Starting phenix.real_space_refine on Mon Mar 25 22:42:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkv_29258/03_2024/8fkv_29258_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkv_29258/03_2024/8fkv_29258.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkv_29258/03_2024/8fkv_29258_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkv_29258/03_2024/8fkv_29258_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkv_29258/03_2024/8fkv_29258_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkv_29258/03_2024/8fkv_29258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkv_29258/03_2024/8fkv_29258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkv_29258/03_2024/8fkv_29258_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkv_29258/03_2024/8fkv_29258_neut_updated.pdb" } resolution = 2.47 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= 0.039 sd= 0.183 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 4 7.16 5 Zn 2 6.06 5 P 2440 5.49 5 Mg 65 5.21 5 S 404 5.16 5 C 84556 2.51 5 N 27531 2.21 5 O 33972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BA TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA GLU 87": "OE1" <-> "OE2" Residue "BA ASP 154": "OD1" <-> "OD2" Residue "BA GLU 161": "OE1" <-> "OE2" Residue "L6 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L6 GLU 80": "OE1" <-> "OE2" Residue "L6 GLU 119": "OE1" <-> "OE2" Residue "L7 TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ASP 100": "OD1" <-> "OD2" Residue "L7 ASP 106": "OD1" <-> "OD2" Residue "L7 ASP 113": "OD1" <-> "OD2" Residue "L7 GLU 158": "OE1" <-> "OE2" Residue "L7 GLU 162": "OE1" <-> "OE2" Residue "L8 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ASP 81": "OD1" <-> "OD2" Residue "L9 GLU 9": "OE1" <-> "OE2" Residue "L9 ASP 17": "OD1" <-> "OD2" Residue "L9 ASP 46": "OD1" <-> "OD2" Residue "L9 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 GLU 131": "OE1" <-> "OE2" Residue "L9 ASP 147": "OD1" <-> "OD2" Residue "LA ASP 7": "OD1" <-> "OD2" Residue "LB ASP 4": "OD1" <-> "OD2" Residue "LB ASP 22": "OD1" <-> "OD2" Residue "LB TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC GLU 69": "OE1" <-> "OE2" Residue "LC ASP 99": "OD1" <-> "OD2" Residue "LE TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 103": "OD1" <-> "OD2" Residue "LE PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE GLU 152": "OE1" <-> "OE2" Residue "LG ASP 30": "OD1" <-> "OD2" Residue "LG ASP 59": "OD1" <-> "OD2" Residue "LG GLU 99": "OE1" <-> "OE2" Residue "LG GLU 111": "OE1" <-> "OE2" Residue "LG GLU 124": "OE1" <-> "OE2" Residue "LI GLU 54": "OE1" <-> "OE2" Residue "LI TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 61": "OD1" <-> "OD2" Residue "LN TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 279": "OE1" <-> "OE2" Residue "LQ ASP 42": "OD1" <-> "OD2" Residue "LQ TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS ASP 8": "OD1" <-> "OD2" Residue "LS GLU 16": "OE1" <-> "OE2" Residue "LS GLU 111": "OE1" <-> "OE2" Residue "LT GLU 38": "OE1" <-> "OE2" Residue "LU TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 54": "OE1" <-> "OE2" Residue "LU GLU 59": "OE1" <-> "OE2" Residue "LU GLU 89": "OE1" <-> "OE2" Residue "NA ASP 326": "OD1" <-> "OD2" Residue "NA PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NB GLU 35": "OE1" <-> "OE2" Residue "NB GLU 63": "OE1" <-> "OE2" Residue "NF TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH ASP 61": "OD1" <-> "OD2" Residue "NH ASP 87": "OD1" <-> "OD2" Residue "NH TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH ASP 157": "OD1" <-> "OD2" Residue "NI PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NI GLU 754": "OE1" <-> "OE2" Residue "NI TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NK GLU 25": "OE1" <-> "OE2" Residue "NK ASP 88": "OD1" <-> "OD2" Residue "NM ASP 5": "OD1" <-> "OD2" Residue "NM ASP 9": "OD1" <-> "OD2" Residue "NM PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NM TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NO PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NO PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NS PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NS GLU 300": "OE1" <-> "OE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 254": "OE1" <-> "OE2" Residue "SA ASP 288": "OD1" <-> "OD2" Residue "SC GLU 119": "OE1" <-> "OE2" Residue "SC ASP 202": "OD1" <-> "OD2" Residue "SC ASP 214": "OD1" <-> "OD2" Residue "SC ASP 234": "OD1" <-> "OD2" Residue "SD PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 203": "OE1" <-> "OE2" Residue "SD GLU 229": "OE1" <-> "OE2" Residue "SD ASP 232": "OD1" <-> "OD2" Residue "SD GLU 237": "OE1" <-> "OE2" Residue "SE GLU 148": "OE1" <-> "OE2" Residue "SE ASP 211": "OD1" <-> "OD2" Residue "SE ASP 231": "OD1" <-> "OD2" Residue "SG ASP 11": "OD1" <-> "OD2" Residue "SG GLU 14": "OE1" <-> "OE2" Residue "SG GLU 44": "OE1" <-> "OE2" Residue "SG ASP 58": "OD1" <-> "OD2" Residue "SG TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG GLU 107": "OE1" <-> "OE2" Residue "SG GLU 120": "OE1" <-> "OE2" Residue "SG ASP 150": "OD1" <-> "OD2" Residue "SG GLU 152": "OE1" <-> "OE2" Residue "SG GLU 183": "OE1" <-> "OE2" Residue "SH GLU 163": "OE1" <-> "OE2" Residue "SH TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH ASP 184": "OD1" <-> "OD2" Residue "SI GLU 62": "OE1" <-> "OE2" Residue "SI ASP 74": "OD1" <-> "OD2" Residue "SI ASP 92": "OD1" <-> "OD2" Residue "SI ASP 106": "OD1" <-> "OD2" Residue "SI GLU 245": "OE1" <-> "OE2" Residue "SJ PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ ASP 831": "OD1" <-> "OD2" Residue "SK GLU 32": "OE1" <-> "OE2" Residue "SK GLU 127": "OE1" <-> "OE2" Residue "SK ASP 144": "OD1" <-> "OD2" Residue "SL PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL GLU 77": "OE1" <-> "OE2" Residue "SL ASP 196": "OD1" <-> "OD2" Residue "SL PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM GLU 316": "OE1" <-> "OE2" Residue "SM TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO ASP 91": "OD1" <-> "OD2" Residue "SO GLU 183": "OE1" <-> "OE2" Residue "SO TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO ASP 301": "OD1" <-> "OD2" Residue "SO GLU 317": "OE1" <-> "OE2" Residue "SQ TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 107": "OD1" <-> "OD2" Residue "SR TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 121": "OD1" <-> "OD2" Residue "SR ASP 194": "OD1" <-> "OD2" Residue "SR PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 301": "OE1" <-> "OE2" Residue "SR PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 434": "OE1" <-> "OE2" Residue "SS PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS GLU 319": "OE1" <-> "OE2" Residue "SS PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 4": "OE1" <-> "OE2" Residue "SV TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 570": "OE1" <-> "OE2" Residue "SW TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY GLU 302": "OE1" <-> "OE2" Residue "SY TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ ASP 61": "OD1" <-> "OD2" Residue "SZ TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ ASP 117": "OD1" <-> "OD2" Residue "SZ GLU 124": "OE1" <-> "OE2" Residue "SZ GLU 128": "OE1" <-> "OE2" Residue "SZ ASP 143": "OD1" <-> "OD2" Residue "SZ ASP 165": "OD1" <-> "OD2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148975 Number of models: 1 Model: "" Number of chains: 71 Chain: "BA" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1208 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "BB" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1057 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 8, 'TRANS': 204} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 686 Unresolved non-hydrogen angles: 858 Unresolved non-hydrogen dihedrals: 573 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 320 Chain: "L1" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3234 Classifications: {'RNA': 152} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 12, 'rna3p_pur': 60, 'rna3p_pyr': 65} Link IDs: {'rna2p': 26, 'rna3p': 125} 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: 47439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2213, 47439 Classifications: {'RNA': 2213} Modifications used: {'rna2p_pur': 209, 'rna2p_pyr': 127, 'rna3p_pur': 1004, 'rna3p_pyr': 873} Link IDs: {'rna2p': 336, 'rna3p': 1876} Chain breaks: 39 Chain: "L6" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 998 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 110} Chain: "L7" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1634 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 189} 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: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1286 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 1 Chain: "LB" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1223 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "LC" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1461 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain: "LE" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 926 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain breaks: 2 Chain: "LG" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "LH" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 813 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 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: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2884 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 345} Chain breaks: 2 Chain: "LP" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 526 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 197 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: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} Chain: "LW" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 612 Classifications: {'peptide': 74} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 70} Chain: "NA" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3658 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 22, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 133 Chain: "NB" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2424 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 22, 'TRANS': 364} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 642 Unresolved non-hydrogen angles: 814 Unresolved non-hydrogen dihedrals: 526 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 3, 'ASN:plan1': 13, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 18, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 296 Chain: "NF" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1783 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain breaks: 3 Chain: "NH" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1441 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "NI" Number of atoms: 5137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5137 Classifications: {'peptide': 647} Link IDs: {'PTRANS': 31, 'TRANS': 615} Chain breaks: 6 Chain: "NK" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 581 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "NM" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1550 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2864 Classifications: {'peptide': 360} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 341} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1491 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 174} Chain: "SG" Number of atoms: 1526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Conformer: "B" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} bond proxies already assigned to first conformer: 1528 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: 1864 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1853 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 225, 1853 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 bond proxies already assigned to first conformer: 1876 Chain: "SJ" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2780 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 327} Chain breaks: 5 Chain: "SK" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1852 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} 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: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3735 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 432} Chain breaks: 3 Chain: "SN" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1350 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "SO" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2544 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 284} Chain: "SQ" Number of atoms: 1778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Conformer: "B" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} bond proxies already assigned to first conformer: 1797 Chain: "SR" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3808 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 19, 'TRANS': 442} Chain: "SS" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2011 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 26, 'TRANS': 216} Chain breaks: 1 Chain: "ST" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 838 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "SU" Number of atoms: 4434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4434 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 539} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 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: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3549 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 19, 'TRANS': 424} Chain breaks: 1 Chain: "SY" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2985 Classifications: {'peptide': 378} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 357} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 51} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "L9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "NI" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "SO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SR" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' K': 1, ' MG': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "SU" 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 75430 SG CYSLW 19 88.449 146.294 148.144 1.00 31.16 S ATOM 75458 SG CYSLW 22 89.203 143.661 150.817 1.00 26.13 S ATOM 75549 SG CYSLW 34 91.121 146.905 150.783 1.00 31.09 S ATOM 75568 SG CYSLW 37 91.751 144.430 148.030 1.00 26.74 S ATOM 91260 SG CYSNM 29 105.765 76.811 192.835 1.00 15.28 S ATOM 91376 SG CYSNM 44 111.750 75.306 191.355 1.00 18.57 S ATOM 91339 SG CYSNM 39 110.419 80.825 194.231 1.00 16.52 S ATOM 91160 SG CYSNM 17 108.328 79.884 188.091 1.00 11.73 S ATOM A0UR0 SG CYSSV 6 57.299 203.042 235.035 1.00 38.09 S ATOM A0URT SG CYSSV 9 53.714 201.968 234.581 1.00 41.80 S ATOM A0UWX SG CYSSV 32 56.438 199.337 235.088 1.00 36.42 S ATOM A0UXR SG CYSSV 36 56.314 201.302 231.832 1.00 39.31 S Time building chain proxies: 57.66, per 1000 atoms: 0.39 Number of scatterers: 148975 At special positions: 0 Unit cell: (239.056, 309.808, 335.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 Fe 4 26.01 K 1 19.00 S 404 16.00 P 2440 15.00 Mg 65 11.99 O 33972 8.00 N 27531 7.00 C 84556 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: 54.77 Conformation dependent library (CDL) restraints added in 13.3 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 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " Number of angles added : 12 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23170 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: 470 helices and 93 sheets defined 52.4% alpha, 11.9% beta 785 base pairs and 1205 stacking pairs defined. Time for finding SS restraints: 91.75 Creating SS restraints... Processing helix chain 'BA' and resid 24 through 36 Proline residue: BA 30 - end of helix Proline residue: BA 34 - end of helix Processing helix chain 'BA' and resid 38 through 51 Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.791A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 91 through 96 removed outlier: 5.032A pdb=" N LYSBA 96 " --> pdb=" O ARGBA 92 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 3.559A pdb=" N ILEBA 109 " --> pdb=" O THRBA 105 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.549A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 Processing helix chain 'BB' and resid 6 through 25 Processing helix chain 'BB' and resid 70 through 81 Processing helix chain 'BB' and resid 86 through 97 removed outlier: 4.308A pdb=" N LYSBB 95 " --> pdb=" O LYSBB 91 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASNBB 96 " --> pdb=" O LYSBB 92 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYSBB 97 " --> pdb=" O LEUBB 93 " (cutoff:3.500A) Processing helix chain 'BB' and resid 98 through 108 removed outlier: 4.856A pdb=" N ASPBB 108 " --> pdb=" O ALABB 104 " (cutoff:3.500A) Processing helix chain 'BB' and resid 113 through 124 removed outlier: 4.332A pdb=" N LYSBB 118 " --> pdb=" O GLUBB 114 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLNBB 119 " --> pdb=" O SERBB 115 " (cutoff:3.500A) Proline residue: BB 121 - end of helix Processing helix chain 'BB' and resid 125 through 132 removed outlier: 3.529A pdb=" N LYSBB 130 " --> pdb=" O PROBB 126 " (cutoff:3.500A) Processing helix chain 'BB' and resid 143 through 154 Processing helix chain 'BB' and resid 175 through 195 removed outlier: 5.258A pdb=" N LYSBB 195 " --> pdb=" O VALBB 191 " (cutoff:3.500A) Processing helix chain 'BB' and resid 197 through 202 removed outlier: 3.995A pdb=" N VALBB 201 " --> pdb=" O ASNBB 197 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ARGBB 202 " --> pdb=" O TRPBB 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 197 through 202' Processing helix chain 'L6' and resid 17 through 22 removed outlier: 4.451A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VALL6 22 " --> pdb=" O TRPL6 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L6' and resid 17 through 22' Processing helix chain 'L6' and resid 27 through 47 Processing helix chain 'L6' and resid 77 through 85 Processing helix chain 'L6' and resid 87 through 95 removed outlier: 4.102A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.712A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.670A pdb=" N GLYL7 30 " --> pdb=" O GLNL7 26 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 60 removed outlier: 3.646A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) Processing helix chain 'L7' and resid 75 through 89 Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 3.681A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.936A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.457A 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 150 through 190 removed outlier: 5.798A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.683A pdb=" N HISL7 199 " --> pdb=" O VALL7 195 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLYL7 200 " --> pdb=" O LEUL7 196 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.934A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.237A 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: 3.515A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.606A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 4.071A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.866A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 4.902A 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: 3.733A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.969A 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: 6.108A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.888A 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: 3.650A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 4.081A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 3.986A 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 70 through 77 removed outlier: 4.398A pdb=" N LYSLA 74 " --> pdb=" O CYSLA 70 