue 228 LEU Chi-restraints excluded: chain NE residue 250 LEU Chi-restraints excluded: chain NE residue 251 ASP Chi-restraints excluded: chain NE residue 260 LYS Chi-restraints excluded: chain NE residue 311 THR Chi-restraints excluded: chain NE residue 332 LYS Chi-restraints excluded: chain NG residue 144 MET Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NN residue 19 LEU Chi-restraints excluded: chain NN residue 70 LEU Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 288 GLU Chi-restraints excluded: chain NO residue 89 THR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NS residue 72 GLN Chi-restraints excluded: chain NS residue 85 LEU Chi-restraints excluded: chain NS residue 334 VAL Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 14 VAL Chi-restraints excluded: chain SD residue 43 ARG Chi-restraints excluded: chain SE residue 106 THR Chi-restraints excluded: chain SE residue 210 GLU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SJ residue 673 VAL Chi-restraints excluded: chain SJ residue 707 GLN Chi-restraints excluded: chain SJ residue 708 GLU Chi-restraints excluded: chain SJ residue 714 ILE Chi-restraints excluded: chain SJ residue 726 HIS Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 80 VAL Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 222 GLN Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SM residue 169 MET Chi-restraints excluded: chain SN residue 67 VAL Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SN residue 241 ARG Chi-restraints excluded: chain SO residue 289 LEU Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 242 ASP Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SZ residue 129 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 946 random chunks: chunk 829 optimal weight: 3.9990 chunk 873 optimal weight: 1.9990 chunk 796 optimal weight: 9.9990 chunk 849 optimal weight: 8.9990 chunk 511 optimal weight: 6.9990 chunk 370 optimal weight: 0.7980 chunk 667 optimal weight: 0.9980 chunk 260 optimal weight: 9.9990 chunk 767 optimal weight: 0.8980 chunk 803 optimal weight: 2.9990 chunk 846 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L8 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 83 ASN L8 125 ASN ** LB 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 67 GLN LS 107 GLN ** LW 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NG 181 GLN NN 134 GLN NO 6 GLN SD 110 GLN SE 64 GLN SI 71 GLN SJ 687 ASN SJ 726 HIS SL 112 GLN SR 421 ASN ** SS 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 106979 Z= 0.191 Angle : 0.503 13.720 152562 Z= 0.258 Chirality : 0.035 0.390 18203 Planarity : 0.004 0.068 12999 Dihedral : 21.533 179.972 36382 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.02 % Favored : 97.96 % Rotamer: Outliers : 1.92 % Allowed : 13.98 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 7811 helix: 2.45 (0.09), residues: 3349 sheet: 0.04 (0.15), residues: 1075 loop : 0.06 (0.10), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPSR 417 HIS 0.030 0.001 HISSJ 726 PHE 0.031 0.001 PHESK 154 TYR 0.027 0.001 TYRLG 38 ARG 0.014 0.000 ARGSK 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 707 time to evaluate : 6.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 52 LEU cc_start: 0.5700 (pp) cc_final: 0.5377 (mt) REVERT: L7 87 MET cc_start: 0.8674 (mtt) cc_final: 0.8437 (mtt) REVERT: L7 144 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7480 (mm-30) REVERT: LA 40 HIS cc_start: 0.6315 (t70) cc_final: 0.5718 (t70) REVERT: LC 28 TYR cc_start: 0.8124 (m-80) cc_final: 0.7824 (m-10) REVERT: LC 54 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6952 (mtm) REVERT: LG 26 ILE cc_start: 0.8346 (pp) cc_final: 0.8031 (pt) REVERT: LG 100 ASP cc_start: 0.7318 (p0) cc_final: 0.7060 (p0) REVERT: LK 65 ARG cc_start: 0.7627 (mmt180) cc_final: 0.7277 (mmt180) REVERT: LQ 133 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: LW 80 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6818 (mt-10) REVERT: NE 314 VAL cc_start: 0.8203 (t) cc_final: 0.7979 (t) REVERT: NE 328 ASN cc_start: 0.7979 (t0) cc_final: 0.7528 (m110) REVERT: NS 72 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.6739 (mp10) REVERT: SC 250 GLN cc_start: 0.8209 (tp40) cc_final: 0.7806 (tp-100) REVERT: SC 254 ASP cc_start: 0.7305 (m-30) cc_final: 0.6854 (m-30) REVERT: SD 43 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6555 (ptp-170) REVERT: SD 71 MET cc_start: 0.7961 (mmp) cc_final: 0.7635 (mmp) REVERT: SJ 708 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: SL 101 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: SL 222 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: SL 244 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7498 (mttm) REVERT: SN 165 GLU cc_start: 0.8334 (tp30) cc_final: 0.7917 (tp30) REVERT: SN 241 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7798 (tpt170) REVERT: SS 141 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7696 (tm) REVERT: ST 213 GLN cc_start: 0.7680 (mt0) cc_final: 0.7383 (mm110) REVERT: SW 202 MET cc_start: 0.7384 (ptp) cc_final: 0.7028 (ptp) REVERT: SW 363 PHE cc_start: 0.6446 (m-10) cc_final: 0.6239 (m-10) REVERT: SZ 10 ARG cc_start: 0.7212 (mpp-170) cc_final: 0.6727 (mtm-85) REVERT: SZ 61 ASP cc_start: 0.7378 (t0) cc_final: 0.7097 (t0) outliers start: 131 outliers final: 96 residues processed: 791 average time/residue: 1.8644 time to fit residues: 2018.1843 Evaluate side-chains 799 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 692 time to evaluate : 6.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 39 GLU Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L7 residue 185 VAL Chi-restraints excluded: chain L8 residue 69 HIS Chi-restraints excluded: chain L8 residue 75 GLN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 109 VAL Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 54 MET Chi-restraints excluded: chain LC residue 87 ARG Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LE residue 150 LEU Chi-restraints excluded: chain LG residue 28 CYS Chi-restraints excluded: chain LG residue 80 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 258 HIS Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LQ residue 8 VAL Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 92 ASN Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 88 THR Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LU residue 9 VAL Chi-restraints excluded: chain LU residue 66 ASP Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain NB residue 354 THR Chi-restraints excluded: chain NE residue 228 LEU Chi-restraints excluded: chain NE residue 250 LEU Chi-restraints excluded: chain NE residue 251 ASP Chi-restraints excluded: chain NE residue 260 LYS Chi-restraints excluded: chain NE residue 311 THR Chi-restraints excluded: chain NE residue 332 LYS Chi-restraints excluded: chain NG residue 144 MET Chi-restraints excluded: chain NG residue 171 VAL Chi-restraints excluded: chain NG residue 206 SER Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NN residue 43 ILE Chi-restraints excluded: chain NN residue 70 LEU Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 199 ILE Chi-restraints excluded: chain NN residue 288 GLU Chi-restraints excluded: chain NO residue 89 THR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NQ residue 284 LEU Chi-restraints excluded: chain NS residue 72 GLN Chi-restraints excluded: chain NS residue 85 LEU Chi-restraints excluded: chain NS residue 334 VAL Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SD residue 14 VAL Chi-restraints excluded: chain SD residue 43 ARG Chi-restraints excluded: chain SE residue 106 THR Chi-restraints excluded: chain SE residue 210 GLU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SJ residue 673 VAL Chi-restraints excluded: chain SJ residue 707 GLN Chi-restraints excluded: chain SJ residue 708 GLU Chi-restraints excluded: chain SJ residue 714 ILE Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SK residue 199 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 80 VAL Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 222 GLN Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SM residue 169 MET Chi-restraints excluded: chain SN residue 67 VAL Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SN residue 241 ARG Chi-restraints excluded: chain SO residue 289 LEU Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 242 ASP Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SW residue 428 LEU Chi-restraints excluded: chain SZ residue 110 THR Chi-restraints excluded: chain SZ residue 129 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 946 random chunks: chunk 557 optimal weight: 1.9990 chunk 898 optimal weight: 5.9990 chunk 548 optimal weight: 0.6980 chunk 426 optimal weight: 5.9990 