Starting phenix.real_space_refine on Sat Feb 17 11:12:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fku_29257/02_2024/8fku_29257_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fku_29257/02_2024/8fku_29257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fku_29257/02_2024/8fku_29257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fku_29257/02_2024/8fku_29257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fku_29257/02_2024/8fku_29257_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fku_29257/02_2024/8fku_29257_neut_updated.pdb" } resolution = 2.82 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= 0.043 sd= 0.159 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 2 6.06 5 P 2412 5.49 5 Mg 58 5.21 5 S 301 5.16 5 C 69937 2.51 5 N 23421 2.21 5 O 29737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BA GLU 9": "OE1" <-> "OE2" Residue "BA TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA GLU 108": "OE1" <-> "OE2" Residue "BA GLU 124": "OE1" <-> "OE2" Residue "BA GLU 131": "OE1" <-> "OE2" Residue "BA ASP 153": "OD1" <-> "OD2" Residue "L6 GLU 119": "OE1" <-> "OE2" Residue "L7 ASP 100": "OD1" <-> "OD2" Residue "L7 ASP 106": "OD1" <-> "OD2" Residue "L7 GLU 144": "OE1" <-> "OE2" Residue "L7 GLU 158": "OE1" <-> "OE2" Residue "L7 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 GLU 194": "OE1" <-> "OE2" Residue "L8 ASP 29": "OD1" <-> "OD2" Residue "L8 ASP 32": "OD1" <-> "OD2" Residue "L8 ASP 81": "OD1" <-> "OD2" Residue "L8 GLU 126": "OE1" <-> "OE2" Residue "L9 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 GLU 9": "OE1" <-> "OE2" Residue "L9 GLU 123": "OE1" <-> "OE2" Residue "L9 ASP 124": "OD1" <-> "OD2" Residue "LA ASP 7": "OD1" <-> "OD2" Residue "LA GLU 99": "OE1" <-> "OE2" Residue "LB ASP 89": "OD1" <-> "OD2" Residue "LB GLU 94": "OE1" <-> "OE2" Residue "LB GLU 147": "OE1" <-> "OE2" Residue "LC GLU 9": "OE1" <-> "OE2" Residue "LC TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC GLU 60": "OE1" <-> "OE2" Residue "LC GLU 69": "OE1" <-> "OE2" Residue "LC ASP 99": "OD1" <-> "OD2" Residue "LC GLU 130": "OE1" <-> "OE2" Residue "LC GLU 131": "OE1" <-> "OE2" Residue "LC ASP 147": "OD1" <-> "OD2" Residue "LE GLU 118": "OE1" <-> "OE2" Residue "LE GLU 137": "OE1" <-> "OE2" Residue "LE GLU 157": "OE1" <-> "OE2" Residue "LG GLU 71": "OE1" <-> "OE2" Residue "LG ASP 92": "OD1" <-> "OD2" Residue "LI ASP 10": "OD1" <-> "OD2" Residue "LI GLU 54": "OE1" <-> "OE2" Residue "LI TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI GLU 88": "OE1" <-> "OE2" Residue "LI GLU 120": "OE1" <-> "OE2" Residue "LK PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 61": "OD1" <-> "OD2" Residue "LN TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 199": "OE1" <-> "OE2" Residue "LN TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 311": "OD1" <-> "OD2" Residue "LN PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 383": "OE1" <-> "OE2" Residue "LQ GLU 113": "OE1" <-> "OE2" Residue "LS GLU 15": "OE1" <-> "OE2" Residue "LS GLU 16": "OE1" <-> "OE2" Residue "LS TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT GLU 40": "OE1" <-> "OE2" Residue "LU GLU 46": "OE1" <-> "OE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 54": "OE1" <-> "OE2" Residue "LU GLU 59": "OE1" <-> "OE2" Residue "LU GLU 88": "OE1" <-> "OE2" Residue "LW GLU 80": "OE1" <-> "OE2" Residue "NB GLU 27": "OE1" <-> "OE2" Residue "NB ASP 47": "OD1" <-> "OD2" Residue "NF TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF GLU 31": "OE1" <-> "OE2" Residue "NF GLU 69": "OE1" <-> "OE2" Residue "NF ASP 158": "OD1" <-> "OD2" Residue "NF PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF GLU 249": "OE1" <-> "OE2" Residue "NH GLU 8": "OE1" <-> "OE2" Residue "NH TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH ASP 87": "OD1" <-> "OD2" Residue "NH TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH GLU 123": "OE1" <-> "OE2" Residue "NH ASP 152": "OD1" <-> "OD2" Residue "NI GLU 577": "OE1" <-> "OE2" Residue "NK GLU 16": "OE1" <-> "OE2" Residue "NK GLU 25": "OE1" <-> "OE2" Residue "SA GLU 13": "OE1" <-> "OE2" Residue "SA GLU 16": "OE1" <-> "OE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA ASP 156": "OD1" <-> "OD2" Residue "SA ASP 261": "OD1" <-> "OD2" Residue "SA TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 119": "OE1" <-> "OE2" Residue "SC ASP 202": "OD1" <-> "OD2" Residue "SC GLU 244": "OE1" <-> "OE2" Residue "SD GLU 68": "OE1" <-> "OE2" Residue "SD GLU 152": "OE1" <-> "OE2" Residue "SD ASP 171": "OD1" <-> "OD2" Residue "SD GLU 188": "OE1" <-> "OE2" Residue "SD ASP 232": "OD1" <-> "OD2" Residue "SD GLU 237": "OE1" <-> "OE2" Residue "SD ASP 238": "OD1" <-> "OD2" Residue "SE TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE ASP 88": "OD1" <-> "OD2" Residue "SE TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE GLU 119": "OE1" <-> "OE2" Residue "SE GLU 165": "OE1" <-> "OE2" Residue "SE ASP 211": "OD1" <-> "OD2" Residue "SG ASP 11": "OD1" <-> "OD2" Residue "SG GLU 14": "OE1" <-> "OE2" Residue "SG ASP 37": "OD1" <-> "OD2" Residue "SG TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG GLU 107": "OE1" <-> "OE2" Residue "SG GLU 113": "OE1" <-> "OE2" Residue "SG GLU 143": "OE1" <-> "OE2" Residue "SG GLU 152": "OE1" <-> "OE2" Residue "SH PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI ASP 92": "OD1" <-> "OD2" Residue "SI ASP 178": "OD1" <-> "OD2" Residue "SI PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ GLU 696": "OE1" <-> "OE2" Residue "SJ ASP 697": "OD1" <-> "OD2" Residue "SJ GLU 708": "OE1" <-> "OE2" Residue "SK GLU 8": "OE1" <-> "OE2" Residue "SK PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL GLU 34": "OE1" <-> "OE2" Residue "SL GLU 60": "OE1" <-> "OE2" Residue "SL ASP 94": "OD1" <-> "OD2" Residue "SL GLU 143": "OE1" <-> "OE2" Residue "SL GLU 239": "OE1" <-> "OE2" Residue "SL PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN ASP 49": "OD1" <-> "OD2" Residue "SN TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN GLU 183": "OE1" <-> "OE2" Residue "SN TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO GLU 183": "OE1" <-> "OE2" Residue "SO GLU 225": "OE1" <-> "OE2" Residue "SO TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ GLU 29": "OE1" <-> "OE2" Residue "SQ PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 55": "OD1" <-> "OD2" Residue "SQ ASP 87": "OD1" <-> "OD2" Residue "SQ PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ GLU 143": "OE1" <-> "OE2" Residue "SQ ASP 180": "OD1" <-> "OD2" Residue "SQ GLU 199": "OE1" <-> "OE2" Residue "SR ASP 17": "OD1" <-> "OD2" Residue "SR PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 270": "OE1" <-> "OE2" Residue "SR PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 298": "OE1" <-> "OE2" Residue "SR PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 370": "OD1" <-> "OD2" Residue "SR GLU 456": "OE1" <-> "OE2" Residue "SS ASP 146": "OD1" <-> "OD2" Residue "SS PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 4": "OE1" <-> "OE2" Residue "SV ASP 66": "OD1" <-> "OD2" Residue "SV PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 70": "OE1" <-> "OE2" Residue "SV PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 72": "OE1" <-> "OE2" Residue "SV GLU 84": "OE1" <-> "OE2" Residue "SV GLU 117": "OE1" <-> "OE2" Residue "SW GLU 262": "OE1" <-> "OE2" Residue "SW PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 344": "OE1" <-> "OE2" Residue "SW PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ GLU 55": "OE1" <-> "OE2" Residue "SZ ASP 129": "OD1" <-> "OD2" Residue "SZ GLU 162": "OE1" <-> "OE2" Residue "SZ GLU 176": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 125869 Number of models: 1 Model: "" Number of chains: 62 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': 11, 'rna3p_pur': 60, 'rna3p_pyr': 66} Link IDs: {'rna2p': 25, 'rna3p': 126} 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: 46844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2185, 46844 Classifications: {'RNA': 2185} Modifications used: {'rna2p_pur': 209, 'rna2p_pyr': 130, 'rna3p_pur': 986, 'rna3p_pyr': 860} Link IDs: {'rna2p': 339, 'rna3p': 1845} Chain breaks: 38 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: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1106 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} 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: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 747 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain breaks: 2 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 4, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "LG" Number