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLNLA 75 " --> pdb=" O ALALA 71 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLYLA 77 " --> pdb=" O ALALA 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 70 through 77' Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LA' and resid 159 through 176 removed outlier: 3.533A pdb=" N LYSLA 167 " --> pdb=" O GLULA 163 " (cutoff:3.500A) Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.162A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.508A 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: 4.244A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 removed outlier: 3.511A pdb=" N SERLC 42 " --> pdb=" O VALLC 38 " (cutoff:3.500A) Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.586A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLNLC 125 " --> pdb=" O ALALC 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 120 through 125' Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.475A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASPLC 147 " --> pdb=" O LYSLC 143 " (cutoff:3.500A) Processing helix chain 'LC' and resid 161 through 166 Proline residue: LC 165 - end of helix No H-bonds generated for 'chain 'LC' and resid 161 through 166' Processing helix chain 'LE' and resid 92 through 97 removed outlier: 3.784A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.213A 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: 4.362A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSLE 120 " --> pdb=" O LYSLE 116 " (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 136 removed outlier: 3.506A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.854A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 93 removed outlier: 3.505A pdb=" N ILELH 90 " --> pdb=" O ALALH 86 " (cutoff:3.500A) Processing helix chain 'LH' and resid 105 through 118 Processing helix chain 'LH' and resid 145 through 154 Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 3.990A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.260A 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: 4.183A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.603A 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: 3.936A pdb=" N LYSLK 10 " --> pdb=" O ARGLK 6 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARGLK 12 " --> pdb=" O THRLK 8 " (cutoff:3.500A) Processing helix chain 'LK' and resid 60 through 67 removed outlier: 3.536A pdb=" N ASNLK 66 " --> pdb=" O HISLK 62 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLNLK 67 " --> pdb=" O LEULK 63 " (cutoff:3.500A) Processing helix chain 'LK' and resid 74 through 83 removed outlier: 3.549A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 94 removed outlier: 4.779A pdb=" N LYSLK 94 " --> pdb=" O ALALK 90 " (cutoff:3.500A) Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.612A 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: 3.971A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 4.225A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 157 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 3.942A pdb=" N LEULN 171 " --> pdb=" O GLNLN 167 " (cutoff:3.500A) Proline residue: LN 172 - end of helix No H-bonds generated for 'chain 'LN' and resid 167 through 172' Processing helix chain 'LN' and resid 189 through 201 Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.816A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 3.942A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) Processing helix chain 'LN' and resid 381 through 390 Processing helix chain 'LN' and resid 392 through 403 Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.766A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) Processing helix chain 'LP' and resid 37 through 58 removed outlier: 4.779A pdb=" N ALALP 42 " --> pdb=" O PHELP 38 " (cutoff:3.500A) Proline residue: LP 43 - end of helix removed outlier: 3.990A pdb=" N GLYLP 58 " --> pdb=" O METLP 54 " (cutoff:3.500A) Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.513A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 4.985A 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 90 removed outlier: 3.762A pdb=" N LEULQ 85 " --> pdb=" O ASNLQ 81 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLULQ 86 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 81 through 90' Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.798A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.788A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 removed outlier: 3.527A pdb=" N VALLS 26 " --> pdb=" O ASPLS 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLULS 27 " --> pdb=" O ASPLS 23 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VALLS 36 " --> pdb=" O ARGLS 32 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLYLS 38 " --> pdb=" O ALALS 34 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.586A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VALLS 49 " --> pdb=" O SERLS 45 " (cutoff:3.500A) Processing helix chain 'LS' and resid 80 through 85 Proline residue: LS 85 - end of helix Processing helix chain 'LS' and resid 88 through 95 removed outlier: 5.690A 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: 3.743A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.549A 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: 4.094A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.183A 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: 3.574A pdb=" N GLULU 46 " --> pdb=" O ASPLU 42 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLYLU 49 " --> pdb=" O ARGLU 45 " (cutoff:3.500A) Processing helix chain 'LU' and resid 51 through 64 Processing helix chain 'LU' and resid 65 through 78 removed outlier: 3.528A pdb=" N LYSLU 75 " --> pdb=" O LYSLU 71 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARGLU 76 " --> pdb=" O PHELU 72 " (cutoff:3.500A) Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.690A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.150A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLYLW 77 " --> pdb=" O ARGLW 73 " (cutoff:3.500A) Processing helix chain 'NA' and resid 150 through 164 Processing helix chain 'NA' and resid 166 through 186 removed outlier: 3.712A pdb=" N VALNA 173 " --> pdb=" O LEUNA 169 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THRNA 184 " --> pdb=" O ALANA 180 " (cutoff:3.500A) Processing helix chain 'NA' and resid 187 through 195 removed outlier: 5.436A pdb=" N LYSNA 195 " --> pdb=" O ALANA 191 " (cutoff:3.500A) Processing helix chain 'NA' and resid 200 through 214 removed outlier: 3.587A pdb=" N ARGNA 213 " --> pdb=" O THRNA 209 " (cutoff:3.500A) Processing helix chain 'NA' and resid 215 through 224 Processing helix chain 'NA' and resid 240 through 247 removed outlier: 4.253A pdb=" N GLYNA 244 " --> pdb=" O SERNA 240 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYSNA 245 " --> pdb=" O PRONA 241 " (cutoff:3.500A) Processing helix chain 'NA' and resid 248 through 265 removed outlier: 3.583A pdb=" N SERNA 262 " --> pdb=" O ILENA 258 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SERNA 265 " --> pdb=" O VALNA 261 " (cutoff:3.500A) Processing helix chain 'NA' and resid 266 through 281 Processing helix chain 'NA' and resid 282 through 288 removed outlier: 3.735A pdb=" N PHENA 287 " --> pdb=" O CYSNA 283 " (cutoff:3.500A) Proline residue: NA 288 - end of helix Processing helix chain 'NA' and resid 289 through 304 Processing helix chain 'NA' and resid 306 through 325 removed outlier: 3.625A pdb=" N VALNA 311 " --> pdb=" O GLUNA 307 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VALNA 316 " --> pdb=" O LEUNA 312 " (cutoff:3.500A) Processing helix chain 'NA' and resid 328 through 346 removed outlier: 3.537A pdb=" N LYSNA 345 " --> pdb=" O VALNA 341 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHENA 346 " --> pdb=" O ARGNA 342 " (cutoff:3.500A) Processing helix chain 'NA' and resid 349 through 370 Proline residue: NA 353 - end of helix removed outlier: 4.221A pdb=" N GLUNA 369 " --> pdb=" O LEUNA 365 " (cutoff:3.500A) Proline residue: NA 370 - end of helix Processing helix chain 'NA' and resid 371 through 395 removed outlier: 3.716A pdb=" N GLNNA 375 " --> pdb=" O GLYNA 371 " (cutoff:3.500A) Processing helix chain 'NA' and resid 396 through 405 removed outlier: 3.609A pdb=" N VALNA 403 " --> pdb=" O THRNA 399 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASNNA 405 " --> pdb=" O GLNNA 401 " (cutoff:3.500A) Processing helix chain 'NA' and resid 406 through 422 removed outlier: 3.510A pdb=" N PHENA 413 " --> pdb=" O VALNA 409 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALANA 422 " --> pdb=" O VALNA 418 " (cutoff:3.500A) Processing helix chain 'NA' and resid 423 through 429 removed outlier: 4.203A pdb=" N ALANA 427 " --> pdb=" O GLYNA 423 " (cutoff:3.500A) Processing helix chain 'NA' and resid 430 through 447 Proline residue: NA 434 - end of helix removed outlier: 4.701A pdb=" N ILENA 446 " --> pdb=" O CYSNA 442 " (cutoff:3.500A) Proline residue: NA 447 - end of helix Processing helix chain 'NA' and resid 448 through 470 removed outlier: 3.646A pdb=" N TYRNA 452 " --> pdb=" O THRNA 448 " (cutoff:3.500A) Proline residue: NA 453 - end of helix Processing helix chain 'NA' and resid 474 through 486 removed outlier: 4.674A pdb=" N PHENA 478 " --> pdb=" O PRONA 474 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILENA 479 " --> pdb=" O VALNA 475 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N METNA 482 " --> pdb=" O PHENA 478 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHENA 483 " --> pdb=" O ILENA 479 " (cutoff:3.500A) Processing helix chain 'NA' and resid 509 through 516 removed outlier: 3.510A pdb=" N GLNNA 514 " --> pdb=" O ASNNA 510 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYSNA 516 " --> pdb=" O ASNNA 512 " (cutoff:3.500A) Processing helix chain 'NA' and resid 517 through 538 Processing helix chain 'NA' and resid 542 through 561 Proline residue: NA 549 - end of helix Processing helix chain 'NA' and resid 564 through 592 removed outlier: 3.501A pdb=" N ARGNA 590 " --> pdb=" O SERNA 586 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SERNA 592 " --> pdb=" O ARGNA 588 " (cutoff:3.500A) Processing helix chain 'NA' and resid 597 through 612 removed outlier: 3.510A pdb=" N VALNA 601 " --> pdb=" O GLUNA 597 " (cutoff:3.500A) Processing helix chain 'NA' and resid 613 through 635 Processing helix chain 'NB' and resid 14 through 36 Processing helix chain 'NB' and resid 56 through 77 Processing helix chain 'NB' and resid 125 through 141 Processing helix chain 'NB' and resid 152 through 158 removed outlier: 3.518A pdb=" N CYSNB 156 " --> pdb=" O ASPNB 152 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N CYSNB 158 " --> pdb=" O LEUNB 154 " (cutoff:3.500A) Processing helix chain 'NB' and resid 159 through 169 Processing helix chain 'NB' and resid 179 through 184 removed outlier: 3.864A pdb=" N VALNB 183 " --> pdb=" O LYSNB 179 " (cutoff:3.500A) Proline residue: NB 184 - end of helix No H-bonds generated for 'chain 'NB' and resid 179 through 184' Processing helix chain 'NB' and resid 185 through 199 removed outlier: 3.636A pdb=" N LYSNB 197 " --> pdb=" O ASNNB 193 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLUNB 198 " --> pdb=" O TYRNB 194 " (cutoff:3.500A) Processing helix chain 'NB' and resid 236 through 252 Processing helix chain 'NB' and resid 266 through 276 Processing helix chain 'NB' and resid 316 through 324 Processing helix chain 'NB' and resid 332 through 345 removed outlier: 3.703A pdb=" N GLNNB 343 " --> pdb=" O ALANB 339 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASPNB 345 " --> pdb=" O LEUNB 341 " (cutoff:3.500A) Processing helix chain 'NB' and resid 346 through 354 Processing helix chain 'NB' and resid 360 through 373 Processing helix chain 'NB' and resid 382 through 396 Processing helix chain 'NB' and resid 416 through 426 removed outlier: 5.085A pdb=" N GLYNB 426 " --> pdb=" O ASPNB 422 " (cutoff:3.500A) Processing helix chain 'NB' and resid 428 through 444 removed outlier: 3.510A pdb=" N LEUNB 432 " --> pdb=" O ASNNB 428 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LYSNB 444 " --> pdb=" O ILENB 440 " (cutoff:3.500A) Processing helix chain 'NB' and resid 447 through 452 removed outlier: 4.963A pdb=" N ILENB 452 " --> pdb=" O LEUNB 448 " (cutoff:3.500A) Processing helix chain 'NF' and resid 5 through 14 Processing helix chain 'NF' and resid 21 through 35 removed outlier: 4.326A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N HISNF 33 " --> pdb=" O SERNF 29 " (cutoff:3.500A) Processing helix chain 'NF' and resid 44 through 72 Processing helix chain 'NF' and resid 97 through 117 Processing helix chain 'NF' and resid 164 through 169 removed outlier: 4.983A pdb=" N ARGNF 169 " --> pdb=" O PRONF 165 " (cutoff:3.500A) Processing helix chain 'NF' and resid 173 through 178 removed outlier: 3.581A pdb=" N ARGNF 177 " --> pdb=" O PRONF 173 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHENF 178 " --> pdb=" O METNF 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'NF' and resid 173 through 178' Processing helix chain 'NF' and resid 205 through 212 Processing helix chain 'NF' and resid 247 through 252 Processing helix chain 'NH' and resid 5 through 20 removed outlier: 4.146A pdb=" N TYRNH 19 " --> pdb=" O LYSNH 15 " (cutoff:3.500A) Processing helix chain 'NH' and resid 22 through 30 removed outlier: 4.382A pdb=" N LEUNH 26 " --> pdb=" O GLUNH 22 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARGNH 30 " --> pdb=" O LEUNH 26 " (cutoff:3.500A) Processing helix chain 'NH' and resid 48 through 59 removed outlier: 4.323A pdb=" N ASNNH 57 " --> pdb=" O LYSNH 53 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILENH 58 " --> pdb=" O LEUNH 54 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SERNH 59 " --> pdb=" O ALANH 55 " (cutoff:3.500A) Processing helix chain 'NH' and resid 82 through 93 removed outlier: 4.151A pdb=" N LEUNH 86 " --> pdb=" O HISNH 82 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASPNH 87 " --> pdb=" O VALNH 83 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYRNH 88 " --> pdb=" O THRNH 84 " (cutoff:3.500A) Proline residue: NH 91 - end of helix Processing helix chain 'NH' and resid 100 through 110 removed outlier: 4.096A pdb=" N GLNNH 105 " --> pdb=" O PRONH 101 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SERNH 106 " --> pdb=" O GLYNH 102 " (cutoff:3.500A) Processing helix chain 'NH' and resid 114 through 119 removed outlier: 5.550A pdb=" N GLYNH 119 " --> pdb=" O LYSNH 115 " (cutoff:3.500A) Processing helix chain 'NH' and resid 149 through 157 removed outlier: 3.862A pdb=" N ARGNH 154 " --> pdb=" O THRNH 150 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYSNH 155 " --> pdb=" O GLNNH 151 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASPNH 157 " --> pdb=" O CYSNH 153 " (cutoff:3.500A) Processing helix chain 'NH' and resid 168 through 175 removed outlier: 4.887A pdb=" N TYRNH 172 " --> pdb=" O ASPNH 168 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VALNH 173 " --> pdb=" O ILENH 169 " (cutoff:3.500A) Processing helix chain 'NI' and resid 97 through 102 removed outlier: 3.887A pdb=" N GLYNI 102 " --> pdb=" O PHENI 98 " (cutoff:3.500A) Processing helix chain 'NI' and resid 104 through 115 Processing helix chain 'NI' and resid 120 through 133 Proline residue: NI 128 - end of helix removed outlier: 3.597A pdb=" N GLYNI 133 " --> pdb=" O VALNI 129 " (cutoff:3.500A) Processing helix chain 'NI' and resid 145 through 159 removed outlier: 3.949A pdb=" N CYSNI 149 " --> pdb=" O GLYNI 145 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHENI 150 " --> pdb=" O LYSNI 146 " (cutoff:3.500A) Proline residue: NI 153 - end of helix removed outlier: 3.913A pdb=" N LYSNI 159 " --> pdb=" O PHENI 155 " (cutoff:3.500A) Processing helix chain 'NI' and resid 175 through 191 Processing helix chain 'NI' and resid 205 through 216 removed outlier: 4.079A pdb=" N ASNNI 216 " --> pdb=" O ALANI 212 " (cutoff:3.500A) Processing helix chain 'NI' and resid 223 through 235 removed outlier: 3.721A pdb=" N HISNI 229 " --> pdb=" O GLYNI 225 " (cutoff:3.500A) Processing helix chain 'NI' and resid 248 through 256 removed outlier: 3.582A pdb=" N GLYNI 256 " --> pdb=" O LEUNI 252 " (cutoff:3.500A) Processing helix chain 'NI' and resid 257 through 269 Proline residue: NI 269 - end of helix Processing helix chain 'NI' and resid 282 through 292 Processing helix chain 'NI' and resid 301 through 307 removed outlier: 3.682A pdb=" N THRNI 305 " --> pdb=" O LEUNI 301 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYSNI 306 " --> pdb=" O ASPNI 302 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEUNI 307 " --> pdb=" O VALNI 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'NI' and resid 301 through 307' Processing helix chain 'NI' and resid 319 through 333 removed outlier: 4.792A pdb=" N ALANI 324 " --> pdb=" O GLUNI 320 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALANI 325 " --> pdb=" O ASPNI 321 " (cutoff:3.500A) Processing helix chain 'NI' and resid 347 through 362 removed outlier: 3.543A pdb=" N GLNNI 361 " --> pdb=" O LEUNI 357 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARGNI 362 " --> pdb=" O LEUNI 358 " (cutoff:3.500A) Processing helix chain 'NI' and resid 373 through 387 Processing helix chain 'NI' and resid 395 through 403 removed outlier: 4.910A pdb=" N GLYNI 401 " --> pdb=" O LEUNI 397 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEUNI 402 " --> pdb=" O ALANI 398 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASPNI 403 " --> pdb=" O ALANI 399 " (cutoff:3.500A) Processing helix chain 'NI' and resid 418 through 427 Processing helix chain 'NI' and resid 443 through 458 removed outlier: 3.508A pdb=" N ILENI 447 " --> pdb=" O ALANI 443 " (cutoff:3.500A) Proline residue: NI 448 - end of helix Processing helix chain 'NI' and resid 472 through 478 removed outlier: 5.434A pdb=" N GLYNI 478 " --> pdb=" O ALANI 474 " (cutoff:3.500A) Processing helix chain 'NI' and resid 486 through 503 removed outlier: 3.557A pdb=" N GLUNI 491 " --> pdb=" O VALNI 487 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLYNI 494 " --> pdb=" O GLUNI 490 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALANI 501 " --> pdb=" O SERNI 497 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEUNI 503 " --> pdb=" O LEUNI 499 " (cutoff:3.500A) Processing helix chain 'NI' and resid 504 through 523 Processing helix chain 'NI' and resid 527 through 543 removed outlier: 5.693A pdb=" N ASPNI 538 " --> pdb=" O ALANI 534 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEUNI 539 " --> pdb=" O LYSNI 535 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VALNI 540 " --> pdb=" O GLUNI 536 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLYNI 541 " --> pdb=" O METNI 537 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEUNI 542 " --> pdb=" O ASPNI 538 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLYNI 543 " --> pdb=" O LEUNI 539 " (cutoff:3.500A) Processing helix chain 'NI' and resid 545 through 553 removed outlier: 4.528A pdb=" N ARGNI 551 " --> pdb=" O LEUNI 547 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHENI 552 " --> pdb=" O PHENI 548 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLUNI 553 " --> pdb=" O SERNI 549 " (cutoff:3.500A) Processing helix chain 'NI' and resid 554 through 569 removed outlier: 3.560A pdb=" N LYSNI 567 " --> pdb=" O VALNI 563 " (cutoff:3.500A) Processing helix chain 'NI' and resid 574 through 579 removed outlier: 5.066A pdb=" N ASNNI 579 " --> pdb=" O ILENI 575 " (cutoff:3.500A) Processing helix chain 'NI' and resid 584 through 598 Processing helix chain 'NI' and resid 599 through 618 Proline residue: NI 618 - end of helix Processing helix chain 'NI' and resid 677 through 682 removed outlier: 5.872A pdb=" N ILENI 682 " --> pdb=" O GLNNI 678 " (cutoff:3.500A) Processing helix chain 'NI' and resid 703 through 712 removed outlier: 3.503A pdb=" N GLYNI 710 " --> pdb=" O GLNNI 706 " (cutoff:3.500A) Processing helix chain 'NI' and