chunk 624 optimal weight: 6.9990 chunk 942 optimal weight: 0.9990 chunk 867 optimal weight: 0.4980 chunk 750 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 579 optimal weight: 1.9990 chunk 460 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L8 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 83 ASN L8 125 ASN ** LB 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 67 GLN LS 107 GLN ** LW 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NE 235 ASN NE 238 GLN NG 181 GLN NO 6 GLN SD 110 GLN SE 64 GLN SI 71 GLN SJ 687 ASN ** SK 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN ** SS 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 333 GLN ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 106979 Z= 0.151 Angle : 0.491 13.580 152562 Z= 0.251 Chirality : 0.034 0.367 18203 Planarity : 0.004 0.050 12999 Dihedral : 21.521 179.833 36382 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.83 % Favored : 98.16 % Rotamer: Outliers : 1.68 % Allowed : 14.34 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 1.68 (0.09), residues: 7811 helix: 2.51 (0.09), residues: 3351 sheet: 0.08 (0.15), residues: 1074 loop : 0.09 (0.10), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPSR 417 HIS 0.004 0.001 HISLA 40 PHE 0.030 0.001 PHEL8 17 TYR 0.025 0.001 TYRLC 84 ARG 0.014 0.000 ARGLA 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15622 Ramachandran restraints generated. 7811 Oldfield, 0 Emsley, 7811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 712 time to evaluate : 6.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 52 LEU cc_start: 0.5729 (pp) cc_final: 0.5422 (mt) REVERT: L7 87 MET cc_start: 0.8605 (mtt) cc_final: 0.8355 (mtt) REVERT: L7 144 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7465 (mm-30) REVERT: LA 10 ASN cc_start: 0.6914 (p0) cc_final: 0.6526 (p0) REVERT: LA 40 HIS cc_start: 0.6281 (t70) cc_final: 0.5696 (t70) REVERT: LG 26 ILE cc_start: 0.8332 (pp) cc_final: 0.8015 (pt) REVERT: LG 107 ASN cc_start: 0.8094 (p0) cc_final: 0.7825 (p0) REVERT: LI 54 GLU cc_start: 0.7422 (mp0) cc_final: 0.7195 (mt-10) REVERT: LI 108 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7805 (ttm170) REVERT: LK 65 ARG cc_start: 0.7563 (mmt180) cc_final: 0.7237 (mmt180) REVERT: LQ 133 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: LS 72 PHE cc_start: 0.8479 (t80) cc_final: 0.8209 (t80) REVERT: LW 80 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: NE 314 VAL cc_start: 0.8205 (t) cc_final: 0.7971 (t) REVERT: NE 328 ASN cc_start: 0.7958 (t0) cc_final: 0.7522 (m110) REVERT: NS 72 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6715 (mp10) REVERT: SC 250 GLN cc_start: 0.8195 (tp40) cc_final: 0.7803 (tp-100) REVERT: SC 254 ASP cc_start: 0.7299 (m-30) cc_final: 0.6855 (m-30) REVERT: SD 43 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6448 (ptp-170) REVERT: SE 226 TYR cc_start: 0.8517 (t80) cc_final: 0.8272 (t80) REVERT: SJ 708 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: SL 101 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7433 (m-30) REVERT: SL 222 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: SL 244 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7514 (mttm) REVERT: SN 165 GLU cc_start: 0.8309 (tp30) cc_final: 0.7885 (tp30) REVERT: SN 241 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7758 (tpt170) REVERT: SS 141 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7691 (tm) REVERT: ST 213 GLN cc_start: 0.7647 (mt0) cc_final: 0.7359 (mm110) REVERT: SW 202 MET cc_start: 0.7327 (ptp) cc_final: 0.6983 (ptp) REVERT: SW 363 PHE cc_start: 0.6443 (m-10) cc_final: 0.6222 (m-10) REVERT: SZ 10 ARG cc_start: 0.7239 (mpp-170) cc_final: 0.6759 (mtm-85) REVERT: SZ 61 ASP cc_start: 0.7365 (t0) cc_final: 0.7072 (t0) outliers start: 115 outliers final: 82 residues processed: 786 average time/residue: 1.8777 time to fit residues: 2019.5545 Evaluate side-chains 778 residues out of total 7002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 686 time to evaluate : 6.