of atoms: 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: "LL" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} 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: "LQ" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "LS" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "LT" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "LU" Number of atoms: 840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} bond proxies already assigned to first conformer: 834 Chain: "LW" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 612 Classifications: {'peptide': 74} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 70} Chain: "NB" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 569 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain breaks: 1 Chain: "NF" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1684 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 196} 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: 3866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 3866 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 240} Link IDs: {'PTRANS': 27, 'TRANS': 570} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 895 Unresolved non-hydrogen angles: 1126 Unresolved non-hydrogen dihedrals: 744 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 18, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 463 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: "SA" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2853 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 339} Chain: "SC" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1627 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Chain: "SD" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} 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: 1887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 228, 1876 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 228, 1876 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain breaks: 1 bond proxies already assigned to first conformer: 1900 Chain: "SJ" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 855 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 2 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: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2460 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 274} Chain breaks: 1 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: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3695 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain breaks: 1 Chain: "SS" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2116 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 28, 'TRANS': 227} Chain breaks: 1 Chain: "ST" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 787 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 87 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Unusual residues: {' MG': 46} Classifications: {'undetermined': 46} Link IDs: {None: 45} Chain: "L9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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: "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: "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 74895 SG CYSLW 19 87.424 125.927 149.521 1.00 24.87 S ATOM 74923 SG CYSLW 22 88.235 123.170 152.063 1.00 24.23 S ATOM 75014 SG CYSLW 34 90.007 126.497 152.198 1.00 25.88 S ATOM 75033 SG CYSLW 37 90.699 124.168 149.282 1.00 24.40 S ATOM A0CXL SG CYSSV 6 56.441 182.963 235.839 1.00 24.43 S ATOM A0CYE SG CYSSV 9 53.056 181.723 235.167 1.00 23.41 S ATOM A0D3I SG CYSSV 32 55.667 179.115 235.839 1.00 22.59 S ATOM A0D4C SG CYSSV 36 55.514 180.875 232.576 1.00 24.05 S Time building chain proxies: 48.89, per 1000 atoms: 0.39 Number of scatterers: 125869 At special positions: 0 Unit cell: (237.984, 234.768, 335.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 1 19.00 S 301 16.00 P 2412 15.00 Mg 58 11.99 O 29737 8.00 N 23421 7.00 C 69937 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: 41.98 Conformation dependent library (CDL) restraints added in 11.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 12 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17822 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: 360 helices and 80 sheets defined 49.7% alpha, 12.8% beta 784 base pairs and 1235 stacking pairs defined. Time for finding SS restraints: 73.28 Creating SS restraints... Processing helix chain 'BA' and resid 24 through 33 Proline residue: BA 30 - end of helix Processing helix chain 'BA' and resid 38 through 51 Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.580A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 5.044A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.571A 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 95 removed outlier: 4.390A pdb=" N LYSBB 95 " --> pdb=" O LYSBB 91 " (cutoff:3.500A) Processing helix chain 'BB' and resid 96 through 108 removed outlier: 4.947A pdb=" N ASPBB 108 " --> pdb=" O ALABB 104 " (cutoff:3.500A) Processing helix chain 'BB' and resid 113 through 124 removed outlier: 4.288A pdb=" N LYSBB 118 " --> pdb=" O GLUBB 114 " (cutoff:3.500A) removed outlier: 4.894A 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: 3.562A 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: 5.282A pdb=" N LYSBB 195 " --> pdb=" O VALBB 191 " (cutoff:3.500A) Processing helix chain 'BB' and resid 197 through 202 removed outlier: 3.957A pdb=" N VALBB 201 " --> pdb=" O ASNBB 197 " (cutoff:3.500A) removed outlier: 5.415A 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: 4.336A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 3.768A 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: 4.209A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.879A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.547A pdb=" N GLYL7 30 " --> pdb=" O GLNL7 26 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 61 removed outlier: 3.663A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARGL7 61 " --> pdb=" O PHEL7 57 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 Proline residue: L7 70 - end of helix 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: 3.659A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.695A 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: 4.139A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.576A 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: 5.576A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.601A pdb=" N HISL7 199 " --> pdb=" O VALL7 195 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLYL7 200 " --> pdb=" O LEUL7 196 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.932A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.514A 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 Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.541A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 Processing helix chain 'L8' and resid 105 through 136 removed outlier: 3.562A pdb=" N ARGL8 121 " --> pdb=" O LYSL8 117 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILEL8 122 " --> pdb=" O METL8 118 " (cutoff:3.500A) Processing helix chain 'L9' and resid 2 through 14 removed outlier: 4.118A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 4.864A 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: 3.805A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.998A 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: 6.403A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.843A 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: 3.605A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 4.092A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 4.053A 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 38 removed outlier: 5.968A pdb=" N GLYLA 38 " --> pdb=" O GLNLA 34 " (cutoff:3.500A) Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 70 through 77 removed outlier: 4.267A pdb=" N LYSLA 74 " --> pdb=" O CYSLA 70 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLNLA 75 " --> pdb=" O ALALA 71 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.155A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.640A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.722A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 removed outlier: 3.634A pdb=" N LEULB 128 " --> pdb=" O ASPLB 124 " (cutoff:3.500A) Processing helix chain 'LB' and resid 146 through 152 removed outlier: 4.253A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) Processing helix chain 'LB' and resid 7 through 12 removed outlier: 3.525A pdb=" N ASPLB 10 " --> pdb=" O HISLB 7 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARGLB 11 " --> pdb=" O ASNLB 8 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LYSLB 12 " --> pdb=" O LYSLB 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 7 through 12' Processing helix chain 'LC' and resid 36 through 52 Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.524A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.352A 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: 4.538A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.313A 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: 3.852A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYSLE 97 " --> pdb=" O ILELE 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 92 through 97' Processing helix chain 'LE' and resid 100 through 121 removed outlier: 3.605A pdb=" N SERLE 104 " --> pdb=" O LYSLE 100 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYSLE 120 " --> pdb=" O LYSLE 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLULE 121 " --> pdb=" O LYSLE 117 " (cutoff:3.500A) Processing helix chain 'LG' and resid 122 through 130 removed outlier: 3.742A pdb=" N LEULG 128 " --> pdb=" O GLULG 124 " (cutoff:3.500A) Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 137 removed outlier: 3.684A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLYLG 137 " --> pdb=" O ALALG 133 " (cutoff:3.500A) Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.681A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 92 removed outlier: 3.501A pdb=" N GLULH 91 " --> pdb=" O METLH 87 " (cutoff:3.500A) Processing helix chain 'LH' and resid 105 through 117 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: 3.741A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.450A 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: 4.168A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.450A 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 removed outlier: 3.544A pdb=" N GLYLI 129 " --> pdb=" O SERLI 125 " (cutoff:3.500A) Processing helix chain 'LK' and resid 6 through 12 removed outlier: 4.073A pdb=" N LYSLK 10 " --> pdb=" O ARGLK 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARGLK 12 " --> pdb=" O THRLK 8 " (cutoff:3.500A) Processing helix chain 'LK' and resid 60 through 67 removed outlier: 5.466A pdb=" N GLNLK 67 " --> pdb=" O LEULK 63 " (cutoff:3.500A) Processing helix chain 'LK' and resid 74 through 83 removed outlier: 4.720A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 94 removed outlier: 4.729A pdb=" N LYSLK 94 " --> pdb=" O ALALK 90 " (cutoff:3.500A) Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.534A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 Processing helix chain 'LL' and resid 2 through 13 removed outlier: 3.512A pdb=" N VALLL 9 " --> pdb=" O LEULL 5 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.615A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 3.922A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYSLL 122 " --> pdb=" O LEULL 118 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LN' and resid 111 through 120 removed outlier: 3.941A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 4.219A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.462A 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: 4.099A pdb=" N LEULN 171 " --> pdb=" O GLNLN 167 " (cutoff:3.500A) Proline residue: LN 172 - end of helix No H-bonds generated for 'chain 'LN' and resid 167 through 172' Processing helix chain 'LN' and resid 189 through 201 removed outlier: 3.586A pdb=" N ARGLN 200 " --> pdb=" O TRPLN 196 " (cutoff:3.500A) Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.885A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 3.986A 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 'LQ' and resid 24 through 29 removed outlier: 3.512A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 5.129A 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: 3.585A pdb=" N LEULQ 85 " --> pdb=" O ASNLQ 81 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLULQ 86 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.191A 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: 3.851A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLNLQ 117 " --> pdb=" O GLULQ 113 " (cutoff:3.500A) Processing helix chain 'LS' and resid 5 through 10 Processing helix chain 'LS' and resid 13 through 38 removed outlier: 3.646A pdb=" N THRLS 37 " --> pdb=" O VALLS 33 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLYLS 38 " --> pdb=" O ALALS 34 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 4.632A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.027A 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: 5.517A 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 114 Processing helix chain 'LT' and resid 35 through 40 removed outlier: 3.720A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.594A 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: 4.154A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.326A 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: 3.736A pdb=" N GLULU 46 " --> pdb=" O ASPLU 42 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLYLU 49 " --> pdb=" O ARGLU 45 " (cutoff:3.500A) Processing helix chain 'LU' and resid 51 through 64 removed outlier: 3.511A pdb=" N VALLU 63 " --> pdb=" O GLULU 59 " (cutoff:3.500A) Processing helix chain 'LU' and resid 65 through 78 Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.617A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.224A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLYLW 77 " --> pdb=" O ARGLW 73 " (cutoff:3.500A) Processing helix chain 'NB' and resid 14 through 36 Processing helix chain 'NB' and resid 56 through 77 Processing helix chain 'NF' and resid 5 through 14 Processing helix chain 'NF' and resid 21 through 35 removed outlier: 4.212A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.770A 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: 3.581A pdb=" N GLUNF 168 " --> pdb=" O PRONF 164 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ARGNF 169 " --> pdb=" O PRONF 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'NF' and resid 164 through 169' Processing helix chain 'NF' and resid 173 through 178 removed outlier: 3.512A pdb=" N ARGNF 177 " --> pdb=" O PRONF 173 " (cutoff:3.500A) removed outlier: 5.707A 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: 4.048A pdb=" N TYRNH 19 " --> pdb=" O LYSNH 15 " (cutoff:3.500A) Processing helix chain 'NH' and resid 22 through 30 removed outlier: 4.511A pdb=" N LEUNH 26 " --> pdb=" O GLUNH 22 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEUNH 27 " --> pdb=" O ASNNH 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARGNH 30 " --> pdb=" O LEUNH 26 " (cutoff:3.500A) Processing helix chain 'NH' and resid 48 through 59 removed outlier: 3.552A pdb=" N ALANH 56 " --> pdb=" O METNH 52 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASNNH 57 " --> pdb=" O LYSNH 53 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILENH 58 " --> pdb=" O LEUNH 54 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SERNH 59 " --> pdb=" O ALANH 55 " (cutoff:3.500A) Processing helix chain 'NH' and resid 82 through 93 removed outlier: 4.488A pdb=" N LEUNH 86 " --> pdb=" O HISNH 82 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASPNH 87 " --> pdb=" O VALNH 83 " (cutoff:3.500A) removed outlier: 5.856A 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: 4.442A pdb=" N GLNNH 105 " --> pdb=" O PRONH 101 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N SERNH 106 " --> pdb=" O GLYNH 102 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLYNH 110 " --> pdb=" O SERNH 106 " (cutoff:3.500A) Processing helix chain 'NH' and resid 114 through 119 removed outlier: 5.748A pdb=" N GLYNH 119 " --> pdb=" O LYSNH 115 " (cutoff:3.500A) Processing helix chain 'NH' and resid 149 through 156 removed outlier: 4.172A pdb=" N LYSNH 155 " --> pdb=" O GLNNH 151 " (cutoff:3.500A) Processing helix chain 'NH' and resid 168 through 175 removed outlier: 4.815A pdb=" N TYRNH 172 " --> pdb=" O ASPNH 168 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VALNH 173 " --> pdb=" O ILENH 169 " (cutoff:3.500A) Processing helix chain 'NI' and resid 97 through 102 removed outlier: 4.150A 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: 3.735A pdb=" N ASPNI 132 " --> pdb=" O PRONI 128 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLYNI 133 " --> pdb=" O VALNI 129 " (cutoff:3.500A) Processing helix chain 'NI' and resid 145 through 159 removed outlier: 4.051A pdb=" N CYSNI 149 " --> pdb=" O GLYNI 145 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHENI 150 " --> pdb=" O LYSNI 