resid 719 through 736 removed outlier: 4.140A pdb=" N THRNI 724 " --> pdb=" O ALANI 720 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARGNI 725 " --> pdb=" O GLNNI 721 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLYNI 726 " --> pdb=" O ASNNI 722 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARGNI 727 " --> pdb=" O LEUNI 723 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEUNI 730 " --> pdb=" O GLYNI 726 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYSNI 731 " --> pdb=" O ARGNI 727 " (cutoff:3.500A) Processing helix chain 'NI' and resid 766 through 776 Processing helix chain 'NI' and resid 825 through 845 Processing helix chain 'NK' and resid 12 through 33 removed outlier: 3.507A pdb=" N LYSNK 20 " --> pdb=" O GLUNK 16 " (cutoff:3.500A) Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 98 through 112 Processing helix chain 'NM' and resid 3 through 12 Processing helix chain 'NM' and resid 44 through 49 removed outlier: 4.938A pdb=" N SERNM 49 " --> pdb=" O PRONM 45 " (cutoff:3.500A) Processing helix chain 'NM' and resid 67 through 72 removed outlier: 3.532A pdb=" N ALANM 71 " --> pdb=" O VALNM 67 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALANM 72 " --> pdb=" O ILENM 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'NM' and resid 67 through 72' Processing helix chain 'NM' and resid 86 through 99 Processing helix chain 'NM' and resid 102 through 129 Processing helix chain 'NM' and resid 138 through 173 removed outlier: 6.157A pdb=" N LEUNM 158 " --> pdb=" O ILENM 154 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ASPNM 159 " --> pdb=" O ALANM 155 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASNNM 160 " --> pdb=" O ALANM 156 " (cutoff:3.500A) Processing helix chain 'NO' and resid 8 through 19 Processing helix chain 'NO' and resid 21 through 43 removed outlier: 5.380A pdb=" N ALANO 43 " --> pdb=" O ARGNO 39 " (cutoff:3.500A) Processing helix chain 'NO' and resid 48 through 67 removed outlier: 3.584A pdb=" N GLNNO 66 " --> pdb=" O CYSNO 62 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASPNO 67 " --> pdb=" O METNO 63 " (cutoff:3.500A) Processing helix chain 'NO' and resid 68 through 86 removed outlier: 4.590A pdb=" N VALNO 83 " --> pdb=" O ILENO 79 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N HISNO 84 " --> pdb=" O SERNO 80 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALANO 85 " --> pdb=" O GLNNO 81 " (cutoff:3.500A) removed outlier: 3.797A 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: 4.245A pdb=" N ASPNO 116 " --> pdb=" O ARGNO 112 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYSNO 117 " --> pdb=" O LEUNO 113 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHENO 118 " --> pdb=" O ARGNO 114 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEUNO 133 " --> pdb=" O SERNO 129 " (cutoff:3.500A) Processing helix chain 'NO' and resid 139 through 154 Processing helix chain 'NO' and resid 162 through 181 removed outlier: 4.826A pdb=" N LEUNO 174 " --> pdb=" O ILENO 170 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLUNO 175 " --> pdb=" O GLUNO 171 " (cutoff:3.500A) Processing helix chain 'NO' and resid 186 through 204 Proline residue: NO 196 - end of helix removed outlier: 3.589A pdb=" N ARGNO 199 " --> pdb=" O ASPNO 195 " (cutoff:3.500A) Processing helix chain 'NO' and resid 206 through 248 removed outlier: 3.547A pdb=" N PHENO 218 " --> pdb=" O THRNO 214 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLUNO 219 " --> pdb=" O ARGNO 215 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THRNO 220 " --> pdb=" O GLYNO 216 " (cutoff:3.500A) Proline residue: NO 226 - end of helix Processing helix chain 'NO' and resid 299 through 312 Processing helix chain 'NO' and resid 317 through 337 removed outlier: 3.519A pdb=" N ARGNO 323 " --> pdb=" O GLNNO 319 " (cutoff:3.500A) Processing helix chain 'NO' and resid 345 through 353 removed outlier: 3.810A pdb=" N LEUNO 352 " --> pdb=" O ALANO 348 " (cutoff:3.500A) Processing helix chain 'NQ' and resid 1 through 10 removed outlier: 4.502A pdb=" N ARGNQ 7 " --> pdb=" O ALANQ 3 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TRPNQ 8 " --> pdb=" O ALANQ 4 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASNNQ 9 " --> pdb=" O ALANQ 5 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N HISNQ 10 " --> pdb=" O ALANQ 6 " (cutoff:3.500A) Processing helix chain 'NS' and resid 59 through 93 removed outlier: 3.789A pdb=" N LYSNS 82 " --> pdb=" O LYSNS 78 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYSNS 83 " --> pdb=" O LEUNS 79 " (cutoff:3.500A) Processing helix chain 'NS' and resid 104 through 109 Processing helix chain 'NS' and resid 120 through 130 Processing helix chain 'NS' and resid 132 through 138 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: 5.429A pdb=" N LYSNS 233 " --> pdb=" O ARGNS 229 " (cutoff:3.500A) Processing helix chain 'NS' and resid 253 through 268 removed outlier: 3.680A pdb=" N LEUNS 266 " --> pdb=" O METNS 262 " (cutoff:3.500A) removed outlier: 4.176A 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: 4.410A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.737A 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: 3.882A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.512A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.841A 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 Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.350A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 156 through 161' Processing helix chain 'SA' and resid 163 through 175 Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.741A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLNSA 187 " --> pdb=" O VALSA 183 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.567A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.626A 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 265 removed outlier: 3.777A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 removed outlier: 3.530A pdb=" N ILESA 292 " --> pdb=" O ASPSA 288 " (cutoff:3.500A) Processing helix chain 'SA' and resid 296 through 303 removed outlier: 4.163A pdb=" N ARGSA 300 " --> pdb=" O PROSA 296 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.227A 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: 4.412A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SC' and resid 47 through 54 Processing helix chain 'SC' and resid 58 through 74 removed outlier: 3.970A pdb=" N TYRSC 73 " --> pdb=" O TYRSC 69 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SERSC 74 " --> pdb=" O LYSSC 70 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.907A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.444A 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: 3.927A 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: 5.298A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.452A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 15 through 79 removed outlier: 3.538A pdb=" N ILESD 30 " --> pdb=" O ALASD 26 " (cutoff:3.500A) removed outlier: 3.686A 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: 3.614A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VALSD 136 " --> pdb=" O METSD 132 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.209A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.802A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.281A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 238 through 248 removed outlier: 4.788A pdb=" N ARGSD 242 " --> pdb=" O ASPSD 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.774A pdb=" N ALASE 68 " --> pdb=" O GLNSE 64 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.694A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.599A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 124 removed outlier: 3.996A pdb=" N GLYSE 124 " --> pdb=" O LYSSE 120 " (cutoff:3.500A) Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 164 through 178 removed outlier: 4.821A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.683A 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: 3.555A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 231 removed outlier: 4.756A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASPSE 228 " --> pdb=" O THRSE 224 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARGSE 229 " --> pdb=" O ASNSE 225 " (cutoff:3.500A) Processing helix chain 'SE' and resid 232 through 237 removed outlier: 4.257A pdb=" N HISSE 236 " --> pdb=" O GLUSE 232 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TRPSE 237 " --> pdb=" O ILESE 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'SE' and resid 232 through 237' Processing helix chain 'SG' and resid 63 through 86 removed outlier: 3.513A pdb=" N ALASG 68 " --> pdb=" O ARGSG 64 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.935A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.819A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.616A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.516A pdb=" N VALSH 126 " --> pdb=" O PROSH 122 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'SH' and resid 122 through 127' Processing helix chain 'SH' and resid 143 through 151 removed outlier: 3.526A 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 34 through 46 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.534A pdb=" N PHESI 64 " --> pdb=" O ARGSI 60 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.218A 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: 3.604A 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: 5.111A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.179A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 5.044A 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: 4.401A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 13 through 23 Processing helix chain 'SJ' and resid 26 through 40 removed outlier: 4.936A pdb=" N PHESJ 30 " --> pdb=" O SERSJ 26 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYSSJ 31 " --> pdb=" O ARGSJ 27 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEUSJ 32 " --> pdb=" O SERSJ 28 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARGSJ 38 " --> pdb=" O GLNSJ 34 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 56 through 66 Processing helix chain 'SJ' and resid 95 through 107 removed outlier: 4.064A pdb=" N ARGSJ 99 " --> pdb=" O THRSJ 95 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 132 through 148 removed outlier: 3.553A pdb=" N ASPSJ 146 " --> pdb=" O ARGSJ 142 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 163 through 175 Processing helix chain 'SJ' and resid 183 through 188 removed outlier: 3.765A pdb=" N ARGSJ 187 " --> pdb=" O PROSJ 183 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N HISSJ 188 " --> pdb=" O GLNSJ 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'SJ' and resid 183 through 188' Processing helix chain 'SJ' and resid 207 through 213 removed outlier: 4.337A pdb=" N PHESJ 211 " --> pdb=" O ASPSJ 207 " (cutoff:3.500A) Proline residue: SJ 213 - end of helix Processing helix chain 'SJ' and resid 519 through 532 removed outlier: 4.336A pdb=" N LYSSJ 532 " --> pdb=" O LEUSJ 528 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 540 through 561 Processing helix chain 'SJ' and resid 664 through 677 Processing helix chain 'SJ' and resid 678 through 690 removed outlier: 4.065A pdb=" N PHESJ 689 " --> pdb=" O ILESJ 685 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASNSJ 690 " --> pdb=" O ASPSJ 686 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 702 through 713 removed outlier: 3.685A pdb=" N GLNSJ 711 " --> pdb=" O GLNSJ 707 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 720 through 731 removed outlier: 4.260A pdb=" N ARGSJ 730 " --> pdb=" O HISSJ 726 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRPSJ 731 " --> pdb=" O TYRSJ 727 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 825 through 843 removed outlier: 4.166A pdb=" N LYSSJ 829 " --> pdb=" O ASPSJ 825 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYSSJ 830 " --> pdb=" O SERSJ 826 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASPSJ 831 " --> pdb=" O ARGSJ 827 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 3.874A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.593A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 4.986A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 88 Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.658A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.268A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 229 through 237 removed outlier: 4.636A pdb=" N ALASK 233 " --> pdb=" O PROSK 229 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THRSK 234 " --> pdb=" O SERSK 230 " (cutoff:3.500A) Processing helix chain 'SK' and resid 238 through 244 Processing helix chain 'SL' and resid 32 through 50 Processing helix chain 'SL' and resid 106 through 122 Processing helix chain 'SL' and resid 131 through 138 Processing helix chain 'SL' and resid 141 through 153 removed outlier: 3.773A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 169 removed outlier: 5.095A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) Proline residue: SL 166 - end of helix Processing helix chain 'SL' and resid 170 through 177 removed outlier: 3.994A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 Processing helix chain 'SL' and resid 222 through 240 Processing helix chain 'SL' and resid 244 through 249 removed outlier: 6.640A pdb=" N VALSL 248 " --> pdb=" O LYSSL 244 " (cutoff:3.500A) removed outlier: 6.438A 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 13 through 18 removed outlier: 4.939A pdb=" N ILESM 18 " --> pdb=" O ALASM 14 " (cutoff:3.500A) Processing helix chain 'SM' and resid 19 through 28 Processing helix chain 'SM' and resid 30 through 42 Processing helix chain 'SM' and resid 50 through 56 removed outlier: 3.553A pdb=" N VALSM 54 " --> pdb=" O HISSM 50 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 77 removed outlier: 3.978A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 3.844A 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: 3.602A 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: 3.518A pdb=" N ALASM 130 " --> pdb=" O THRSM 126 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) Processing helix chain 'SM' and resid 136 through 148 removed outlier: 3.876A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 3.690A 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: 3.551A pdb=" N METSM 220 " --> pdb=" O ASPSM 216 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEUSM 242 " --> pdb=" O LEUSM 238 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 3.854A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.684A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEUSM 326 " --> pdb=" O LYSSM 322 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.516A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.435A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.606A 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 543 through 586 removed outlier: 3.508A pdb=" N ARGSM 557 " --> pdb=" O PHESM 553 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYSSM 558 " --> pdb=" O GLYSM 554 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILESM 559 " --> pdb=" O LYSSM 555 " (cutoff:3.500A) 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 removed outlier: 3.614A pdb=" N ARGSN 69 " --> pdb=" O GLUSN 65 " (cutoff:3.500A) 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 Processing helix chain 'SN' and resid 178 through 205 Processing helix chain 'SO' and resid 71 through 86 Proline residue: SO 86 - end of helix Processing helix chain 'SO' and resid 99 through 111 removed outlier: 4.258A pdb=" N ILESO 103 " --> pdb=" O LYSSO 99 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASNSO 104 " --> pdb=" O LEUSO 100 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLUSO 105 " --> pdb=" O PHESO 101 " (cutoff:3.500A) Processing helix chain 'SO' and resid 170 through 176 removed outlier: 3.720A pdb=" N GLUSO 174 " --> pdb=" O PROSO 170 " (cutoff:3.500A) removed outlier: 3.981A 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 170 through 176' Processing helix chain 'SO' and resid 177 through 190 Processing helix chain 'SO' and resid 261 through 293 removed outlier: 3.689A pdb=" N HISSO 265 " --> pdb=" O SERSO 261 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEUSO 289 " --> pdb=" O ASPSO 285 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYSSO 292 " --> pdb=" O LYSSO 288 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLUSO 293 " --> pdb=" O LEUSO 289 " (cutoff:3.500A) Processing helix chain 'SO' and resid 337 through 353 Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.220A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 61 removed outlier: 4.021A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 3.981A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.314A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 149 through 157 Processing helix chain 'SQ' and resid 183 through 194 Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 70 removed outlier: 3.581A pdb=" N LYSSR 50 " --> pdb=" O PHESR 46 " (cutoff:3.500A) Proline residue: SR 70 - end of helix Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 121 removed outlier: 3.586A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ASPSR 121 " --> pdb=" O METSR 117 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 145 removed outlier: 3.664A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) Processing helix chain 'SR' and resid 146 through 161 Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.654A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) Processing helix chain 'SR' and resid 229 through 234 removed outlier: 5.741A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) Processing helix chain 'SR' and resid 235 through 247 removed outlier: 4.084A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 Proline residue: SR 277 - end of helix removed outlier: 4.669A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 295 through 300 removed outlier: 5.264A pdb=" N SERSR 300 " --> pdb=" O ILESR 296 " (cutoff:3.500A) Processing helix chain 'SR' and resid 301 through 314 removed outlier: 3.643A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 3.568A pdb=" N GLYSR 350 " --> pdb=" O THRSR 346 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 4.254A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEUSR 357 " --> pdb=" O VALSR 353 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) Processing helix chain 'SR' and resid 380 through 391 removed outlier: 4.520A pdb=" N GLUSR 389 " --> pdb=" O ARGSR 385 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THRSR 390 " --> pdb=" O LYSSR 386 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.187A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 418 removed outlier: 4.831A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASPSR 418 " --> pdb=" O GLNSR 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 418' Processing helix chain 'SR' and resid 421 through 426 removed outlier: 4.249A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HISSR 426 " --> pdb=" O LEUSR 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 421 through 426' Processing helix chain 'SR' and resid 437 through 442 removed outlier: 4.162A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.784A 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 463 removed outlier: 3.573A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SS' and resid 140 through 146 removed outlier: 4.618A pdb=" N TYRSS 144 " --> pdb=" O PROSS 140 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASPSS 145 " --> pdb=" O LEUSS 141 " (cutoff:3.500A) removed outlier: 4.676A 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: 3.909A pdb=" N PHESS 246 " --> pdb=" O ASPSS 242 " (cutoff:3.500A) Proline residue: SS 248 - end of helix Processing helix chain 'SS' and resid 249 through 266 removed outlier: 3.717A pdb=" N LYSSS 253 " --> pdb=" O