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 63 THR Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 39 GLU Chi-restraints excluded: chain L7 residue 43 ILE Chi-restraints excluded: chain L8 residue 69 HIS Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 109 VAL Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 85 THR Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 174 THR Chi-restraints excluded: chain LE residue 150 LEU Chi-restraints excluded: chain LG residue 28 CYS Chi-restraints excluded: chain LG residue 80 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 79 VAL Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 258 HIS Chi-restraints excluded: chain LQ residue 8 VAL Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 102 ASN Chi-restraints excluded: chain LQ residue 131 SER Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LU residue 9 VAL Chi-restraints excluded: chain LU residue 66 ASP Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain NB residue 354 THR Chi-restraints excluded: chain NE residue 228 LEU Chi-restraints excluded: chain NE residue 250 LEU Chi-restraints excluded: chain NE residue 260 LYS Chi-restraints excluded: chain NE residue 311 THR Chi-restraints excluded: chain NE residue 332 LYS Chi-restraints excluded: chain NG residue 171 VAL Chi-restraints excluded: chain NG residue 206 SER Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NN residue 43 ILE Chi-restraints excluded: chain NN residue 70 LEU Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 156 MET Chi-restraints excluded: chain NN residue 288 GLU Chi-restraints excluded: chain NO residue 89 THR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NQ residue 240 ASN Chi-restraints excluded: chain NS residue 72 GLN Chi-restraints excluded: chain NS residue 85 LEU Chi-restraints excluded: chain NS residue 334 VAL Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 57 LEU Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 14 VAL Chi-restraints excluded: chain SD residue 43 ARG Chi-restraints excluded: chain SE residue 106 THR Chi-restraints excluded: chain SE residue 210 GLU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SJ residue 673 VAL Chi-restraints excluded: chain SJ residue 707 GLN Chi-restraints excluded: chain SJ residue 708 GLU Chi-restraints excluded: chain SJ residue 714 ILE Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SK residue 199 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 80 VAL Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 222 GLN Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SM residue 169 MET Chi-restraints excluded: chain SN residue 67 VAL Chi-restraints excluded: chain SN residue 77 VAL Chi-restraints excluded: chain SN residue 241 ARG Chi-restraints excluded: chain SO residue 289 LEU Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SV residue 19 MET Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SW residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 946 random chunks: chunk 596 optimal weight: 5.9990 chunk 799 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 691 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 751 optimal weight: 5.9990 chunk 314 optimal weight: 0.5980 chunk 771 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L8 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 125 ASN L9 8 GLN ** LB 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LK 67 GLN LS 107 GLN ** LW 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NE 235 ASN NE 238 GLN NG 181 GLN NN 134 GLN NO 6 GLN NO 142 GLN SD 248 ASN SE 64 GLN SI 71 GLN SJ 687 ASN SJ 726 HIS ** SK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN ** SR 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.091977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.064234 restraints weight = 272715.131| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.80 r_work: 0.2941 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 106979 Z= 0.366 Angle : 0.587 13.040 152562 Z= 0.299 Chirality : 0.039 0.299 18203 Planarity : 0.005 0.051 12999 Dihedral : 21.511 179.493 36382 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.33 % Favored : 97.66 % Rotamer: Outliers : 1.96 % Allowed : 14.29 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.21 % 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: 7811 helix: 2.25 (0.09), residues: 3350 sheet: -0.06 (0.15), residues: 1067 loop : -0.04 (0.10), residues: 3394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPSR 417 HIS 0.008 0.001 HISSH 51 PHE 0.034 0.002 PHESK 154 TYR 0.033 0.002 TYRLC 84 ARG 0.012 0.001 ARGLA 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32838.55 seconds wall clock time: 573 minutes 23.64 seconds (34403.64 seconds total)