146 " (cutoff:3.500A) Proline residue: NI 153 - end of helix removed outlier: 4.172A 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: 4.246A pdb=" N ASNNI 216 " --> pdb=" O ALANI 212 " (cutoff:3.500A) Processing helix chain 'NI' and resid 223 through 235 removed outlier: 3.543A pdb=" N HISNI 229 " --> pdb=" O GLYNI 225 " (cutoff:3.500A) Processing helix chain 'NI' and resid 248 through 256 Processing helix chain 'NI' and resid 257 through 269 removed outlier: 3.748A pdb=" N GLUNI 263 " --> pdb=" O GLUNI 259 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEUNI 268 " --> pdb=" O ILENI 264 " (cutoff:3.500A) Proline residue: NI 269 - end of helix Processing helix chain 'NI' and resid 282 through 292 removed outlier: 3.567A pdb=" N ALANI 291 " --> pdb=" O GLUNI 287 " (cutoff:3.500A) Processing helix chain 'NI' and resid 301 through 307 removed outlier: 3.656A pdb=" N THRNI 305 " --> pdb=" O LEUNI 301 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYSNI 306 " --> pdb=" O ASPNI 302 " (cutoff:3.500A) removed outlier: 5.136A 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: 4.791A pdb=" N ALANI 324 " --> pdb=" O GLUNI 320 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALANI 325 " --> pdb=" O ASPNI 321 " (cutoff:3.500A) Processing helix chain 'NI' and resid 347 through 362 removed outlier: 3.545A pdb=" N GLNNI 361 " --> pdb=" O LEUNI 357 " (cutoff:3.500A) removed outlier: 4.304A 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: 4.989A pdb=" N GLYNI 401 " --> pdb=" O LEUNI 397 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEUNI 402 " --> pdb=" O ALANI 398 " (cutoff:3.500A) removed outlier: 5.334A 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: 3.539A 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 477 Processing helix chain 'NI' and resid 486 through 503 removed outlier: 3.566A pdb=" N GLUNI 491 " --> pdb=" O VALNI 487 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLYNI 494 " --> pdb=" O GLUNI 490 " (cutoff:3.500A) removed outlier: 4.783A 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: 5.604A pdb=" N ASPNI 538 " --> pdb=" O ALANI 534 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEUNI 539 " --> pdb=" O LYSNI 535 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VALNI 540 " --> pdb=" O GLUNI 536 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLYNI 541 " --> pdb=" O METNI 537 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEUNI 542 " --> pdb=" O ASPNI 538 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLYNI 543 " --> pdb=" O LEUNI 539 " (cutoff:3.500A) Processing helix chain 'NI' and resid 545 through 553 removed outlier: 4.332A pdb=" N ARGNI 551 " --> pdb=" O LEUNI 547 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHENI 552 " --> pdb=" O PHENI 548 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLUNI 553 " --> pdb=" O SERNI 549 " (cutoff:3.500A) Processing helix chain 'NI' and resid 554 through 569 removed outlier: 3.582A pdb=" N LYSNI 567 " --> pdb=" O VALNI 563 " (cutoff:3.500A) Processing helix chain 'NI' and resid 574 through 579 removed outlier: 4.885A pdb=" N ASNNI 579 " --> pdb=" O ILENI 575 " (cutoff:3.500A) Processing helix chain 'NI' and resid 584 through 598 removed outlier: 3.523A pdb=" N ALANI 592 " --> pdb=" O GLNNI 588 " (cutoff:3.500A) 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: 3.522A pdb=" N TYRNI 681 " --> pdb=" O ASPNI 677 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILENI 682 " --> pdb=" O GLNNI 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'NI' and resid 677 through 682' Processing helix chain 'NI' and resid 703 through 712 removed outlier: 3.760A pdb=" N GLYNI 710 " --> pdb=" O GLNNI 706 " (cutoff:3.500A) Processing helix chain 'NI' and resid 719 through 737 removed outlier: 4.292A pdb=" N THRNI 724 " --> pdb=" O ALANI 720 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARGNI 725 " --> pdb=" O GLNNI 721 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLYNI 726 " --> pdb=" O ASNNI 722 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARGNI 727 " --> pdb=" O LEUNI 723 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEUNI 730 " --> pdb=" O GLYNI 726 " (cutoff:3.500A) Processing helix chain 'NI' and resid 766 through 775 Processing helix chain 'NK' and resid 12 through 33 removed outlier: 3.537A 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 removed outlier: 3.611A pdb=" N ARGNK 112 " --> pdb=" O LYSNK 108 " (cutoff:3.500A) Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.398A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.673A 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: 3.866A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.687A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEUSA 133 " --> pdb=" O ALASA 129 " (cutoff:3.500A) Proline residue: SA 134 - end of helix Processing helix chain 'SA' and resid 135 through 141 removed outlier: 3.648A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.280A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.034A 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: 3.840A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.513A 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: 3.520A pdb=" N LYSSA 259 " --> pdb=" O SERSA 255 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 Processing helix chain 'SA' and resid 296 through 303 removed outlier: 3.870A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.601A 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: 4.488A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SC' and resid 58 through 64 Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.953A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.412A 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: 3.723A 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: 5.175A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.660A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.547A pdb=" N GLUSD 68 " --> pdb=" O METSD 64 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.576A pdb=" N METSD 132 " --> pdb=" O ALASD 128 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.158A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.717A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 3.598A pdb=" N LEUSD 208 " --> pdb=" O ALASD 204 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 238 through 248 removed outlier: 4.724A pdb=" N ARGSD 242 " --> pdb=" O ASPSD 238 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.572A pdb=" N ALASE 68 " --> pdb=" O GLNSE 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.492A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.639A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARGSE 103 " --> pdb=" O ALASE 99 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 124 removed outlier: 3.547A pdb=" N ARGSE 117 " --> pdb=" O ARGSE 113 " (cutoff:3.500A) removed outlier: 3.772A 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: 4.850A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.978A 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: 3.679A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 231 removed outlier: 4.658A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASPSE 228 " --> pdb=" O THRSE 224 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARGSE 229 " --> pdb=" O ASNSE 225 " (cutoff:3.500A) Processing helix chain 'SE' and resid 232 through 237 removed outlier: 4.314A pdb=" N HISSE 236 " --> pdb=" O GLUSE 232 " (cutoff:3.500A) removed outlier: 5.376A 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: 3.540A pdb=" N ALASG 68 " --> pdb=" O ARGSG 64 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILESG 73 " --> pdb=" O THRSG 69 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.510A pdb=" N THRSG 165 " --> pdb=" O ILESG 161 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.894A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 4.115A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLYSH 69 " --> pdb=" O PHESH 65 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SH' and resid 122 through 127 removed outlier: 5.915A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) Processing helix chain 'SH' and resid 143 through 151 Processing helix chain 'SH' and resid 154 through 180 removed outlier: 3.555A pdb=" N LYSSH 174 " --> pdb=" O ARGSH 170 " (cutoff:3.500A) Processing helix chain 'SI' and resid 34 through 46 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.622A pdb=" N PHESI 64 " --> pdb=" O ARGSI 60 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VALSI 83 " --> pdb=" O ARGSI 79 " (cutoff:3.500A) Processing