SERSS 249 " (cutoff:3.500A) Processing helix chain 'SS' and resid 323 through 334 removed outlier: 5.597A pdb=" N GLUSS 334 " --> pdb=" O TRPSS 330 " (cutoff:3.500A) Processing helix chain 'SS' and resid 349 through 354 removed outlier: 3.584A pdb=" N VALSS 353 " --> pdb=" O SERSS 349 " (cutoff:3.500A) Proline residue: SS 354 - end of helix No H-bonds generated for 'chain 'SS' and resid 349 through 354' Processing helix chain 'SS' and resid 358 through 372 removed outlier: 3.620A pdb=" N TYRSS 371 " --> pdb=" O CYSSS 367 " (cutoff:3.500A) Processing helix chain 'ST' and resid 169 through 198 removed outlier: 4.841A pdb=" N LYSST 198 " --> pdb=" O ALAST 194 " (cutoff:3.500A) Processing helix chain 'ST' and resid 214 through 229 removed outlier: 3.687A pdb=" N THRST 229 " --> pdb=" O ALAST 225 " (cutoff:3.500A) Processing helix chain 'ST' and resid 260 through 276 removed outlier: 3.954A pdb=" N LYSST 265 " --> pdb=" O PHEST 261 " (cutoff:3.500A) Processing helix chain 'SU' and resid 199 through 229 Proline residue: SU 229 - end of helix Processing helix chain 'SU' and resid 232 through 246 removed outlier: 3.548A pdb=" N LEUSU 236 " --> pdb=" O ASNSU 232 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEUSU 243 " --> pdb=" O LEUSU 239 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N METSU 244 " --> pdb=" O ARGSU 240 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLUSU 245 " --> pdb=" O SERSU 241 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLNSU 246 " --> pdb=" O METSU 242 " (cutoff:3.500A) Processing helix chain 'SU' and resid 251 through 270 Processing helix chain 'SU' and resid 279 through 286 removed outlier: 5.535A pdb=" N LYSSU 286 " --> pdb=" O GLUSU 282 " (cutoff:3.500A) Processing helix chain 'SU' and resid 288 through 322 Processing helix chain 'SU' and resid 332 through 353 removed outlier: 4.548A pdb=" N LYSSU 336 " --> pdb=" O LEUSU 332 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLYSU 337 " --> pdb=" O LYSSU 333 " (cutoff:3.500A) Processing helix chain 'SU' and resid 358 through 371 removed outlier: 3.575A pdb=" N ILESU 362 " --> pdb=" O PHESU 358 " (cutoff:3.500A) Proline residue: SU 368 - end of helix removed outlier: 3.802A pdb=" N ASNSU 371 " --> pdb=" O VALSU 367 " (cutoff:3.500A) Processing helix chain 'SU' and resid 374 through 392 Processing helix chain 'SU' and resid 395 through 413 Processing helix chain 'SU' and resid 417 through 427 removed outlier: 4.299A pdb=" N LEUSU 421 " --> pdb=" O ARGSU 417 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHESU 424 " --> pdb=" O METSU 420 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEUSU 425 " --> pdb=" O LEUSU 421 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N CYSSU 426 " --> pdb=" O LYSSU 422 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEUSU 427 " --> pdb=" O THRSU 423 " (cutoff:3.500A) Processing helix chain 'SU' and resid 464 through 480 removed outlier: 4.570A pdb=" N GLUSU 477 " --> pdb=" O ARGSU 473 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALASU 478 " --> pdb=" O GLUSU 474 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLUSU 479 " --> pdb=" O LEUSU 475 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALASU 480 " --> pdb=" O ARGSU 476 " (cutoff:3.500A) Processing helix chain 'SU' and resid 483 through 509 Processing helix chain 'SU' and resid 514 through 526 Processing helix chain 'SU' and resid 530 through 548 removed outlier: 3.567A pdb=" N ASPSU 535 " --> pdb=" O VALSU 531 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASPSU 536 " --> pdb=" O GLUSU 532 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLYSU 548 " --> pdb=" O LEUSU 544 " (cutoff:3.500A) Processing helix chain 'SU' and resid 551 through 569 removed outlier: 4.034A pdb=" N GLYSU 568 " --> pdb=" O HISSU 564 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLNSU 569 " --> pdb=" O ILESU 565 " (cutoff:3.500A) Processing helix chain 'SU' and resid 577 through 589 removed outlier: 5.135A pdb=" N PHESU 589 " --> pdb=" O TYRSU 585 " (cutoff:3.500A) Processing helix chain 'SU' and resid 596 through 611 removed outlier: 4.246A pdb=" N VALSU 600 " --> pdb=" O THRSU 596 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLUSU 601 " --> pdb=" O ASNSU 597 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILESU 602 " --> pdb=" O GLUSU 598 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLNSU 605 " --> pdb=" O GLUSU 601 " (cutoff:3.500A) Processing helix chain 'SU' and resid 619 through 637 removed outlier: 3.517A pdb=" N LEUSU 635 " --> pdb=" O CYSSU 631 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HISSU 636 " --> pdb=" O THRSU 632 " (cutoff:3.500A) Processing helix chain 'SU' and resid 638 through 656 removed outlier: 3.557A pdb=" N GLYSU 644 " --> pdb=" O ASNSU 640 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HISSU 654 " --> pdb=" O ARGSU 650 " (cutoff:3.500A) Processing helix chain 'SU' and resid 658 through 665 removed outlier: 4.763A pdb=" N LEUSU 662 " --> pdb=" O LYSSU 658 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEUSU 663 " --> pdb=" O THRSU 659 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SERSU 665 " --> pdb=" O LEUSU 661 " (cutoff:3.500A) Processing helix chain 'SU' and resid 679 through 684 removed outlier: 3.977A pdb=" N CYSSU 683 " --> pdb=" O GLUSU 679 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASNSU 684 " --> pdb=" O PROSU 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 679 through 684' Processing helix chain 'SU' and resid 690 through 699 removed outlier: 5.016A pdb=" N HISSU 694 " --> pdb=" O LEUSU 690 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALASU 695 " --> pdb=" O TRPSU 691 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HISSU 699 " --> pdb=" O ALASU 695 " (cutoff:3.500A) Processing helix chain 'SU' and resid 701 through 714 removed outlier: 3.590A pdb=" N GLNSU 705 " --> pdb=" O HISSU 701 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALASU 713 " --> pdb=" O ALASU 709 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLYSU 714 " --> pdb=" O HISSU 710 " (cutoff:3.500A) Processing helix chain 'SU' and resid 724 through 731 removed outlier: 3.521A pdb=" N SERSU 728 " --> pdb=" O LYSSU 724 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARGSU 730 " --> pdb=" O GLUSU 726 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SERSU 731 " --> pdb=" O LEUSU 727 " (cutoff:3.500A) Processing helix chain 'SU' and resid 732 through 740 removed outlier: 4.428A pdb=" N SERSU 740 " --> pdb=" O PHESU 736 " (cutoff:3.500A) Processing helix chain 'SU' and resid 769 through 786 removed outlier: 3.593A pdb=" N LEUSU 775 " --> pdb=" O ASPSU 771 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THRSU 785 " --> pdb=" O SERSU 781 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLUSU 786 " --> pdb=" O GLUSU 782 " (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 removed outlier: 3.517A pdb=" N ARGSV 56 " --> pdb=" O THRSV 52 " (cutoff:3.500A) Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.103A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.444A 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: 3.516A pdb=" N ARGSV 95 " --> pdb=" O ASPSV 91 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARGSV 111 " --> pdb=" O PHESV 107 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILESV 134 " --> pdb=" O ASNSV 130 " (cutoff:3.500A) Processing helix chain 'SW' and resid 178 through 183 removed outlier: 4.179A pdb=" N LEUSW 182 " --> pdb=" O SERSW 178 " (cutoff:3.500A) Processing helix chain 'SW' and resid 187 through 198 Processing helix chain 'SW' and resid 203 through 216 removed outlier: 4.478A 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: 3.508A pdb=" N LEUSW 234 " --> pdb=" O THRSW 230 " (cutoff:3.500A) Proline residue: SW 236 - end of helix Processing helix chain 'SW' and resid 260 through 276 Processing helix chain 'SW' and resid 290 through 301 Processing helix chain 'SW' and resid 308 through 318 Processing helix chain 'SW' and resid 334 through 342 Processing helix chain 'SW' and resid 343 through 355 Proline residue: SW 355 - end of helix Processing helix chain 'SW' and resid 368 through 379 removed outlier: 3.583A pdb=" N ILESW 377 " --> pdb=" O ASPSW 373 " (cutoff:3.500A) Processing helix chain 'SW' and resid 408 through 424 removed outlier: 4.918A pdb=" N PHESW 413 " --> pdb=" O SERSW 409 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEUSW 414 " --> pdb=" O GLUSW 410 " (cutoff:3.500A) Processing helix chain 'SW' and resid 434 through 449 Processing helix chain 'SW' and resid 460 through 475 removed outlier: 5.284A pdb=" N ASPSW 475 " --> pdb=" O PHESW 471 " (cutoff:3.500A) Processing helix chain 'SW' and resid 482 through 488 removed outlier: 5.749A pdb=" N GLYSW 488 " --> pdb=" O VALSW 484 " (cutoff:3.500A) Processing helix chain 'SW' and resid 505 through 516 Processing helix chain 'SW' and resid 531 through 545 removed outlier: 5.278A pdb=" N GLYSW 536 " --> pdb=" O PROSW 532 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHESW 537 " --> pdb=" O GLUSW 533 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEUSW 538 " --> pdb=" O GLUSW 534 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARGSW 539 " --> pdb=" O LEUSW 535 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYRSW 540 " --> pdb=" O GLYSW 536 " (cutoff:3.500A) Processing helix chain 'SW' and resid 561 through 573 removed outlier: 5.048A pdb=" N TYRSW 573 " --> pdb=" O ILESW 569 " (cutoff:3.500A) Processing helix chain 'SW' and resid 574 through 593 Processing helix chain 'SW' and resid 595 through 600 removed outlier: 3.538A pdb=" N ASNSW 600 " --> pdb=" O LYSSW 596 " (cutoff:3.500A) Processing helix chain 'SW' and resid 605 through 614 Processing helix chain 'SY' and resid 223 through 234 removed outlier: 3.524A pdb=" N GLUSY 228 " --> pdb=" O ALASY 224 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLNSY 229 " --> pdb=" O GLYSY 225 " (cutoff:3.500A) Proline residue: SY 234 - end of helix Processing helix chain 'SY' and resid 235 through 253 Processing helix chain 'SY' and resid 262 through 279 removed outlier: 3.578A pdb=" N TYRSY 266 " --> pdb=" O SERSY 262 " (cutoff:3.500A) Processing helix chain 'SY' and resid 281 through 293 removed outlier: 3.512A pdb=" N ASPSY 290 " --> pdb=" O GLYSY 286 " (cutoff:3.500A) Proline residue: SY 293 - end of helix Processing helix chain 'SY' and resid 294 through 307 removed outlier: 4.205A pdb=" N VALSY 298 " --> pdb=" O LEUSY 294 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLUSY 299 " --> pdb=" O SERSY 295 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUSY 305 " --> pdb=" O LEUSY 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VALSY 306 " --> pdb=" O GLUSY 302 " (cutoff:3.500A) Proline residue: SY 307 - end of helix Processing helix chain 'SY' and resid 320 through 332 Processing helix chain 'SY' and resid 358 through 364 Processing helix chain 'SY' and resid 370 through 381 Proline residue: SY 376 - end of helix Processing helix chain 'SY' and resid 396 through 407 Processing helix chain 'SY' and resid 419 through 433 removed outlier: 4.127A pdb=" N LYSSY 423 " --> pdb=" O ALASY 419 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SERSY 424 " --> pdb=" O GLUSY 420 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VALSY 425 " --> pdb=" O ARGSY 421 " (cutoff:3.500A) Processing helix chain 'SY' and resid 468 through 473 Proline residue: SY 473 - end of helix Processing helix chain 'SY' and resid 480 through 503 removed outlier: 5.434A pdb=" N ASNSY 503 " --> pdb=" O ILESY 499 " (cutoff:3.500A) Processing helix chain 'SY' and resid 520 through 535 removed outlier: 4.496A pdb=" N TRPSY 526 " --> pdb=" O GLUSY 522 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VALSY 527 " --> pdb=" O GLUSY 523 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VALSY 528 " --> pdb=" O ASNSY 524 " (cutoff:3.500A) Processing helix chain 'SY' and resid 562 through 567 removed outlier: 4.603A pdb=" N THRSY 566 " --> pdb=" O SERSY 562 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ARGSY 567 " --> pdb=" O LEUSY 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'SY' and resid 562 through 567' Processing helix chain 'SY' and resid 570 through 575 removed outlier: 3.615A pdb=" N ASNSY 575 " --> pdb=" O TYRSY 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'SY' and resid 570 through 575' Processing helix chain 'SZ' and resid 6 through 12 removed outlier: 3.710A pdb=" N ARGSZ 10 " --> pdb=" O GLYSZ 6 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYSSZ 12 " --> pdb=" O THRSZ 8 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 18 through 32 Proline residue: SZ 32 - end of helix Processing helix chain 'SZ' and resid 36 through 43 Processing helix chain 'SZ' and resid 48 through 57 Processing helix chain 'SZ' and resid 61 through 67 Proline residue: SZ 67 - end of helix Processing helix chain 'SZ' and resid 90 through 103 removed outlier: 4.676A pdb=" N LEUSZ 94 " --> pdb=" O LYSSZ 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASNSZ 95 " --> pdb=" O PROSZ 91 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUSZ 103 " --> pdb=" O ALASZ 99 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 112 through 126 Processing helix chain 'SZ' and resid 129 through 137 removed outlier: 3.591A pdb=" N ARGSZ 135 " --> pdb=" O LYSSZ 131 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLUSZ 137 " --> pdb=" O METSZ 133 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 144 through 159 Processing helix chain 'SZ' and resid 160 through 178 Processing sheet with id= 1, first strand: chain 'BA' and resid 11 through 17 removed outlier: 4.318A pdb=" N THRBA 59 " --> pdb=" O VALBA 74 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'BB' and resid 50 through 53 Processing sheet with id= 3, first strand: chain 'BB' and resid 65 through 68 Processing sheet with id= 4, first strand: chain 'BB' and resid 163 through 169 removed outlier: 6.727A pdb=" N LEUBB 163 " --> pdb=" O LEUBB 38 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VALBB 32 " --> pdb=" O VALBB 169 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 6, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 7, first strand: chain 'L8' and resid 11 through 16 removed outlier: 4.587A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEUL8 37 " --> pdb=" O VALL8 28 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.251A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.896A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LA' and resid 14 through 20 removed outlier: 7.535A pdb=" N SERLA 111 " --> pdb=" O LYSLA 153 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LA' and resid 57 through 60 removed outlier: 5.369A pdb=" N GLNLA 80 " --> pdb=" O PHELA 60 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LA' and resid 116 through 122 Processing sheet with id= 13, first strand: chain 'LB' and resid 78 through 82 Processing sheet with id= 14, first strand: chain 'LB' and resid 98 through 101 Processing sheet with id= 15, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.664A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.165A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.775A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LE' and resid 38 through 43 removed outlier: 4.260A pdb=" N ASPLE 38 " --> pdb=" O VALLE 64 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LG' and resid 24 through 27 removed outlier: 4.730A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LG' and resid 60 through 63 removed outlier: 6.795A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LG' and resid 87 through 90 removed outlier: 4.314A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.732A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.690A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LI' and resid 71 through 75 removed outlier: 3.523A pdb=" N GLNLI 72 " --> pdb=" O TYRLI 81 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.630A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 27, first strand: chain 'LN' and resid 53 through 59 removed outlier: 6.746A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.779A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LN' and resid 179 through 184 removed outlier: 4.948A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LN' and resid 286 through 289 removed outlier: 3.666A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LN' and resid 77 through 80 Processing sheet with id= 32, first strand: chain 'LN' and resid 88 through 93 removed outlier: 3.761A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.830A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 35, first strand: chain 'LT' and resid 56 through 60 removed outlier: 6.022A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THRLT 59 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LT' and resid 8 through 12 removed outlier: 5.933A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LT' and resid 6 through 10 Processing sheet with id= 38, first strand: chain 'LW' and resid 15 through 18 removed outlier: 8.435A pdb=" N THRLW 15 " --> pdb=" O HISLW 28 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HISLW 28 " --> pdb=" O THRLW 15 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N THRLW 17 " --> pdb=" O ALALW 26 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'NB' and resid 200 through 204 removed outlier: 4.058A pdb=" N LYSNB 172 " --> pdb=" O ASPNB 142 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VALNB 174 " --> pdb=" O VALNB 144 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLYNB 261 " --> pdb=" O SERNB 306 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'NF' and resid 189 through 194 removed outlier: 3.688A pdb=" N ALANF 190 " --> pdb=" O HISNF 185 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASNNF 255 " --> pdb=" O THRNF 245 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYRNF 241 " --> pdb=" O LEUNF 259 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THRNF 218 " --> pdb=" O VALNF 244 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'NH' and resid 36 through 39 Processing sheet with id= 42, first strand: chain 'NH' and resid 95 through 99 removed outlier: 4.946A pdb=" N TYRNH 95 " --> pdb=" O GLYNH 130 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'NI' and resid 196 through 200 removed outlier: 3.584A pdb=" N ALANI 169 " --> pdb=" O ASPNI 218 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VALNI 136 " --> pdb=" O THRNI 274 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'NI' and resid 364 through 368 removed outlier: 4.144A pdb=" N METNI 479 " --> pdb=" O THRNI 313 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'NM' and resid 19 through 22 removed outlier: 7.375A pdb=" N PHENM 19 " --> pdb=" O ARGNM 30 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'NM' and resid 51 through 56 removed outlier: 5.291A pdb=" N CYSNM 61 " --> pdb=" O LEUNM 83 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'NQ' and resid 28 through 34 removed outlier: 4.293A pdb=" N ILENQ 19 " --> pdb=" O THRNQ 15 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYSNQ 316 " --> pdb=" O GLYNQ 14 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'NQ' and resid 46 through 51 removed outlier: 4.211A pdb=" N ALANQ 47 " --> pdb=" O GLYNQ 61 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLNNQ 57 " --> pdb=" O GLYNQ 51 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THRNQ 56 " --> pdb=" O THRNQ 72 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRNQ 66 " --> pdb=" O CYSNQ 62 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARGNQ 65 " --> pdb=" O CYSNQ 83 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLYNQ 79 " --> pdb=" O HISNQ 69 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'NQ' and resid 92 through 95 removed outlier: 3.825A pdb=" N GLYNQ 92 " --> pdb=" O CYSNQ 103 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEUNQ 125 " --> pdb=" O VALNQ 111 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'NQ' and resid 135 through 139 removed outlier: 5.555A pdb=" N VALNQ 145 " --> pdb=" O ASPNQ 139 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N HISNQ 144 " --> pdb=" O LEUNQ 160 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEUNQ 160 " --> pdb=" O HISNQ 144 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'NQ' and resid 188 through 192 removed outlier: 3.638A pdb=" N ASPNQ 188 " --> pdb=" O CYSNQ 201 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LYSNQ 197 " --> pdb=" O LEUNQ 192 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N HISNQ 205 " --> pdb=" O TYRNQ 225 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYRNQ 225 " --> pdb=" O HISNQ 205 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEUNQ 221 " --> pdb=" O VALNQ 209 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'NQ' and resid 232 through 236 removed outlier: 5.804A pdb=" N SERNQ 241 " --> pdb=" O THRNQ 236 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ASNNQ 240 " --> pdb=" O LEUNQ 256 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLUNQ 253 " --> pdb=" O LEUNQ 262 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGNQ 260 " --> pdb=" O ASPNQ 255 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'NQ' and resid 273 through 278 removed outlier: 5.530A pdb=" N LEUNQ 283 " --> pdb=" O HISNQ 278 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLYNQ 288 " --> pdb=" O VALNQ 292 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VALNQ 292 " --> pdb=" O GLYNQ 288 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'NS' and resid 169 through 173 removed outlier: 4.859A pdb=" N THRNS 148 " --> pdb=" O TYRNS 173 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLUNS 200 " --> pdb=" O SERNS 149 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLYNS 207 " --> pdb=" O ASNNS 199 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASNNS 206 " --> pdb=" O METNS 223 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N HISNS 220 " --> pdb=" O ARGNS 317 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHENS 312 " --> pdb=" O PHENS 290 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SA' and resid 7 through 10 removed outlier: 5.009A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.421A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SC' and resid 147 through 153 removed outlier: 4.313A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 59, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.378A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'SD' and resid 159 through 162 Processing sheet with id= 61, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 62, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.758A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 64, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.490A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.522A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'SH' and resid 72 through 76 removed outlier: 3.738A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SI' and resid 147 through 151 removed outlier: 4.201A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SJ' and resid 86 through 91 removed outlier: 3.637A pdb=" N GLNSJ 91 " --> pdb=" O ASPSJ 76 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASPSJ 117 " --> pdb=" O LEUSJ 51 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSSJ 157 " --> pdb=" O ASNSJ 116 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 70, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 71, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 72, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 73, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.514A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEUSL 78 " --> pdb=" O ILESL 205 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'SL' and resid 127 through 130 Processing sheet with id= 75, first strand: chain 'SL' and resid 210 through 217 removed outlier: 6.156A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEUSL 251 " --> pdb=" O ILESL 263 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SM' and resid 179 through 184 Processing sheet with id= 77, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 78, first strand: chain 'SO' and resid 87 through 91 removed outlier: 3.986A pdb=" N ASPSO 91 " --> pdb=" O ILESO 64 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SERSO 66 " --> pdb=" O ASPSO 91 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALASO 120 " --> pdb=" O SERSO 67 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEUSO 126 " --> pdb=" O VALSO 143 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYSSO 140 " --> pdb=" O ILESO 241 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALASO 228 " --> pdb=" O ILESO 223 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASNSO 219 " --> pdb=" O ILESO 232 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHESO 217 " --> pdb=" O PROSO 234 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHESO 236 " --> pdb=" O ILESO 215 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILESO 215 " --> pdb=" O PHESO 236 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASPSO 203 " --> pdb=" O ILESO 222 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'SO' and resid 137 through 140 removed outlier: 3.612A pdb=" N LYSSO 242 " --> pdb=" O LYSSO 140 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 5.156A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.804A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 83, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.733A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.488A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'SR' and resid 205 through 211 removed outlier: 5.288A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEUSR 173 " --> pdb=" O VALSR 220 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLYSR 224 " --> pdb=" O GLYSR 175 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEUSR 172 " --> pdb=" O ALASR 250 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N CYSSR 174 " --> pdb=" O LEUSR 252 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VALSR 254 " --> pdb=" O CYSSR 174 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYRSR 176 " --> pdb=" O VALSR 254 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASPSR 256 " --> pdb=" O TYRSR 176 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'SS' and resid 183 through 188 removed outlier: 6.590A pdb=" N ARGSS 183 " --> pdb=" O LEUSS 196 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEUSS 196 " --> pdb=" O ARGSS 183 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARGSS 192 " --> pdb=" O ASPSS 187 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'SV' and resid 3 through 6 removed outlier: 6.456A pdb=" N GLUSV 4 " --> pdb=" O PROSV 12 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N CYSSV 6 " --> pdb=" O SERSV 10 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'SV' and resid 18 through 22 Processing sheet with id= 89, first strand: chain 'SW' and resid 281 through 285 Processing sheet with id= 90, first strand: chain 'SW' and resid 400 through 406 removed outlier: 3.538A pdb=" N ILESW 529 " --> pdb=" O GLNSW 499 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'SW' and resid 452 through 455 Processing sheet with id= 92, first strand: chain 'SY' and resid 334 through 337 removed outlier: 6.681A pdb=" N ASNSY 334 " --> pdb=" O TYRSY 349 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THRSY 344 " --> pdb=" O THRSY 314 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VALSY 310 " --> pdb=" O VALSY 348 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N HISSY 365 " --> pdb=" O ASNSY 315 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'SY' and resid 436 through 442 removed outlier: 5.635A pdb=" N ASNSY 436 " --> pdb=" O GLYSY 410 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYRSY 442 " --> pdb=" O ASPSY 416 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASPSY 460 " --> pdb=" O METSY 391 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLYSY 510 " --> pdb=" O LYSSY 586 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYSSY 583 " --> pdb=" O VALSY 540 " (cutoff:3.500A) 4751 hydrogen bonds defined for protein. 14132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2059 hydrogen bonds 3574 hydrogen bond angles 0 basepair planarities 785 basepair parallelities 1205 stacking parallelities Total time for adding SS restraints: 165.91 Time building geometry restraints manager: 59.75 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: 62300 1.41 - 1.64: 93895 1.64 - 1.86: 641 1.86 - 2.09: 0 2.09 - 2.31: 12 Bond restraints: 156848 Sorted by residual: bond pdb=" N7 GDPSR1001 " pdb=" C5 GDPSR1001 " ideal model delta sigma weight residual 1.350 1.518 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C6 GDPSR1001 " pdb=" O6 GDPSR1001 " ideal model delta sigma weight residual 1.250 1.398 -0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" C2 GDPSR1001 " pdb=" N2 GDPSR1001 " ideal model delta sigma weight residual 1.355 1.451 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" N1 GDPSR1001 " pdb=" C2 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.406 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1' GDPSR1001 " pdb=" N9 GDPSR1001 " ideal model delta sigma weight residual 1.485 1.426 0.059 2.00e-02 2.50e+03 8.67e+00 ... (remaining 156843 not shown) Histogram of bond angle deviations from ideal: 71.97 - 85.45: 12 85.45 - 98.93: 2 98.93 - 112.42: 98041 112.42 - 125.90: 116411 125.90 - 139.38: 8998 Bond angle restraints: 223464 Sorted by residual: angle pdb=" C TRPNO 64 " pdb=" N METNO 65 " pdb=" CA METNO 65 " ideal model delta sigma weight residual 120.28 126.29 -6.01 1.34e+00 5.57e-01 2.01e+01 angle pdb=" C8 GDPSR1001 " pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 108.00 120.88 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" N ILESO 232 " pdb=" CA ILESO 232 " pdb=" C ILESO 232 " ideal model delta sigma weight residual 111.90 108.79 3.11 8.10e-01 1.52e+00 1.47e+01 angle pdb=" CA PROSC 48 " pdb=" N PROSC 48 " pdb=" CD PROSC 48 " ideal model delta sigma weight residual 112.00 107.36 4.64 1.40e+00 5.10e-01 1.10e+01 angle pdb=" N GLYL9 186 " pdb=" CA GLYL9 186 " pdb=" C GLYL9 186 " ideal model delta sigma weight residual 113.79 110.21 3.58 1.17e+00 7.31e-01 9.35e+00 ... (remaining 223459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 92590 35.79 - 71.59: 5904 71.59 - 107.38: 811 107.38 - 143.17: 6 143.17 - 178.96: 11 Dihedral angle restraints: 99322 sinusoidal: 63638 harmonic: 35684 Sorted by residual: dihedral pdb=" O4' UL31381 " pdb=" C1' UL31381 " pdb=" N1 UL31381 " pdb=" C2 UL31381 " ideal model delta sinusoidal sigma weight residual 200.00 33.05 166.95 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' CL2 61 " pdb=" C1' CL2 61 " pdb=" N1 CL2 61 " pdb=" C2 CL2 61 " ideal model delta sinusoidal sigma weight residual 200.00 46.85 153.15 1 1.50e+01 4.44e-03 8.07e+01 dihedral pdb=" O4' CL32814 " pdb=" C1' CL32814 " pdb=" N1 CL32814 " pdb=" C2 CL32814 " ideal model delta sinusoidal sigma weight residual 232.00 53.04 178.96 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 99319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 22479 0.041 - 0.083: 3233 0.083 - 0.124: 960 0.124 - 0.166: 147 0.166 - 0.207: 12 Chirality restraints: 26831 Sorted by residual: chirality pdb=" C3' AL32798 " pdb=" C4' AL32798 " pdb=" O3' AL32798 " pdb=" C2' AL32798 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C1' AL3 746 " pdb=" O4' AL3 746 " pdb=" C2' AL3 746 " pdb=" N9 AL3 746 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb="FE1 SF4NM 401 " pdb=" S2 SF4NM 401 " pdb=" S3 SF4NM 401 " pdb=" S4 SF4NM 401 " both_signs ideal model delta sigma weight residual False -10.55 -10.35 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 26828 not shown) Planarity restraints: 19436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASNSC 47 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PROSC 48 " 0.188 5.00e-02 4.00e+02 pdb=" CA PROSC 48 " -0.057 5.00e-02 4.00e+02 pdb=" CD PROSC 48 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' GL1 39 " -0.047 2.00e-02 2.50e+03 1.94e-02 1.12e+01 pdb=" N9 GL1 39 " 0.042 2.00e-02 2.50e+03 pdb=" C8 GL1 39 " 0.010 2.00e-02 2.50e+03 pdb=" N7 GL1 39 " 0.000 2.00e-02 2.50e+03 pdb=" C5 GL1 39 " 0.000 2.00e-02 2.50e+03 pdb=" C6 GL1 39 " -0.007 2.00e-02 2.50e+03 pdb=" O6 GL1 39 " -0.014 2.00e-02 2.50e+03 pdb=" N1 GL1 39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GL1 39 " 0.003 2.00e-02 2.50e+03 pdb=" N2 GL1 39 " 0.002 2.00e-02 2.50e+03 pdb=" N3 GL1 39 " 0.009 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=" CD ARGSC 71 " -0.248 9.50e-02 1.11e+02 1.11e-01 8.07e+00 pdb=" NE ARGSC 71 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARGSC 71 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARGSC 71 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARGSC 71 " -0.005 2.00e-02 2.50e+03 ... (remaining 19433 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.59: 1167 2.59 - 3.23: 134807 3.23 - 3.87: 316126 3.87 - 4.50: 439134 4.50 - 5.14: 617003 Nonbonded interactions: 1508237 Sorted by model distance: nonbonded pdb=" OP2 GL3 356 " pdb="MG MGL36008 " model vdw 1.957 2.170 nonbonded pdb=" O6 GL3 356 " pdb="MG MGL36010 " model vdw 1.970 2.170 nonbonded pdb=" OG1 THRBA 105 " pdb=" OE1 GLUBA 108 " model vdw 1.972 2.440 nonbonded pdb=" OP1 AL32279 " pdb="MG MGL36017 " model vdw 1.988 2.170 nonbonded pdb=" OG1 THRSR 202 " pdb="MG MGSR1003 " model vdw 1.990 2.170 ... (remaining 1508232 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: 0.010 Normalize map: mean=0, sd=1: 6.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 25.990 Check model and map are aligned: 1.590 Set scattering table: 0.990 Process input model: 530.330 Find NCS groups from input model: 4.610 Set up NCS constraints: 0.510 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: 0.040 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 583.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 156848 Z= 0.172 Angle : 0.530 12.884 223464 Z= 0.279 Chirality : 0.035 0.207 26831 Planarity : 0.004 0.111 19436 Dihedral : 19.428 178.964 76152 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 2.08 (0.07), residues: 12058 helix: 2.36 (0.07), residues: 5344 sheet: 0.99 (0.13), residues: 1552 loop : 0.56 (0.08), residues: 5162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPNI 732 HIS 0.011 0.001 HISLA 25 PHE 0.021 0.001 PHENA 354 TYR 0.025 0.001 TYRSR 176 ARG 0.031 0.001 ARGNA 494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1337 time to evaluate : 9.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LN 301 ASN cc_start: 0.7695 (m-40) cc_final: 0.7468 (m-40) REVERT: NO 313 ARG cc_start: 0.6908 (mtp-110) cc_final: 0.6518 (mtp-110) REVERT: SA 156 ASP cc_start: 0.7802 (m-30) cc_final: 0.7578 (m-30) REVERT: SC 62 MET cc_start: 0.8146 (ttp) cc_final: 0.7927 (ttm) outliers start: 0 outliers final: 0 residues processed: 1337 average time/residue: 2.4145 time to fit residues: 4511.6592 Evaluate side-chains 1039 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1039 time to evaluate : 8.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1445 random chunks: chunk 1220 optimal weight: 7.9990 chunk 1095 optimal weight: 3.9990 chunk 607 optimal weight: 30.0000 chunk 374 optimal weight: 0.9990 chunk 738 optimal weight: 0.5980 chunk 585 optimal weight: 4.9990 chunk 1132 optimal weight: 0.1980 chunk 438 optimal weight: 8.9990 chunk 688 optimal weight: 8.9990 chunk 842 optimal weight: 9.9990 chunk 1312 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 104 ASN L7 46 ASN L7 90 HIS LA 75 GLN LA 97 ASN LA 116 HIS LB 93 GLN LC 37 HIS LC 50 GLN LC 125 GLN LE 127 GLN LH 57 GLN LI 96 HIS LK 62 HIS LN 42 HIS LS 30 GLN LW 66 HIS NA 259 GLN NA 376 HIS NA 501 ASN NA 510 ASN NB 450 ASN NI 333 ASN NI 409 ASN NI 454 HIS NI 722 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NM 172 GLN ** NO 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NO 127 ASN NO 212 ASN NS 139 GLN NS 212 HIS NS 277 GLN SA 178 ASN SA 245 HIS SA 276 ASN SC 190 HIS SC 211 HIS SC 227 HIS SC 266 GLN SC 268 GLN SD 63 GLN SE 64 GLN SE 149 ASN SE 225 ASN SG 42 ASN SG 140 GLN SH 60 GLN SH 67 GLN SI 113 GLN ** SI 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 166 GLN SI 219 HIS SI 249 GLN SJ 165 GLN SJ 527 ASN SJ 712 HIS SK 83 HIS SK 157 GLN SL 112 GLN SL 218 HIS SM 16 ASN SM 154 HIS SQ 186 GLN SR 157 HIS SR 209 HIS SR 239 GLN SR 246 HIS SR 304 GLN SR 342 HIS SS 238 ASN SS 310 HIS ST 213 GLN ST 267 ASN SU 203 HIS SU 217 HIS SU 359 HIS SU 542 HIS SU 592 HIS SU 701 HIS SV 17 HIS SV 45 ASN SV 104 GLN SW 266 GLN SW 499 GLN SW 593 HIS SY 430 HIS Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 156848 Z= 0.239 Angle : 0.547 17.208 223464 Z= 0.285 Chirality : 0.038 0.235 26831 Planarity : 0.005 0.068 19436 Dihedral : 21.234 178.739 51995 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.15 % Allowed : 6.64 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 2.08 (0.07), residues: 12058 helix: 2.43 (0.07), residues: 5446 sheet: 0.83 (0.13), residues: 1551 loop : 0.48 (0.08), residues: 5061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPSU 464 HIS 0.013 0.001 HISLA 25 PHE 0.028 0.002 PHESW 233 TYR 0.027 0.002 TYRNA 400 ARG 0.009 0.001 ARGSH 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1098 time to evaluate : 9.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LA 69 ARG cc_start: 0.8121 (mpp80) cc_final: 0.7766 (mtm-85) REVERT: LN 156 TYR cc_start: 0.8789 (m-80) cc_final: 0.8566 (m-80) REVERT: LN 301 ASN cc_start: 0.7940 (m-40) cc_final: 0.7653 (m-40) REVERT: LS 7 ARG cc_start: 0.7063 (mtm110) cc_final: 0.6812 (mtm110) REVERT: NA 280 LEU cc_start: 0.7443 (tp) cc_final: 0.7241 (tp) REVERT: NA 354 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: NI 570 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.6262 (mmp-170) REVERT: NO 135 MET cc_start: 0.8171 (mtp) cc_final: 0.7970 (mtp) REVERT: NO 313 ARG cc_start: 0.7042 (mtp-110) cc_final: 0.6713 (mtp-110) REVERT: SA 156 ASP cc_start: 0.7900 (m-30) cc_final: 0.7657 (m-30) REVERT: SC 62 MET cc_start: 0.8060 (ttp) cc_final: 0.7822 (ttm) REVERT: SH 183 TYR cc_start: 0.8590 (t80) cc_final: 0.8339 (t80) REVERT: SN 100 ASP cc_start: 0.6460 (t0) cc_final: 0.6054 (t0) REVERT: SR 238 MET cc_start: 0.8420 (mmm) cc_final: 0.8059 (mmm) REVERT: SR 294 LYS cc_start: 0.7846 (mmtp) cc_final: 0.7624 (tppp) REVERT: SR 395 LYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5810 (pttm) REVERT: SS 333 GLN cc_start: 0.8399 (tt0) cc_final: 0.8016 (tt0) REVERT: SV 109 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7786 (mmp) outliers start: 114 outliers final: 45 residues processed: 1153 average time/residue: 2.3431 time to fit residues: 3816.8680 Evaluate side-chains 1055 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1006 time to evaluate : 9.