helix chain 'SI' and resid 109 through 120 Processing helix chain 'SI' and resid 133 through 144 Processing helix chain 'SI' and resid 153 through 163 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 3.679A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 3.534A pdb=" N LEUSI 215 " --> pdb=" O ILESI 211 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.177A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 5.094A 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: 4.613A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 664 through 677 Processing helix chain 'SJ' and resid 678 through 690 removed outlier: 4.114A pdb=" N PHESJ 689 " --> pdb=" O ILESJ 685 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASNSJ 690 " --> pdb=" O ASPSJ 686 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 702 through 713 removed outlier: 3.603A pdb=" N GLNSJ 711 " --> pdb=" O GLNSJ 707 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HISSJ 712 " --> pdb=" O GLUSJ 708 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 720 through 731 removed outlier: 4.158A pdb=" N ARGSJ 730 " --> pdb=" O HISSJ 726 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRPSJ 731 " --> pdb=" O TYRSJ 727 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 825 through 843 removed outlier: 4.354A pdb=" N LYSSJ 829 " --> pdb=" O ASPSJ 825 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYSSJ 830 " --> pdb=" O SERSJ 826 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASPSJ 831 " --> pdb=" O ARGSJ 827 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 4.013A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.636A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 3.810A 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: 3.580A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.201A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 3.722A pdb=" N SERSK 235 " --> pdb=" O THRSK 231 " (cutoff:3.500A) Processing helix chain 'SK' and resid 238 through 244 Processing helix chain 'SL' and resid 32 through 51 removed outlier: 5.734A pdb=" N LYSSL 51 " --> pdb=" O CYSSL 47 " (cutoff:3.500A) Processing helix chain 'SL' and resid 106 through 122 Processing helix chain 'SL' and resid 131 through 138 Processing helix chain 'SL' and resid 141 through 153 removed outlier: 3.722A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 166 removed outlier: 3.627A pdb=" N ARGSL 162 " --> pdb=" O ASPSL 158 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.478A 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: 3.996A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 removed outlier: 3.516A pdb=" N GLUSL 193 " --> pdb=" O ASNSL 189 " (cutoff:3.500A) Processing helix chain 'SL' and resid 222 through 241 Processing helix chain 'SM' and resid 13 through 18 removed outlier: 3.603A pdb=" N TYRSM 17 " --> pdb=" O SERSM 13 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILESM 18 " --> pdb=" O ALASM 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'SM' and resid 13 through 18' 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: 3.507A pdb=" N VALSM 54 " --> pdb=" O HISSM 50 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 77 removed outlier: 3.987A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 3.965A 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: 3.589A 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 148 removed outlier: 3.514A pdb=" N ASPSM 133 " --> pdb=" O ASPSM 129 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASPSM 136 " --> pdb=" O ARGSM 132 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALASM 137 " --> pdb=" O ASPSM 133 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 3.877A 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: 3.530A pdb=" N METSM 220 " --> pdb=" O ASPSM 216 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHESM 226 " --> pdb=" O THRSM 222 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 4.103A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.585A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEUSM 326 " --> pdb=" O LYSSM 322 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.522A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLYSM 351 " --> pdb=" O ILESM 347 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.415A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.490A 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: 3.633A pdb=" N LYSSM 550 " --> pdb=" O TYRSM 546 " (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: 3.561A 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 removed outlier: 3.703A pdb=" N METSN 195 " --> pdb=" O GLUSN 191 " (cutoff:3.500A) Processing helix chain 'SO' and resid 71 through 86 Proline residue: SO 86 - end of helix Processing helix chain 'SO' and resid 99 through 111 removed outlier: 4.313A pdb=" N ILESO 103 " --> pdb=" O LYSSO 99 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASNSO 104 " --> pdb=" O LEUSO 100 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLUSO 105 " --> pdb=" O PHESO 101 " (cutoff:3.500A) Processing helix chain 'SO' and resid 169 through 176 removed outlier: 4.689A pdb=" N ASPSO 173 " --> pdb=" O ASPSO 169 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLUSO 174 " --> pdb=" O PROSO 170 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEUSO 175 " --> pdb=" O ALASO 171 " (cutoff:3.500A) Proline residue: SO 176 - end of helix No H-bonds generated for 'chain 'SO' and resid 169 through 176' Processing helix chain 'SO' and resid 177 through 190 Processing helix chain 'SO' and resid 261 through 294 removed outlier: 3.581A pdb=" N HISSO 265 " --> pdb=" O SERSO 261 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEUSO 289 " --> pdb=" O ASPSO 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLUSO 293 " --> pdb=" O LEUSO 289 " (cutoff:3.500A) Proline residue: SO 294 - end of helix Processing helix chain 'SO' and resid 328 through 333 removed outlier: 5.621A pdb=" N LYSSO 333 " --> pdb=" O LEUSO 329 " (cutoff:3.500A) Processing helix chain 'SO' and resid 337 through 353 Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.235A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASNSQ 25 " --> pdb=" O GLUSQ 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 50 through 61 removed outlier: 4.705A pdb=" N LYSSQ 54 " --> pdb=" O ASNSQ 50 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASPSQ 55 " --> pdb=" O SERSQ 51 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 4.274A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 119 Processing helix chain 'SQ' and resid 149 through 157 Processing helix chain 'SQ' and resid 183 through 194 removed outlier: 3.516A pdb=" N ARGSQ 188 " --> pdb=" O PROSQ 184 " (cutoff:3.500A) Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 68 removed outlier: 3.549A pdb=" N PHESR 46 " --> pdb=" O ARGSR 42 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYRSR 47 " --> pdb=" O ILESR 43 " (cutoff:3.500A) Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 120 removed outlier: 3.502A pdb=" N ALASR 110 " --> pdb=" O VALSR 106 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 145 removed outlier: 3.668A pdb=" N ILESR 141 " --> pdb=" O METSR 137 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) Processing helix chain 'SR' and resid 146 through 161 removed outlier: 3.661A pdb=" N GLNSR 153 " --> pdb=" O GLUSR 149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEUSR 161 " --> pdb=" O HISSR 157 " (cutoff:3.500A) Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.706A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.595A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 229 through 234' Processing helix chain 'SR' and resid 235 through 246 removed outlier: 4.147A 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: 4.671A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 295 through 300 removed outlier: 5.282A pdb=" N SERSR 300 " --> pdb=" O ILESR 296 " (cutoff:3.500A) Processing helix chain 'SR' and resid 301 through 314 removed outlier: 3.645A pdb=" N LEUSR 310 " --> pdb=" O ILESR 306 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 4.803A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 4.096A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HISSR 361 " --> pdb=" O LEUSR 357 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.268A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 417 removed outlier: 4.837A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 417' Processing helix chain 'SR' and resid 421 through 426 removed outlier: 4.354A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.181A 