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 77 SER Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 92 LEU Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 67 ILE Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LB residue 107 SER Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 74 ILE Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NA residue 323 HIS Chi-restraints excluded: chain NA residue 354 PHE Chi-restraints excluded: chain NA residue 566 TYR Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NF residue 204 SER Chi-restraints excluded: chain NH residue 152 ASP Chi-restraints excluded: chain NI residue 570 ARG Chi-restraints excluded: chain NM residue 11 LEU Chi-restraints excluded: chain NM residue 25 THR Chi-restraints excluded: chain NS residue 79 LEU Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SJ residue 168 LEU Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SQ residue 122 MET Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 395 LYS Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain SU residue 589 PHE Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 286 MET Chi-restraints excluded: chain SW residue 292 SER Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 294 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1445 random chunks: chunk 729 optimal weight: 20.0000 chunk 407 optimal weight: 8.9990 chunk 1092 optimal weight: 5.9990 chunk 893 optimal weight: 8.9990 chunk 361 optimal weight: 0.9980 chunk 1314 optimal weight: 1.9990 chunk 1420 optimal weight: 8.9990 chunk 1170 optimal weight: 3.9990 chunk 1303 optimal weight: 7.9990 chunk 448 optimal weight: 30.0000 chunk 1054 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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** L7 167 HIS LA 155 GLN LB 93 GLN LC 125 GLN LE 114 GLN LK 67 GLN LN 328 ASN LS 20 GLN LS 30 GLN LU 26 HIS NA 565 ASN NA 572 GLN NB 16 HIS NB 450 ASN NH 111 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NO 101 GLN NO 127 ASN NO 212 ASN ** NQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SA 299 GLN SC 245 GLN SC 268 GLN SG 140 GLN SI 71 GLN SI 113 GLN SI 166 GLN SL 46 HIS SM 16 ASN SM 209 HIS SM 563 ASN SQ 58 ASN SR 35 HIS SR 37 HIS SS 208 GLN SS 238 ASN ST 163 ASN SV 45 ASN SV 115 ASN SW 206 GLN SW 456 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 156848 Z= 0.366 Angle : 0.591 17.709 223464 Z= 0.305 Chirality : 0.041 0.262 26831 Planarity : 0.005 0.063 19436 Dihedral : 21.223 179.636 51995 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.82 % Allowed : 8.22 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 1.83 (0.07), residues: 12058 helix: 2.30 (0.07), residues: 5447 sheet: 0.66 (0.13), residues: 1539 loop : 0.27 (0.08), residues: 5072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPNI 732 HIS 0.020 0.002 HISLA 25 PHE 0.028 0.002 PHENH 143 TYR 0.028 0.002 TYRNM 119 ARG 0.009 0.001 ARGNI 533 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1041 time to evaluate : 10.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 114 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7310 (mtt180) REVERT: L9 161 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7062 (mmm) REVERT: LA 56 GLN cc_start: 0.8398 (mt0) cc_final: 0.8191 (mt0) REVERT: LA 69 ARG cc_start: 0.8156 (mpp80) cc_final: 0.7704 (mtm-85) REVERT: LN 168 MET cc_start: 0.7662 (mmm) cc_final: 0.7395 (mmt) REVERT: LN 174 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7416 (ptt90) REVERT: LQ 133 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: LS 7 ARG cc_start: 0.7095 (mtm110) cc_final: 0.6819 (mtm110) REVERT: NA 280 LEU cc_start: 0.7534 (tp) cc_final: 0.7262 (tp) REVERT: NA 354 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: NB 360 ASN cc_start: 0.7595 (p0) cc_final: 0.7302 (p0) REVERT: NH 54 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8333 (mm) REVERT: NI 321 ASP cc_start: 0.6532 (OUTLIER) cc_final: 0.6151 (p0) REVERT: NI 570 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.6249 (mmp-170) REVERT: NO 135 MET cc_start: 0.8131 (mtp) cc_final: 0.7827 (mtp) REVERT: NO 313 ARG cc_start: 0.7024 (mtp-110) cc_final: 0.6745 (mtp-110) REVERT: NQ 137 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.7934 (tpm170) REVERT: NS 298 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7007 (mmp80) REVERT: SA 156 ASP cc_start: 0.7933 (m-30) cc_final: 0.7702 (m-30) REVERT: SG 140 GLN cc_start: 0.7885 (tt0) cc_final: 0.7680 (tt0) REVERT: SM 441 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8154 (tppt) REVERT: SQ 118 LYS cc_start: 0.8198 (pptt) cc_final: 0.7812 (ptmm) REVERT: SR 294 LYS cc_start: 0.7795 (mmtp) cc_final: 0.7577 (tppp) REVERT: SR 388 MET cc_start: 0.5215 (ppp) cc_final: 0.4933 (mmt) REVERT: SR 455 LYS cc_start: 0.7985 (pttt) cc_final: 0.7659 (ptmt) REVERT: SS 333 GLN cc_start: 0.8419 (tt0) cc_final: 0.8193 (tt0) REVERT: SY 227 MET cc_start: 0.2184 (mmt) cc_final: 0.0394 (ptp) outliers start: 181 outliers final: 82 residues processed: 1128 average time/residue: 2.3387 time to fit residues: 3727.6997 Evaluate side-chains 1083 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 990 time to evaluate : 9.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 77 SER Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L6 residue 129 ARG Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 92 LEU Chi-restraints excluded: chain L9 residue 155 VAL Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LB residue 107 SER Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 74 ILE Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 54 LEU Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 292 LEU Chi-restraints excluded: chain LN residue 386 LYS Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 110 LYS Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 95 LYS Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain NA residue 267 THR Chi-restraints excluded: chain NA residue 323 HIS Chi-restraints excluded: chain NA residue 354 PHE Chi-restraints excluded: chain NA residue 504 VAL Chi-restraints excluded: chain NA residue 520 ASP Chi-restraints excluded: chain NB residue 47 ASP Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NF residue 171 ILE Chi-restraints excluded: chain NF residue 204 SER Chi-restraints excluded: chain NH residue 25 GLN Chi-restraints excluded: chain NH residue 26 LEU Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 321 ASP Chi-restraints excluded: chain NI residue 389 CYS Chi-restraints excluded: chain NI residue 410 VAL Chi-restraints excluded: chain NI residue 570 ARG Chi-restraints excluded: chain NM residue 11 LEU Chi-restraints excluded: chain NM residue 25 THR Chi-restraints excluded: chain NO residue 315 SER Chi-restraints excluded: chain NQ residue 137 ARG Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 85 LEU Chi-restraints excluded: chain NS residue 298 ARG Chi-restraints excluded: chain SD residue 224 THR Chi-restraints excluded: chain SE residue 223 ARG Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SH residue 95 SER Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SI residue 209 GLN Chi-restraints excluded: chain SJ residue 168 LEU Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 272 CYS Chi-restraints excluded: chain SM residue 441 LYS Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 266 LYS Chi-restraints excluded: chain SU residue 589 PHE Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 292 SER Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 241 LYS Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SZ residue 12 LYS Chi-restraints excluded: chain SZ residue 124 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1445 random chunks: chunk 1298 optimal weight: 3.9990 chunk 988 optimal weight: 7.9990 chunk 682 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 627 optimal weight: 0.0170 chunk 882 optimal weight: 4.9990 chunk 1319 optimal weight: 0.9990 chunk 1396 optimal weight: 10.0000 chunk 689 optimal weight: 3.9990 chunk 1250 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 44 GLN LA 25 HIS LA 155 GLN LC 125 GLN LE 58 HIS LE 95 HIS LE 114 GLN LI 14 ASN LK 67 GLN LS 30 GLN LT 20 ASN NA 565 ASN NH 105 GLN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN NM 160 ASN NO 127 ASN NO 332 GLN ** NQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 268 GLN SI 71 GLN SI 113 GLN SI 166 GLN ** SJ 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 30 GLN SM 16 ASN SM 563 ASN SQ 58 ASN SR 342 HIS SS 208 GLN ST 267 ASN SU 232 ASN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 156848 Z= 0.263 Angle : 0.527 18.106 223464 Z= 0.273 Chirality : 0.038 0.249 26831 Planarity : 0.004 0.049 19436 Dihedral : 21.183 179.128 51995 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.81 % Allowed : 9.23 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 1.87 (0.07), residues: 12058 helix: 2.38 (0.07), residues: 5452 sheet: 0.62 (0.13), residues: 1554 loop : 0.24 (0.08), residues: 5052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPNI 732 HIS 0.009 0.001 HISLA 25 PHE 0.026 0.002 PHESW 233 TYR 0.024 0.002 TYRNM 119 ARG 0.009 0.000 ARGNK 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1014 time to evaluate : 9.732 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: BA 114 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7257 (mtt180) REVERT: LA 56 GLN cc_start: 0.8402 (mt0) cc_final: 0.8162 (mt0) REVERT: LA 69 ARG cc_start: 0.8156 (mpp80) cc_final: 0.7653 (mtm-85) REVERT: LC 50 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: LN 174 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7323 (ptt90) REVERT: LQ 133 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: LS 7 ARG cc_start: 0.7116 (mtm110) cc_final: 0.6802 (mtm110) REVERT: LS 20 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7656 (tp-100) REVERT: LU 99 LYS cc_start: 0.8301 (mtpp) cc_final: 0.8070 (ttmp) REVERT: LW 80 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6876 (mt-10) REVERT: NA 280 LEU cc_start: 0.7565 (tp) cc_final: 0.7307 (tp) REVERT: NA 354 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: NA 433 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.6651 (t80) REVERT: NB 360 ASN cc_start: 0.7528 (p0) cc_final: 0.7285 (p0) REVERT: NH 54 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8283 (mm) REVERT: NI 321 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.6119 (p0) REVERT: NO 313 ARG cc_start: 0.6938 (mtp-110) cc_final: 0.6648 (mtp-110) REVERT: NS 234 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7541 (mtm180) REVERT: NS 298 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7013 (mmp80) REVERT: SA 156 ASP cc_start: 0.7906 (m-30) cc_final: 0.7674 (m-30) REVERT: SK 236 MET cc_start: 0.6003 (ptt) cc_final: 0.5537 (ppp) REVERT: SM 441 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8146 (tppt) REVERT: SO 329 LEU cc_start: 0.7722 (mp) cc_final: 0.7491 (mp) REVERT: SQ 118 LYS cc_start: 0.8200 (pptt) cc_final: 0.7822 (ptmm) REVERT: SQ 130 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7941 (mptp) REVERT: SR 294 LYS cc_start: 0.7783 (mmtp) cc_final: 0.7581 (tppp) REVERT: SR 388 MET cc_start: 0.5240 (ppp) cc_final: 0.4953 (mmt) REVERT: SR 452 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6390 (tp30) REVERT: SR 455 LYS cc_start: 0.7960 (pttt) cc_final: 0.7753 (ptmt) REVERT: ST 227 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8601 (p) REVERT: SV 109 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7803 (mmp) REVERT: SY 227 MET cc_start: 0.2060 (mmt) cc_final: 0.0447 (ptp) REVERT: SZ 5 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6963 (mtpt) outliers start: 180 outliers final: 85 residues processed: 1108 average time/residue: 2.3037 time to fit residues: 3608.3547 Evaluate side-chains 1092 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 990 time to evaluate : 8.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 25 THR Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain L6 residue 77 SER Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 92 LEU Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LB residue 107 SER Chi-restraints excluded: chain LC residue 50 GLN Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 54 LEU Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 292 LEU Chi-restraints excluded: chain LN residue 386 LYS Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain LW residue 85 LYS Chi-restraints excluded: chain NA residue 267 THR Chi-restraints excluded: chain NA residue 323 HIS Chi-restraints excluded: chain NA residue 354 PHE Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 433 TYR Chi-restraints excluded: chain NA residue 504 VAL Chi-restraints excluded: chain NA residue 520 ASP Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NF residue 171 ILE Chi-restraints excluded: chain NF residue 204 SER Chi-restraints excluded: chain NH residue 26 LEU Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 152 ASP Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 67 THR Chi-restraints excluded: chain NI residue 321 ASP Chi-restraints excluded: chain NI residue 410 VAL Chi-restraints excluded: chain NI residue 495 LEU Chi-restraints excluded: chain NM residue 11 LEU Chi-restraints excluded: chain NM residue 25 THR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NO residue 315 SER Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 113 HIS Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 140 THR Chi-restraints excluded: chain NS residue 234 ARG Chi-restraints excluded: chain NS residue 298 ARG Chi-restraints excluded: chain SD residue 46 ARG Chi-restraints excluded: chain SD residue 224 THR Chi-restraints excluded: chain SE residue 228 ASP Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SM residue 441 LYS Chi-restraints excluded: chain SN residue 134 THR Chi-restraints excluded: chain SO residue 100 LEU Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SQ residue 122 MET Chi-restraints excluded: chain SQ residue 130 LYS Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 452 GLU Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain ST residue 266 LYS Chi-restraints excluded: chain SU residue 366 ILE Chi-restraints excluded: chain SU residue 589 PHE Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 292 SER Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 294 LEU Chi-restraints excluded: chain SZ residue 5 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1445 random chunks: chunk 1163 optimal weight: 0.8980 chunk 792 optimal weight: 0.0570 chunk 20 optimal weight: 20.0000 chunk 1039 optimal weight: 8.9990 chunk 576 optimal weight: 0.9980 chunk 1191 optimal weight: 10.0000 chunk 965 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 713 optimal weight: 0.9980 chunk 1253 optimal weight: 0.9990 chunk 352 optimal weight: 3.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L8 44 GLN LA 155 GLN LC 125 GLN LE 58 HIS LE 114 GLN LE 127 GLN LI 14 ASN LK 60 HIS LK 67 GLN LS 30 GLN NA 290 GLN NA 501 ASN NA 565 ASN ** NB 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NM 160 ASN NO 127 ASN NQ 10 HIS SC 245 GLN SC 268 GLN SG 140 GLN SI 71 GLN SI 113 GLN SI 166 GLN ** SJ 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 82 GLN SK 86 ASN SM 16 ASN SM 563 ASN SN 148 GLN SQ 58 ASN SR 342 HIS SS 208 GLN ST 267 ASN SU 654 HIS SW 206 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 156848 Z= 0.124 Angle : 0.461 18.710 223464 Z= 0.239 Chirality : 0.034 0.224 26831 Planarity : 0.004 0.043 19436 Dihedral : 21.101 178.050 51995 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.31 % Allowed : 10.15 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 2.12 (0.08), residues: 12058 helix: 2.64 (0.07), residues: 5464 sheet: 0.58 (0.13), residues: 1555 loop : 0.35 (0.08), residues: 5039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPNI 732 HIS 0.005 0.001 HISSN 124 PHE 0.025 0.001 PHESW 233 TYR 0.018 0.001 TYRNM 119 ARG 0.009 0.000 ARGSH 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1032 time to evaluate : 9.846 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: L9 124 ASP cc_start: 0.8541 (p0) cc_final: 0.8083 (p0) REVERT: LA 56 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: LA 69 ARG cc_start: 0.8100 (mpp80) cc_final: 0.7611 (mtm-85) REVERT: LC 50 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: LK 65 ARG cc_start: 0.7372 (mmt180) cc_final: 0.6258 (mmt180) REVERT: LN 168 MET cc_start: 0.7656 (mmm) cc_final: 0.7253 (mmt) REVERT: LQ 133 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: LS 7 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6822 (mtm110) REVERT: LW 80 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6812 (mt-10) REVERT: NA 280 LEU cc_start: 0.7591 (tp) cc_final: 0.7290 (tp) REVERT: NA 354 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: NA 433 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6920 (t80) REVERT: NA 625 LEU cc_start: 0.7830 (mm) cc_final: 0.7626 (mp) REVERT: NH 54 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8159 (mm) REVERT: NO 313 ARG cc_start: 0.6938 (mtp-110) cc_final: 0.6657 (mtp-110) REVERT: NS 234 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7453 (mtm180) REVERT: SA 156 ASP cc_start: 0.7840 (m-30) cc_final: 0.7607 (m-30) REVERT: SK 236 MET cc_start: 0.5918 (ptt) cc_final: 0.5655 (ppp) REVERT: SL 67 MET cc_start: 0.8228 (mmm) cc_final: 0.7724 (mmt) REVERT: SM 441 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8135 (tppt) REVERT: SR 388 MET cc_start: 0.5329 (ppp) cc_final: 0.5006 (mmt) REVERT: ST 227 VAL cc_start: 0.8770 (t) cc_final: 0.8562 (p) REVERT: ST 251 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8266 (mtpt) REVERT: SV 109 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7832 (mmp) REVERT: SY 227 MET cc_start: 0.2378 (mmt) cc_final: 0.0868 (ptp) REVERT: SZ 122 MET cc_start: 0.8298 (mmt) cc_final: 0.8036 (mmt) outliers start: 130 outliers final: 51 residues processed: 1097 average time/residue: 2.3753 time to fit residues: 3691.9297 Evaluate side-chains 1047 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 985 time to evaluate : 9.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 25 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 77 SER Chi-restraints excluded: chain L7 residue 120 VAL Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 92 LEU Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 56 GLN Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 107 SER Chi-restraints excluded: chain LC residue 50 GLN Chi-restraints excluded: chain LE residue 74 ILE Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 292 LEU Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LN residue 386 LYS Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 27 GLU Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain NA residue 354 PHE Chi-restraints excluded: chain NA residue 433 TYR Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NF residue 171 ILE Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 495 LEU Chi-restraints excluded: chain NM residue 25 THR Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NO residue 236 LEU Chi-restraints excluded: chain NO residue 315 SER Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NS residue 234 ARG Chi-restraints excluded: chain SD residue 63 GLN Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SM residue 272 CYS Chi-restraints excluded: chain SM residue 441 LYS Chi-restraints excluded: chain SN residue 134 THR Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain ST residue 217 GLU Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain ST residue 251 LYS Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 292 SER Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 516 THR Chi-restraints excluded: chain SY residue 545 ASP Chi-restraints excluded: chain SZ residue 124 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1445 random chunks: chunk 469 optimal weight: 4.9990 chunk 1257 optimal weight: 2.9990 chunk 276 optimal weight: 10.0000 chunk 820 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 1398 optimal weight: 7.9990 chunk 1160 optimal weight: 1.9990 chunk 647 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 462 optimal weight: 9.9990 chunk 733 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 15 HIS L8 44 GLN ** LA 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 155 GLN LE 58 HIS LE 95 HIS LE 114 GLN LE 127 GLN LE 131 GLN LH 57 GLN LK 60 HIS ** LK 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 30 GLN NA 501 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NM 160 ASN NO 127 ASN NQ 57 GLN SA 43 ASN ** SC 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 268 GLN SE 206 GLN SG 106 GLN SG 140 GLN SI 113 GLN SI 166 GLN SK 82 GLN SK 86 ASN SM 16 ASN SM 563 ASN SQ 58 ASN SR 342 HIS SS 208 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 156848 Z= 0.331 Angle : 0.549 17.908 223464 Z= 0.282 Chirality : 0.039 0.250 26831 Planarity : 0.005 0.055 19436 Dihedral : 21.095 179.478 51995 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.82 % Allowed : 10.59 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 1.90 (0.07), residues: 12058 helix: 2.45 (0.07), residues: 5463 sheet: 0.57 (0.13), residues: 1563 loop : 0.21 (0.08), residues: 5032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPSA 108 HIS 0.009 0.001 HISNS 220 PHE 0.026 0.002 PHENH 143 TYR 0.022 0.002 TYRSJ 16 ARG 0.010 0.001 ARGLB 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1010 time to evaluate : 9.990 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: L9 161 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7048 (mmm) REVERT: LA 56 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: LA 156 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7726 (mp) REVERT: LK 65 ARG cc_start: 0.7351 (mmt180) cc_final: 0.6183 (mmt180) REVERT: LN 168 MET cc_start: 0.7701 (mmm) cc_final: 0.7309 (mmt) REVERT: LN 174 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7363 (ptt90) REVERT: LQ 133 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: LS 7 ARG cc_start: 0.7206 (mtm110) cc_final: 0.6929 (mtm110) REVERT: LS 20 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7707 (tp-100) REVERT: LW 80 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6875 (mt-10) REVERT: NA 280 LEU cc_start: 0.7780 (tp) cc_final: 0.7429 (tp) REVERT: NA 354 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: NA 433 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6563 (t80) REVERT: NH 54 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8277 (mm) REVERT: NI 321 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6124 (p0) REVERT: NO 313 ARG cc_start: 0.7060 (mtp-110) cc_final: 0.6771 (mtp-110) REVERT: NS 234 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7571 (mtm180) REVERT: NS 298 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7027 (mmp80) REVERT: SG 106 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: SJ 139 MET cc_start: 0.6406 (mmm) cc_final: 0.6049 (mmt) REVERT: SK 236 MET cc_start: 0.5926 (ptt) cc_final: 0.5597 (ppp) REVERT: SL 67 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7818 (mmt) REVERT: SM 441 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8146 (tppt) REVERT: SO 344 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7595 (ttmt) REVERT: SQ 130 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7830 (mtmm) REVERT: SR 388 MET cc_start: 0.5385 (ppp) cc_final: 0.5079 (mmt) REVERT: SU 410 LYS cc_start: 0.5034 (tmtm) cc_final: 0.4597 (tmtp) REVERT: SV 109 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7811 (mmp) REVERT: SY 227 MET cc_start: 0.2411 (mmt) cc_final: 0.0894 (ptp) REVERT: SY 312 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7626 (mt) REVERT: SY 421 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7090 (mtp180) REVERT: SZ 5 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7026 (tttt) outliers start: 181 outliers final: 108 residues processed: 1119 average time/residue: 2.3618 time to fit residues: 3745.0726 Evaluate side-chains 1115 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 986 time to evaluate : 8.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 77 SER Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L7 residue 120 VAL Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 92 LEU Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 56 GLN Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LA residue 156 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LB residue 107 SER Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LE residue 74 ILE Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 26 LYS Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 292 LEU Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LN residue 386 LYS Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 27 GLU Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LS residue 54 ILE Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 95 LYS Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain NA residue 267 THR Chi-restraints excluded: chain NA residue 354 PHE Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 433 TYR Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NF residue 171 ILE Chi-restraints excluded: chain NH residue 26 LEU Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NH residue 152 ASP Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 67 THR Chi-restraints excluded: chain NI residue 321 ASP Chi-restraints excluded: chain NI residue 389 CYS Chi-restraints excluded: chain NI residue 410 VAL Chi-restraints excluded: chain NI residue 495 LEU Chi-restraints excluded: chain NM residue 11 LEU Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NO residue 315 SER Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 113 HIS Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 234 ARG Chi-restraints excluded: chain NS residue 298 ARG Chi-restraints excluded: chain SA residue 310 HIS Chi-restraints excluded: chain SD residue 63 GLN Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SD residue 224 THR Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 106 GLN Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SJ residue 168 LEU Chi-restraints excluded: chain SK residue 90 ASP Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 67 MET Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 228 THR Chi-restraints excluded: chain SM residue 272 CYS Chi-restraints excluded: chain SM residue 441 LYS Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 344 LYS Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SQ residue 122 MET Chi-restraints excluded: chain SQ residue 130 LYS Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 265 MET Chi-restraints excluded: chain SS residue 333 GLN Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 217 GLU Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 366 ILE Chi-restraints excluded: chain SU residue 589 PHE Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 292 SER Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 241 LYS Chi-restraints excluded: chain SY residue 312 LEU Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 421 ARG Chi-restraints excluded: chain SY residue 516 THR Chi-restraints excluded: chain SY residue 517 CYS Chi-restraints excluded: chain SY residue 545 ASP Chi-restraints excluded: chain SZ residue 5 LYS Chi-restraints excluded: chain SZ residue 124 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1445 random chunks: chunk 1347 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 796 optimal weight: 9.9990 chunk 1020 optimal weight: 5.9990 chunk 791 optimal weight: 9.9990 chunk 1176 optimal weight: 1.9990 chunk 780 optimal weight: 9.9990 chunk 1392 optimal weight: 1.9990 chunk 871 optimal weight: 1.9990 chunk 849 optimal weight: 0.9990 chunk 643 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 15 HIS L8 44 GLN LA 155 GLN LE 58 HIS LE 114 GLN LE 127 GLN LE 131 GLN LK 60 HIS ** LK 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 30 GLN NA 501 ASN NA 565 ASN NF 72 ASN NI 579 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NM 160 ASN NO 127 ASN NQ 57 GLN ** SC 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 268 GLN SE 206 GLN ** SG 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN SI 71 GLN SI 113 GLN SI 166 GLN SK 82 GLN SK 86 ASN SM 16 ASN SM 563 ASN SQ 58 ASN SR 342 HIS SS 208 GLN ST 267 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 156848 Z= 0.259 Angle : 0.519 17.847 223464 Z= 0.268 Chirality : 0.037 0.243 26831 Planarity : 0.004 0.047 19436 Dihedral : 21.105 179.022 51995 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.82 % Allowed : 10.95 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 1.88 (0.07), residues: 12058 helix: 2.46 (0.07), residues: 5457 sheet: 0.54 (0.13), residues: 1567 loop : 0.19 (0.08), residues: 5034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPLN 196 HIS 0.007 0.001 HISNS 220 PHE 0.026 0.001 PHESW 233 TYR 0.021 0.002 TYRNA 400 ARG 0.011 0.000 ARGSW 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1006 time to evaluate : 9.837 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: L9 161 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7006 (mmm) REVERT: LA 56 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: LK 65 ARG cc_start: 0.7289 (mmt180) cc_final: 0.6137 (mmt180) REVERT: LN 174 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7397 (ptt90) REVERT: LQ 133 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: LS 7 ARG cc_start: 0.7216 (mtm110) cc_final: 0.6947 (mtm110) REVERT: LS 20 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7652 (tp-100) REVERT: LW 80 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: NA 280 LEU cc_start: 0.7621 (tp) cc_final: 0.7252 (tp) REVERT: NA 312 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7422 (mp) REVERT: NA 354 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: NA 433 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.6810 (t80) REVERT: NH 54 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8270 (mm) REVERT: NI 321 ASP cc_start: 0.6496 (OUTLIER) cc_final: 0.6114 (p0) REVERT: NI 479 MET cc_start: 0.7681 (ttm) cc_final: 0.7006 (tpp) REVERT: NO 313 ARG cc_start: 0.7057 (mtp-110) cc_final: 0.6775 (mtp-110) REVERT: NS 234 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7489 (mtm180) REVERT: NS 298 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7027 (mmp80) REVERT: SK 236 MET cc_start: 0.5967 (ptt) cc_final: 0.5661 (ppp) REVERT: SL 67 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7825 (mmt) REVERT: SM 441 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8140 (tppt) REVERT: SM 552 MET cc_start: 0.5356 (mpm) cc_final: 0.5149 (mmm) REVERT: SO 344 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7591 (ttmt) REVERT: SQ 130 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7961 (mptp) REVERT: SR 388 MET cc_start: 0.5405 (OUTLIER) cc_final: 0.5132 (mmt) REVERT: SU 410 LYS cc_start: 0.4699 (tmtm) cc_final: 0.4245 (tmtp) REVERT: SV 109 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7842 (mmp) REVERT: SY 227 MET cc_start: 0.2288 (mmt) cc_final: 0.0895 (ptp) REVERT: SY 312 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7676 (mt) REVERT: SY 421 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7048 (mtp180) REVERT: SZ 5 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6917 (mtpt) REVERT: SZ 137 GLU cc_start: 0.7173 (tp30) cc_final: 0.6951 (tp30) outliers start: 181 outliers final: 103 residues processed: 1118 average time/residue: 2.3723 time to fit residues: 3761.5596 Evaluate side-chains 1108 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 984 time to evaluate : 9.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 77 SER Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L7 residue 120 VAL Chi-restraints excluded: chain L8 residue 2 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 92 LEU Chi-restraints excluded: chain L9 residue 155 VAL Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 56 GLN Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 71 LYS Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LB residue 107 SER Chi-restraints excluded: chain LE residue 74 ILE Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 26 LYS Chi-restraints excluded: chain LH residue 54 LEU Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 292 LEU Chi-restraints excluded: chain LN residue 386 LYS Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 27 GLU Chi-restraints excluded: chain LS residue 54 ILE Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain NA residue 267 THR Chi-restraints excluded: chain NA residue 294 LEU Chi-restraints excluded: chain NA residue 312 LEU Chi-restraints excluded: chain NA residue 354 PHE Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 433 TYR Chi-restraints excluded: chain NA residue 520 ASP Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NF residue 171 ILE Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 67 THR Chi-restraints excluded: chain NI residue 321 ASP Chi-restraints excluded: chain NI residue 389 CYS Chi-restraints excluded: chain NI residue 410 VAL Chi-restraints excluded: chain NI residue 495 LEU Chi-restraints excluded: chain NM residue 11 LEU Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NO residue 315 SER Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 113 HIS Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 234 ARG Chi-restraints excluded: chain NS residue 298 ARG Chi-restraints excluded: chain SA residue 310 HIS Chi-restraints excluded: chain SD residue 63 GLN Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SD residue 224 THR Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SI residue 30 LYS Chi-restraints excluded: chain SJ residue 168 LEU Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 67 MET Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 228 THR Chi-restraints excluded: chain SM residue 272 CYS Chi-restraints excluded: chain SM residue 441 LYS Chi-restraints excluded: chain SN residue 71 ASP Chi-restraints excluded: chain SO residue 65 PHE Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 344 LYS Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SQ residue 122 MET Chi-restraints excluded: chain SQ residue 130 LYS Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 388 MET Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 265 MET Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 217 GLU Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 366 ILE Chi-restraints excluded: chain SU residue 589 PHE Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SV residue 62 GLU Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 292 SER Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 241 LYS Chi-restraints excluded: chain SY residue 312 LEU Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 402 MET Chi-restraints excluded: chain SY residue 421 ARG Chi-restraints excluded: chain SY residue 516 THR Chi-restraints excluded: chain SY residue 517 CYS Chi-restraints excluded: chain SY residue 545 ASP Chi-restraints excluded: chain SZ residue 5 LYS Chi-restraints excluded: chain SZ residue 124 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1445 random chunks: chunk 861 optimal weight: 0.6980 chunk 556 optimal weight: 9.9990 chunk 831 optimal weight: 8.9990 chunk 419 optimal weight: 50.0000 chunk 273 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 885 optimal weight: 5.9990 chunk 948 optimal weight: 0.8980 chunk 688 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 1094 optimal weight: 4.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 15 HIS L8 44 GLN LA 155 GLN LE 58 HIS LE 95 HIS LE 114 GLN LE 127 GLN LE 131 GLN LH 57 GLN LK 60 HIS ** LK 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 30 GLN NA 501 ASN NF 72 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 92 GLN NM 160 ASN NO 20 ASN NO 127 ASN NQ 57 GLN ** SC 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 268 GLN SE 236 HIS SG 106 GLN SG 140 GLN SI 71 GLN SI 113 GLN SI 166 GLN SK 82 GLN SK 86 ASN SM 16 ASN SM 563 ASN SQ 58 ASN SR 342 HIS SS 208 GLN ST 267 ASN SU 232 ASN SW 277 HIS ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 156848 Z= 0.394 Angle : 0.599 17.019 223464 Z= 0.307 Chirality : 0.041 0.263 26831 Planarity : 0.005 0.063 19436 Dihedral : 21.153 179.961 51995 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.91 % Allowed : 10.99 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 1.66 (0.07), residues: 12058 helix: 2.26 (0.07), residues: 5450 sheet: 0.48 (0.13), residues: 1575 loop : 0.07 (0.08), residues: 5033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPSA 108 HIS 0.010 0.001 HISNS 220 PHE 0.030 0.002 PHENH 143 TYR 0.026 0.002 TYRNO 61 ARG 0.010 0.001 ARGSW 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1011 time to evaluate : 9.931 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: L9 161 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7167 (mmm) REVERT: LA 56 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: LA 156 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7680 (mp) REVERT: LK 65 ARG cc_start: 0.7363 (mmt180) cc_final: 0.6172 (mmt180) REVERT: LN 174 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7538 (ptt90) REVERT: LQ 133 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: LS 7 ARG cc_start: 0.7273 (mtm110) cc_final: 0.6982 (mtm110) REVERT: LS 20 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7590 (tp-100) REVERT: LW 80 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6940 (mt-10) REVERT: NA 312 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7544 (mp) REVERT: NA 354 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: NA 433 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7101 (t80) REVERT: NH 54 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8328 (mm) REVERT: NI 321 ASP cc_start: 0.6539 (OUTLIER) cc_final: 0.6167 (p0) REVERT: NI 479 MET cc_start: 0.7821 (ttm) cc_final: 0.7192 (tpp) REVERT: NO 313 ARG cc_start: 0.7041 (mtp-110) cc_final: 0.6765 (mtp-110) REVERT: NS 298 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7132 (mmp80) REVERT: SG 106 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: SK 236 MET cc_start: 0.5962 (ptt) cc_final: 0.5534 (ppp) REVERT: SL 67 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8047 (mmt) REVERT: SM 441 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8142 (tppt) REVERT: SM 552 MET cc_start: 0.5283 (OUTLIER) cc_final: 0.5052 (mmm) REVERT: SQ 130 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7974 (mptp) REVERT: SR 388 MET cc_start: 0.5554 (ppp) cc_final: 0.5170 (mmt) REVERT: SU 410 LYS cc_start: 0.4808 (tmtm) cc_final: 0.4094 (tmtm) REVERT: SV 109 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7830 (mmp) REVERT: SY 227 MET cc_start: 0.2253 (mmt) cc_final: 0.0880 (ptp) REVERT: SY 312 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7697 (mt) REVERT: SY 421 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7123 (mtp180) REVERT: SZ 5 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6880 (mtpt) REVERT: SZ 137 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.7032 (tp30) outliers start: 190 outliers final: 121 residues processed: 1117 average time/residue: 2.4231 time to fit residues: 3836.1422 Evaluate side-chains 1129 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 986 time to evaluate : 8.