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: 4.168A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.915A 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: 4.226A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SS' and resid 140 through 146 removed outlier: 4.442A pdb=" N TYRSS 144 " --> pdb=" O PROSS 140 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASPSS 146 " --> pdb=" O GLUSS 142 " (cutoff:3.500A) Processing helix chain 'SS' and resid 197 through 210 Processing helix chain 'SS' and resid 242 through 248 removed outlier: 4.370A pdb=" N PHESS 246 " --> pdb=" O ASPSS 242 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILESS 247 " --> pdb=" O LYSSS 243 " (cutoff:3.500A) Proline residue: SS 248 - end of helix No H-bonds generated for 'chain 'SS' and resid 242 through 248' Processing helix chain 'SS' and resid 249 through 266 removed outlier: 3.649A pdb=" N LYSSS 253 " --> pdb=" O SERSS 249 " (cutoff:3.500A) Processing helix chain 'SS' and resid 323 through 334 removed outlier: 5.570A pdb=" N GLUSS 334 " --> pdb=" O TRPSS 330 " (cutoff:3.500A) Processing helix chain 'SS' and resid 358 through 372 removed outlier: 3.685A pdb=" N TYRSS 371 " --> pdb=" O CYSSS 367 " (cutoff:3.500A) Processing helix chain 'SS' and resid 384 through 390 removed outlier: 3.689A pdb=" N LEUSS 388 " --> pdb=" O ASPSS 384 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILESS 389 " --> pdb=" O PROSS 385 " (cutoff:3.500A) Proline residue: SS 390 - end of helix No H-bonds generated for 'chain 'SS' and resid 384 through 390' Processing helix chain 'ST' and resid 169 through 198 removed outlier: 4.750A pdb=" N LYSST 198 " --> pdb=" O ALAST 194 " (cutoff:3.500A) Processing helix chain 'ST' and resid 214 through 229 removed outlier: 4.340A pdb=" N THRST 229 " --> pdb=" O ALAST 225 " (cutoff:3.500A) Processing helix chain 'ST' and resid 260 through 276 Processing helix chain 'SV' and resid 33 through 43 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.460A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 removed outlier: 3.644A pdb=" N ARGSV 56 " --> pdb=" O THRSV 52 " (cutoff:3.500A) Processing helix chain 'SV' and resid 66 through 72 removed outlier: 4.017A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLUSV 72 " --> pdb=" O SERSV 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 72' Processing helix chain 'SV' and resid 82 through 135 removed outlier: 4.336A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASNSV 87 " --> pdb=" O ARGSV 83 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASPSV 91 " --> pdb=" O ASNSV 87 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARGSV 111 " --> pdb=" O PHESV 107 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEUSV 118 " --> pdb=" O LYSSV 114 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) Processing helix chain 'SW' and resid 178 through 184 removed outlier: 3.912A pdb=" N LEUSW 182 " --> pdb=" O SERSW 178 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYSSW 183 " --> pdb=" O PHESW 179 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASNSW 184 " --> pdb=" O ALASW 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'SW' and resid 178 through 184' Processing helix chain 'SW' and resid 187 through 198 Processing helix chain 'SW' and resid 203 through 216 removed outlier: 4.380A 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 Proline residue: SW 236 - end of helix Processing helix chain 'SW' and resid 260 through 276 removed outlier: 3.724A pdb=" N THRSW 276 " --> pdb=" O LYSSW 272 " (cutoff:3.500A) Processing helix chain 'SW' and resid 290 through 301 Processing helix chain 'SW' and resid 308 through 318 removed outlier: 3.575A pdb=" N LEUSW 312 " --> pdb=" O THRSW 308 " (cutoff:3.500A) Processing helix chain 'SW' and resid 334 through 342 removed outlier: 3.749A pdb=" N GLYSW 342 " --> pdb=" O ILESW 338 " (cutoff:3.500A) 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: 3.573A pdb=" N ILESW 377 " --> pdb=" O ASPSW 373 " (cutoff:3.500A) Processing helix chain 'SW' and resid 408 through 424 removed outlier: 4.976A pdb=" N PHESW 413 " --> pdb=" O SERSW 409 " (cutoff:3.500A) removed outlier: 5.269A 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 474 Processing helix chain 'SW' and resid 482 through 488 removed outlier: 5.774A 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 534 through 545 removed outlier: 4.564A pdb=" N LEUSW 538 " --> pdb=" O GLUSW 534 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARGSW 539 " --> pdb=" O LEUSW 535 " (cutoff:3.500A) Processing helix chain 'SW' and resid 561 through 572 Processing helix chain 'SW' and resid 573 through 593 removed outlier: 3.537A pdb=" N GLUSW 581 " --> pdb=" O LYSSW 577 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HISSW 593 " --> pdb=" O ALASW 589 " (cutoff:3.500A) Processing helix chain 'SW' and resid 595 through 600 Processing helix chain 'SW' and resid 605 through 614 removed outlier: 3.677A pdb=" N LEUSW 611 " --> pdb=" O PROSW 607 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHESW 613 " --> pdb=" O VALSW 609 " (cutoff:3.500A) Processing helix chain 'SY' and resid 223 through 234 Proline residue: SY 234 - end of helix Processing helix chain 'SY' and resid 235 through 253 removed outlier: 3.609A pdb=" N ASPSY 252 " --> pdb=" O GLYSY 248 " (cutoff:3.500A) Processing helix chain 'SY' and resid 262 through 279 Processing helix chain 'SY' and resid 281 through 293 Proline residue: SY 293 - end of helix Processing helix chain 'SY' and resid 294 through 307 removed outlier: 4.244A pdb=" N VALSY 298 " --> pdb=" O LEUSY 294 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLUSY 299 " --> pdb=" O SERSY 295 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLUSY 305 " --> pdb=" O LEUSY 301 " (cutoff:3.500A) removed outlier: 3.638A 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 removed outlier: 3.791A pdb=" N LEUSY 375 " --> pdb=" O ALASY 371 " (cutoff:3.500A) Proline residue: SY 376 - end of helix Processing helix chain 'SY' and resid 396 through 407 removed outlier: 3.549A pdb=" N TYRSY 401 " --> pdb=" O GLYSY 397 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N METSY 406 " --> pdb=" O METSY 402 " (cutoff:3.500A) Processing helix chain 'SY' and resid 419 through 433 removed outlier: 4.006A pdb=" N LYSSY 423 " --> pdb=" O ALASY 419 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SERSY 424 " --> pdb=" O GLUSY 420 " (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: 3.717A pdb=" N GLUSY 493 " --> pdb=" O HISSY 489 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASNSY 503 " --> pdb=" O ILESY 499 " (cutoff:3.500A) Processing helix chain 'SY' and resid 520 through 535 removed outlier: 3.501A pdb=" N GLUSY 525 " --> pdb=" O VALSY 521 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TRPSY 526 " --> pdb=" O GLUSY 522 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VALSY 527 " --> pdb=" O GLUSY 523 " (cutoff:3.500A) Processing helix chain 'SY' and resid 560 through 566 Processing helix chain 'SZ' and resid 6 through 12 removed outlier: 3.842A pdb=" N ARGSZ 10 " --> pdb=" O GLYSZ 6 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLNSZ 11 " --> pdb=" O LYSSZ 7 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LYSSZ 12 " --> pdb=" O THRSZ 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'SZ' and resid 6 through 12' 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: 4.560A pdb=" N LEUSZ 94 " --> pdb=" O LYSSZ 90 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASNSZ 95 " --> pdb=" O PROSZ 91 " (cutoff:3.500A) removed outlier: 3.563A 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: 5.881A 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: 4.382A 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: 6.938A pdb=" N LEUBB 163 " --> pdb=" O LEUBB 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VALBB 32 " --> pdb=" O VALBB 169 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 6, first strand: chain 'L8' and resid 11 through 15 removed outlier: 4.387A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEUL8 37 " --> pdb=" O VALL8 28 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.239A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.759A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LA' and resid 13 through 20 removed outlier: 6.348A pdb=" N LYSLA 13 " --> pdb=" O GLULA 152 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SERLA 17 " --> pdb=" O METLA 148 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILELA 149 " --> pdb=" O GLULA 115 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LA' and