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 77 SER Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L7 residue 120 VAL Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 2 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 92 LEU Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 155 VAL Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 56 GLN Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LA residue 156 ILE Chi-restraints excluded: chain LB residue 71 LYS Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LB residue 107 SER Chi-restraints excluded: chain LC residue 48 VAL Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LE residue 74 ILE Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 26 LYS Chi-restraints excluded: chain LH residue 54 LEU Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 216 MET Chi-restraints excluded: chain LN residue 292 LEU Chi-restraints excluded: chain LN residue 386 LYS Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 27 GLU Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 95 LYS Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain NA residue 267 THR Chi-restraints excluded: chain NA residue 312 LEU Chi-restraints excluded: chain NA residue 323 HIS Chi-restraints excluded: chain NA residue 354 PHE Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 433 TYR Chi-restraints excluded: chain NA residue 520 ASP Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NF residue 171 ILE Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 67 THR Chi-restraints excluded: chain NI residue 321 ASP Chi-restraints excluded: chain NI residue 389 CYS Chi-restraints excluded: chain NI residue 410 VAL Chi-restraints excluded: chain NI residue 495 LEU Chi-restraints excluded: chain NI residue 678 GLN Chi-restraints excluded: chain NM residue 11 LEU Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NO residue 315 SER Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 113 HIS Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 52 PHE Chi-restraints excluded: chain NS residue 298 ARG Chi-restraints excluded: chain SA residue 310 HIS Chi-restraints excluded: chain SD residue 63 GLN Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SD residue 224 THR Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 106 GLN Chi-restraints excluded: chain SJ residue 168 LEU Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 67 MET Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 228 THR Chi-restraints excluded: chain SM residue 272 CYS Chi-restraints excluded: chain SM residue 441 LYS Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SO residue 65 PHE Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 343 MET Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SQ residue 122 MET Chi-restraints excluded: chain SQ residue 130 LYS Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 208 GLN Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 265 MET Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 217 GLU Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 366 ILE Chi-restraints excluded: chain SU residue 396 GLN Chi-restraints excluded: chain SU residue 589 PHE Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SU residue 638 LEU Chi-restraints excluded: chain SV residue 62 GLU Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 292 SER Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 241 LYS Chi-restraints excluded: chain SY residue 312 LEU Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 421 ARG Chi-restraints excluded: chain SY residue 479 LYS Chi-restraints excluded: chain SY residue 516 THR Chi-restraints excluded: chain SY residue 517 CYS Chi-restraints excluded: chain SY residue 545 ASP Chi-restraints excluded: chain SZ residue 5 LYS Chi-restraints excluded: chain SZ residue 124 GLU Chi-restraints excluded: chain SZ residue 137 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1445 random chunks: chunk 1266 optimal weight: 0.9980 chunk 1334 optimal weight: 5.9990 chunk 1217 optimal weight: 0.0470 chunk 1297 optimal weight: 5.9990 chunk 1333 optimal weight: 5.9990 chunk 781 optimal weight: 3.9990 chunk 565 optimal weight: 4.9990 chunk 1019 optimal weight: 0.2980 chunk 398 optimal weight: 9.9990 chunk 1172 optimal weight: 2.9990 chunk 1227 optimal weight: 3.9990 overall best weight: 1.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 15 HIS ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L8 44 GLN LA 155 GLN LE 58 HIS LE 95 HIS LE 114 GLN LE 127 GLN LH 57 GLN LK 60 HIS ** LK 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 30 GLN LT 20 ASN ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NA 501 ASN NF 72 ASN NI 579 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NO 20 ASN ** NO 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NO 127 ASN ** SC 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 268 GLN SE 206 GLN SG 140 GLN SI 71 GLN SI 113 GLN SI 166 GLN ** SJ 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 82 GLN SK 86 ASN SM 16 ASN SM 563 ASN SQ 58 ASN SR 342 HIS SS 208 GLN ST 267 ASN SU 232 ASN SU 496 ASN ** SW 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 156848 Z= 0.192 Angle : 0.505 17.887 223464 Z= 0.261 Chirality : 0.036 0.237 26831 Planarity : 0.004 0.059 19436 Dihedral : 21.124 179.723 51995 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.41 % Allowed : 11.95 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 1.86 (0.08), residues: 12058 helix: 2.46 (0.07), residues: 5460 sheet: 0.54 (0.13), residues: 1552 loop : 0.15 (0.08), residues: 5046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPLN 196 HIS 0.006 0.001 HISNS 220 PHE 0.027 0.001 PHESW 233 TYR 0.021 0.001 TYRSJ 16 ARG 0.010 0.000 ARGSW 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 999 time to evaluate : 9.685 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: L9 161 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.6976 (mmm) REVERT: LA 56 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: LC 50 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: LK 65 ARG cc_start: 0.7359 (mmt180) cc_final: 0.6210 (mmt180) REVERT: LN 168 MET cc_start: 0.7677 (mmm) cc_final: 0.7287 (mmt) REVERT: LN 174 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7434 (ptt90) REVERT: LQ 133 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: LS 7 ARG cc_start: 0.7256 (mtm110) cc_final: 0.6977 (mtm110) REVERT: LW 80 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6773 (mt-10) REVERT: NA 280 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6779 (tm) REVERT: NA 312 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7452 (mp) REVERT: NA 354 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: NA 433 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6834 (t80) REVERT: NA 625 LEU cc_start: 0.7782 (mm) cc_final: 0.7530 (mp) REVERT: NH 54 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8253 (mm) REVERT: NI 321 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.6112 (p0) REVERT: NI 479 MET cc_start: 0.7759 (ttm) cc_final: 0.7142 (tpp) REVERT: NO 313 ARG cc_start: 0.7053 (mtp-110) cc_final: 0.6776 (mtp-110) REVERT: NS 298 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7053 (mmp80) REVERT: SK 236 MET cc_start: 0.5892 (ptt) cc_final: 0.5646 (ppp) REVERT: SM 441 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8129 (tppt) REVERT: SM 552 MET cc_start: 0.5302 (OUTLIER) cc_final: 0.5063 (mmm) REVERT: SO 329 LEU cc_start: 0.7823 (mp) cc_final: 0.7508 (mp) REVERT: SR 388 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.5086 (mmt) REVERT: SU 326 LYS cc_start: 0.4134 (pmtt) cc_final: 0.3847 (pmtt) REVERT: SU 410 LYS cc_start: 0.4609 (tmtm) cc_final: 0.3854 (tmtp) REVERT: SV 109 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7806 (mmp) REVERT: SY 227 MET cc_start: 0.2125 (mmt) cc_final: 0.0859 (ptp) REVERT: SY 312 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7625 (mt) REVERT: SY 421 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7048 (mtp180) REVERT: SZ 5 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6908 (mtpt) outliers start: 140 outliers final: 97 residues processed: 1083 average time/residue: 2.3479 time to fit residues: 3609.7056 Evaluate side-chains 1104 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 987 time to evaluate : 9.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 77 SER Chi-restraints excluded: chain L7 residue 120 VAL Chi-restraints excluded: chain L8 residue 2 VAL Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 92 LEU Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 56 GLN Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 107 SER Chi-restraints excluded: chain LC residue 48 VAL Chi-restraints excluded: chain LC residue 50 GLN Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LC residue 82 LEU Chi-restraints excluded: chain LE residue 74 ILE Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 26 LYS Chi-restraints excluded: chain LH residue 54 LEU Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 292 LEU Chi-restraints excluded: chain LN residue 386 LYS Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 27 GLU Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain NA residue 280 LEU Chi-restraints excluded: chain NA residue 312 LEU Chi-restraints excluded: chain NA residue 329 LEU Chi-restraints excluded: chain NA residue 354 PHE Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 433 TYR Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 374 MET Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NF residue 171 ILE Chi-restraints excluded: chain NH residue 26 LEU Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 321 ASP Chi-restraints excluded: chain NI residue 389 CYS Chi-restraints excluded: chain NI residue 495 LEU Chi-restraints excluded: chain NM residue 11 LEU Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NO residue 315 SER Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 298 ARG Chi-restraints excluded: chain SA residue 310 HIS Chi-restraints excluded: chain SD residue 63 GLN Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SJ residue 136 LEU Chi-restraints excluded: chain SJ residue 168 LEU Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 128 ILE Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 272 CYS Chi-restraints excluded: chain SM residue 441 LYS Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SO residue 65 PHE Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 343 MET Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SQ residue 122 MET Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 388 MET Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 208 GLN Chi-restraints excluded: chain SS residue 265 MET Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 217 GLU Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain ST residue 266 LYS Chi-restraints excluded: chain SU residue 396 GLN Chi-restraints excluded: chain SU residue 589 PHE Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SU residue 638 LEU Chi-restraints excluded: chain SV residue 62 GLU Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 292 SER Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 312 LEU Chi-restraints excluded: chain SY residue 421 ARG Chi-restraints excluded: chain SY residue 479 LYS Chi-restraints excluded: chain SY residue 517 CYS Chi-restraints excluded: chain SY residue 545 ASP Chi-restraints excluded: chain SZ residue 5 LYS Chi-restraints excluded: chain SZ residue 124 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1445 random chunks: chunk 1293 optimal weight: 0.6980 chunk 852 optimal weight: 4.9990 chunk 1372 optimal weight: 1.9990 chunk 837 optimal weight: 6.9990 chunk 651 optimal weight: 10.0000 chunk 954 optimal weight: 7.9990 chunk 1439 optimal weight: 7.9990 chunk 1324 optimal weight: 5.9990 chunk 1146 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 885 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 15 HIS L8 44 GLN LA 155 GLN LB 93 GLN LE 58 HIS LE 95 HIS LE 127 GLN LH 57 GLN LK 60 HIS ** LK 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 501 ASN NA 565 ASN NF 72 ASN NI 579 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NO 20 ASN NO 127 ASN SA 60 HIS SC 268 GLN SE 206 GLN SG 140 GLN SG 188 GLN SI 33 GLN SI 71 GLN SI 113 GLN SI 166 GLN SK 82 GLN SK 86 ASN SM 16 ASN SM 563 ASN SQ 58 ASN SR 342 HIS SS 208 GLN ST 267 ASN SU 232 ASN ** SW 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 156848 Z= 0.378 Angle : 0.590 17.340 223464 Z= 0.302 Chirality : 0.041 0.267 26831 Planarity : 0.005 0.062 19436 Dihedral : 21.123 179.738 51995 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.48 % Allowed : 11.97 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 1.65 (0.07), residues: 12058 helix: 2.28 (0.07), residues: 5451 sheet: 0.48 (0.13), residues: 1570 loop : 0.04 (0.08), residues: 5037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPLN 196 HIS 0.010 0.001 HISNS 220 PHE 0.028 0.002 PHENH 143 TYR 0.029 0.002 TYRNA 400 ARG 0.009 0.001 ARGSW 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24116 Ramachandran restraints generated. 12058 Oldfield, 0 Emsley, 12058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 988 time to evaluate : 9.914 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: L9 161 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7161 (mmm) REVERT: LA 56 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: LK 65 ARG cc_start: 0.7440 (mmt180) cc_final: 0.6254 (mmt180) REVERT: LN 174 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7542 (ptt90) REVERT: LQ 133 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: LS 7 ARG cc_start: 0.7245 (mtm110) cc_final: 0.6959 (mtm110) REVERT: LS 20 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7621 (tp-100) REVERT: LW 80 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6855 (mt-10) REVERT: NA 280 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6942 (tm) REVERT: NA 354 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: NA 433 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6963 (t80) REVERT: NH 54 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8318 (mm) REVERT: NI 321 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.6163 (p0) REVERT: NI 479 MET cc_start: 0.7813 (ttm) cc_final: 0.7192 (tpp) REVERT: NO 313 ARG cc_start: 0.7058 (mtp-110) cc_final: 0.6710 (mtp-110) REVERT: NS 298 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7108 (mmp80) REVERT: SK 236 MET cc_start: 0.5974 (ptt) cc_final: 0.5651 (ppp) REVERT: SL 67 MET cc_start: 0.8236 (mmm) cc_final: 0.8007 (mmt) REVERT: SM 441 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8123 (tppt) REVERT: SM 552 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4676 (mmm) REVERT: SQ 73 MET cc_start: 0.8449 (mtt) cc_final: 0.8246 (mtt) REVERT: SR 388 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.5088 (mmm) REVERT: SU 326 LYS cc_start: 0.4625 (pmtt) cc_final: 0.3941 (pmtt) REVERT: SU 410 LYS cc_start: 0.4413 (tmtm) cc_final: 0.3686 (tmtm) REVERT: SV 109 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7831 (mmp) REVERT: SY 227 MET cc_start: 0.2198 (mmt) cc_final: 0.0846 (ptp) REVERT: SY 312 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7693 (mt) REVERT: SY 421 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7116 (mtp180) REVERT: SZ 5 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7075 (mtpt) REVERT: SZ 122 MET cc_start: 0.8245 (mmt) cc_final: 0.7916 (mmt) outliers start: 147 outliers final: 106 residues processed: 1075 average time/residue: 2.4473 time to fit residues: 3743.9301 Evaluate side-chains 1106 residues out of total 10752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 982 time to evaluate : 9.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 77 SER Chi-restraints excluded: chain L6 residue 94 ILE Chi-restraints excluded: chain L7 residue 120 VAL Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 2 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 92 LEU Chi-restraints excluded: chain L9 residue 155 VAL Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LA residue 56 GLN Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 22 ASP Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 107 SER Chi-restraints excluded: chain LC residue 48 VAL Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LE residue 74 ILE Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 26 LYS Chi-restraints excluded: chain LH residue 54 LEU Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 292 LEU Chi-restraints excluded: chain LN residue 386 LYS Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 133 GLU Chi-restraints excluded: chain LS residue 27 GLU Chi-restraints excluded: chain LS residue 45 SER Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 32 SER Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain NA residue 267 THR Chi-restraints excluded: chain NA residue 280 LEU Chi-restraints excluded: chain NA residue 354 PHE Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 433 TYR Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 374 MET Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NF residue 171 ILE Chi-restraints excluded: chain NH residue 26 LEU Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 67 THR Chi-restraints excluded: chain NI residue 321 ASP Chi-restraints excluded: chain NI residue 389 CYS Chi-restraints excluded: chain NI residue 495 LEU Chi-restraints excluded: chain NM residue 11 LEU Chi-restraints excluded: chain NM residue 119 TYR Chi-restraints excluded: chain NO residue 167 SER Chi-restraints excluded: chain NO residue 315 SER Chi-restraints excluded: chain NQ residue 1 MET Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 298 ARG Chi-restraints excluded: chain SA residue 310 HIS Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SJ residue 136 LEU Chi-restraints excluded: chain SJ residue 168 LEU Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 228 THR Chi-restraints excluded: chain SM residue 272 CYS Chi-restraints excluded: chain SM residue 441 LYS Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SO residue 65 PHE Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SO residue 296 THR Chi-restraints excluded: chain SO residue 343 MET Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SQ residue 122 MET Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 303 ASP Chi-restraints excluded: chain SR residue 388 MET Chi-restraints excluded: chain SS residue 141 LEU Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 265 MET Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 217 GLU Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain ST residue 266 LYS Chi-restraints excluded: chain SU residue 396 GLN Chi-restraints excluded: chain SU residue 589 PHE Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SU residue 638 LEU Chi-restraints excluded: chain SV residue 62 GLU Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 292 SER Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 312 LEU Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 421 ARG Chi-restraints excluded: chain SY residue 479 LYS Chi-restraints excluded: chain SY residue 517 CYS Chi-restraints excluded: chain SY residue 545 ASP Chi-restraints excluded: chain SZ residue 5 LYS Chi-restraints excluded: chain SZ residue 124 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1445 random chunks: chunk 702 optimal weight: 0.9990 chunk 910 optimal weight: 2.9990 chunk 1221 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 1057 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 318 optimal weight: 2.9990 chunk 1148 optimal weight: 2.9990 chunk 480 optimal weight: 0.7980 chunk 1178 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 15 HIS ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L8 44 GLN LA 155 GLN LB 93 GLN LE 58 HIS LE 95 HIS LE 114 GLN LE 127 GLN LH 57 GLN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 20 ASN ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NA 501 ASN NF 72 ASN NI 332 HIS NI 579 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NO 20 ASN ** NO 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NO 127 ASN SC 268 GLN SE 206 GLN SE 236 HIS SG 106 GLN SG 140 GLN SG 188 GLN SI 33 GLN SI 71 GLN SI 113 GLN SI 166 GLN SK 82 GLN SK 86 ASN SM 16 ASN SM 563 ASN SQ 58 ASN SR 342 HIS SS 208 GLN ST 267 ASN SU 232 ASN ** SW 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.099298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.069891 restraints weight = 332522.543| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.77 r_work: 0.2944 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 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 = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 156848 Z= 0.230 Angle : 0.520 17.685 223464 Z= 0.267 Chirality : 0.036 0.242 26831 Planarity : 0.004 0.046 19436 Dihedral : 21.100 178.877 51995 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.47 % Allowed : 12.06 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % 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: 1.79 (0.08), residues: 12058 helix: 2.40 (0.07), residues: 5468 sheet: 0.47 (0.13), residues: 1582 loop : 0.11 (0.08), residues: 5008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPLN 196 HIS 0.007 0.001 HISNS 220 PHE 0.027 0.001 PHESW 233 TYR 0.021 0.001 TYRSJ 16 ARG 0.019 0.000 ARGSJ 558 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 58752.17 seconds wall clock time: 1016 minutes 52.76 seconds (61012.76 seconds total)