resid 116 through 122 removed outlier: 3.726A pdb=" N ALALA 122 " --> pdb=" O PROLA 143 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LB' and resid 99 through 102 removed outlier: 4.746A pdb=" N LYSLB 99 " --> pdb=" O LYSLB 78 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LC' and resid 27 through 34 removed outlier: 6.486A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.206A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.834A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LE' and resid 38 through 43 removed outlier: 4.086A pdb=" N ASPLE 38 " --> pdb=" O VALLE 64 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) removed outlier: 14.316A pdb=" N GLYLE 59 " --> pdb=" O GLNLE 79 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N GLNLE 79 " --> pdb=" O GLYLE 59 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THRLE 61 " --> pdb=" O ASNLE 77 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASNLE 77 " --> pdb=" O THRLE 61 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLYLE 73 " --> pdb=" O TYRLE 65 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LG' and resid 24 through 27 removed outlier: 4.562A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LG' and resid 59 through 63 removed outlier: 4.587A pdb=" N ASPLG 59 " --> pdb=" O VALLG 81 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LG' and resid 87 through 90 removed outlier: 4.081A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.597A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.961A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LI' and resid 71 through 75 Processing sheet with id= 22, first strand: chain 'LI' and resid 86 through 89 removed outlier: 3.538A pdb=" N LYSLI 89 " --> pdb=" O THRLI 93 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.118A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LN' and resid 41 through 44 removed outlier: 6.387A pdb=" N GLNLN 184 " --> pdb=" O THRLN 44 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILELN 160 " --> pdb=" O VALLN 185 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LN' and resid 53 through 59 removed outlier: 6.752A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 12.818A pdb=" N LYSLN 342 " --> pdb=" O LYSLN 224 " (cutoff:3.500A) removed outlier: 11.242A pdb=" N LYSLN 224 " --> pdb=" O LYSLN 342 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HISLN 275 " --> pdb=" O THRLN 223 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.767A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LN' and resid 77 through 80 Processing sheet with id= 28, first strand: chain 'LN' and resid 88 through 93 removed outlier: 3.621A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LN' and resid 215 through 218 removed outlier: 4.137A pdb=" N GLULN 215 " --> pdb=" O ILELN 284 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 31, first strand: chain 'LT' and resid 56 through 60 removed outlier: 5.732A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THRLT 59 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LT' and resid 8 through 12 removed outlier: 6.001A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LT' and resid 6 through 10 Processing sheet with id= 34, first strand: chain 'LW' and resid 15 through 18 removed outlier: 8.382A pdb=" N THRLW 15 " --> pdb=" O HISLW 28 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N HISLW 28 " --> pdb=" O THRLW 15 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N THRLW 17 " --> pdb=" O ALALW 26 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'NF' and resid 189 through 194 removed outlier: 3.602A pdb=" N ALANF 190 " --> pdb=" O HISNF 185 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TYRNF 241 " --> pdb=" O LEUNF 259 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THRNF 218 " --> pdb=" O VALNF 244 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'NH' and resid 36 through 39 removed outlier: 6.947A pdb=" N VALNH 44 " --> pdb=" O PHENH 70 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THRNH 68 " --> pdb=" O TYRNH 46 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'NH' and resid 95 through 99 removed outlier: 4.871A pdb=" N TYRNH 95 " --> pdb=" O GLYNH 130 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'NI' and resid 196 through 200 removed outlier: 3.879A pdb=" N ALANI 169 " --> pdb=" O ASPNI 218 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VALNI 136 " --> pdb=" O THRNI 274 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SERNI 278 " --> pdb=" O ALANI 138 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALANI 140 " --> pdb=" O SERNI 278 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'NI' and resid 364 through 368 removed outlier: 4.194A pdb=" N METNI 479 " --> pdb=" O THRNI 313 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'SA' and resid 7 through 10 removed outlier: 4.940A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.327A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'SC' and resid 90 through 93 removed outlier: 8.850A pdb=" N ALASC 90 " --> pdb=" O LEUSC 109 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'SC' and resid 147 through 153 removed outlier: 4.354A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 45, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.115A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SD' and resid 158 through 162 removed outlier: 6.703A pdb=" N GLYSD 158 " --> pdb=" O LEUSD 169 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 48, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.661A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 50, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.595A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.328A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'SH' and resid 72 through 77 removed outlier: 3.607A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TYRSH 88 " --> pdb=" O SERSH 77 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SI' and resid 147 through 151 removed outlier: 3.524A pdb=" N ARGSI 101 " --> pdb=" O SERSI 126 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SK' and resid 1 through 4 removed outlier: 3.644A pdb=" N ALASK 204 " --> pdb=" O METSK 1 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 56, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 57, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 58, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 59, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.573A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEUSL 78 " --> pdb=" O ILESL 205 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'SL' and resid 127 through 130 Processing sheet with id= 61, first strand: chain 'SL' and resid 210 through 216 removed outlier: 6.185A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYSSL 249 " --> pdb=" O SERSL 266 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHESL 264 " --> pdb=" O LEUSL 251 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'SM' and resid 179 through 184 removed outlier: 3.596A pdb=" N GLYSM 187 " --> pdb=" O SERSM 184 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 64, first strand: chain 'SO' and resid 87 through 91 removed outlier: 4.327A pdb=" N ASPSO 91 " --> pdb=" O ILESO 64 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SERSO 66 " --> pdb=" O ASPSO 91 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALASO 120 " --> pdb=" O SERSO 67 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEUSO 126 " --> pdb=" O VALSO 143 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYSSO 140 " --> pdb=" O ILESO 241 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALASO 228 " --> pdb=" O ILESO 223 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASNSO 219 " --> pdb=" O ILESO 232 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHESO 217 " --> pdb=" O PROSO 234 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHESO 236 " --> pdb=" O ILESO 215 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILESO 215 " --> pdb=" O PHESO 236 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASPSO 203 " --> pdb=" O ILESO 222 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SO' and resid 137 through 140 removed outlier: 3.518A pdb=" N LYSSO 242 " --> pdb=" O LYSSO 140 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 6.639A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.829A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 69, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.920A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.390A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SR' and resid 205 through 211 removed outlier: 5.188A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEUSR 173 " --> pdb=" O VALSR 220 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N CYSSR 174 " --> pdb=" O LEUSR 252 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VALSR 254 " --> pdb=" O CYSSR 174 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'SS' and resid 183 through 188 removed outlier: 6.726A pdb=" N ARGSS 183 " --> pdb=" O LEUSS 196 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARGSS 192 " --> pdb=" O ASPSS 187 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'SV' and resid 3 through 6 removed outlier: 4.282A pdb=" N GLYSV 11 " --> pdb=" O CYSSV 6 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'SV' and resid 18 through 23 removed outlier: 5.341A pdb=" N LYSSV 27 " --> pdb=" O ARGSV 23 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SW' and resid 281 through 285 removed outlier: 3.517A pdb=" N ALASW 222 " --> pdb=" O VALSW 386 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VALSW 388 " --> pdb=" O ALASW 222 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SW' and resid 400 through 407 removed outlier: 3.575A pdb=" N ILESW 529 " --> pdb=" O GLNSW 499 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'SW' and resid 452 through 455 Processing sheet with id= 78, first strand: chain 'SY' and resid 334 through 337 removed outlier: 6.895A pdb=" N ASNSY 334 " --> pdb=" O TYRSY 349 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THRSY 344 " --> pdb=" O THRSY 314 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VALSY 310 " --> pdb=" O VALSY 348 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N HISSY 365 " --> pdb=" O ASNSY 315 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'SY' and resid 436 through 442 removed outlier: 5.654A pdb=" N ASNSY 436 " --> pdb=" O GLYSY 410 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYRSY 442 " --> pdb=" O ASPSY 416 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASPSY 460 " --> pdb=" O METSY 391 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLYSY 510 " --> pdb=" O LYSSY 586 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEUSY 512 " --> pdb=" O PHESY 584 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYSSY 583 " --> pdb=" O VALSY 540 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'SY' and resid 567 through 571 removed outlier: 6.697A pdb=" N ASPSY 577 " --> pdb=" O PROSY 571 " (cutoff:3.500A) 3451 hydrogen bonds defined for protein. 10238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2058 hydrogen bonds 3568 hydrogen bond angles 0 basepair planarities 784 basepair parallelities 1235 stacking parallelities Total time for adding SS restraints: 120.18 Time building geometry restraints manager: 46.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 19840 1.33 - 1.45: 47300 1.45 - 1.58: 60818 1.58 - 1.70: 4781 1.70 - 1.83: 489 Bond restraints: 133228 Sorted by residual: bond pdb=" N7 GDPSR1001 " pdb=" C5 GDPSR1001 " ideal model delta sigma weight residual 1.350 1.516 -0.166 2.00e-02 2.50e+03 6.93e+01 bond pdb=" C6 GDPSR1001 " pdb=" O6 GDPSR1001 " ideal model delta sigma weight residual 1.250 1.396 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C2 GDPSR1001 " pdb=" N2 GDPSR1001 " ideal model delta sigma weight residual 1.355 1.449 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" N1 GDPSR1001 " pdb=" C2 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.405 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1' GDPSR1001 " pdb=" N9 GDPSR1001 " ideal model delta sigma weight residual 1.485 1.420 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 133223 not shown) Histogram of bond angle deviations from ideal: 96.66 - 105.20: 12250 105.20 - 113.73: 81706 113.73 - 122.26: 74901 122.26 - 130.80: 21682 130.80 - 139.33: 916 Bond angle restraints: 191455 Sorted by residual: angle pdb=" C8 GDPSR1001 " pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 108.00 121.21 -13.21 3.00e+00 1.11e-01 1.94e+01 angle pdb=" CB LYSSA 14 " pdb=" CG LYSSA 14 " pdb=" CD LYSSA 14 " ideal model delta sigma weight residual 111.30 120.27 -8.97 2.30e+00 1.89e-01 1.52e+01 angle pdb=" O4' GL3 417 " pdb=" C1' GL3 417 " pdb=" N9 GL3 417 " ideal model delta sigma weight residual 108.20 112.86 -4.66 1.50e+00 4.44e-01 9.64e+00 angle pdb=" C2' AL34510 " pdb=" C1' AL34510 " pdb=" N9 AL34510 " ideal model delta sigma weight residual 112.00 116.52 -4.52 1.50e+00 4.44e-01 9.08e+00 angle pdb=" C4' GL34520 " pdb=" C3' GL34520 " pdb=" O3' GL34520 " ideal model delta sigma weight residual 109.40 113.90 -4.50 1.50e+00 4.44e-01 9.01e+00 ... (remaining 191450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 78320 35.67 - 71.34: 5763 71.34 - 107.01: 794 107.01 - 142.68: 5 142.68 - 178.35: 7 Dihedral angle restraints: 84889 sinusoidal: 57420 harmonic: 27469 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 25.05 174.95 1 1.50e+01 4.44e-03 8.52e+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 47.21 152.79 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' CL32091 " pdb=" C1' CL32091 " pdb=" N1 CL32091 " pdb=" C2 CL32091 " ideal model delta sinusoidal sigma weight residual 232.00 53.65 178.35 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 84886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 18657 0.047 - 0.094: 3673 0.094 - 0.141: 808 0.141 - 0.188: 93 0.188 - 0.235: 5 Chirality restraints: 23236 Sorted by residual: chirality pdb=" C1' AL32042 " pdb=" O4' AL32042 " pdb=" C2' AL32042 " pdb=" N9 AL32042 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C3' GL34520 " pdb=" C4' GL34520 " pdb=" O3' GL34520 " pdb=" C2' GL34520 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C3' GL1 39 " pdb=" C4' GL1 39 " pdb=" O3' GL1 39 " pdb=" C2' GL1 39 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.72e-01 ... (remaining 23233 not shown) Planarity restraints: 15438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GL1 39 " -0.056 2.00e-02 2.50e+03 2.32e-02 1.61e+01 pdb=" N9 GL1 39 " 0.051 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 " 0.002 2.00e-02 2.50e+03 pdb=" C6 GL1 39 " -0.007 2.00e-02 2.50e+03 pdb=" O6 GL1 39 " -0.018 2.00e-02 2.50e+03 pdb=" N1 GL1 39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GL1 39 " 0.002 2.00e-02 2.50e+03 pdb=" N2 GL1 39 " 0.002 2.00e-02 2.50e+03 pdb=" N3 GL1 39 " 0.011 2.00e-02 2.50e+03 pdb=" C4 GL1 39 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPSV 86 " -0.021 2.00e-02 2.50e+03 2.28e-02 1.30e+01 pdb=" CG TRPSV 86 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRPSV 86 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRPSV 86 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRPSV 86 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRPSV 86 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRPSV 86 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRPSV 86 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRPSV 86 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRPSV 86 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AL34510 " 0.039 2.00e-02 2.50e+03 1.86e-02 9.48e+00 pdb=" N9 AL34510 " -0.046 2.00e-02 2.50e+03 pdb=" C8 AL34510 " -0.002 2.00e-02 2.50e+03 pdb=" N7 AL34510 " 0.003 2.00e-02 2.50e+03 pdb=" C5 AL34510 " 0.000 2.00e-02 2.50e+03 pdb=" C6 AL34510 " 0.006 2.00e-02 2.50e+03 pdb=" N6 AL34510 " 0.008 2.00e-02 2.50e+03 pdb=" N1 AL34510 " 0.002 2.00e-02 2.50e+03 pdb=" C2 AL34510 " -0.000 2.00e-02 2.50e+03 pdb=" N3 AL34510 " -0.007 2.00e-02 2.50e+03 pdb=" C4 AL34510 " -0.003 2.00e-02 2.50e+03 ... (remaining 15435 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.58: 738 2.58 - 3.22: 110617 3.22 - 3.86: 264783 3.86 - 4.50: 374863 4.50 - 5.14: 524947 Nonbonded interactions: 1275948 Sorted by model distance: nonbonded pdb=" O1B ADPNI1001 " pdb="MG MGNI1002 " model vdw 1.935 2.170 nonbonded pdb=" OG SERSR 182 " pdb="MG MGSR1003 " model vdw 1.948 2.170 nonbonded pdb=" OP2 GL1 75 " pdb=" OH TYRLI 74 " model vdw 1.977 2.440 nonbonded pdb=" O1B GDPSR1001 " pdb="MG MGSR1003 " model vdw 1.990 2.170 nonbonded pdb=" O2' UL34946 " pdb=" OG SERLT 2 " model vdw 1.995 2.440 ... (remaining 1275943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 22.950 Check model and map are aligned: 1.210 Set scattering table: 0.760 Process input model: 395.840 Find NCS groups from input model: 3.510 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 441.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.006 0.166 133228 Z= 0.365 Angle : 0.636 13.208 191455 Z= 0.335 Chirality : 0.041 0.235 23236 Planarity : 0.006 0.098 15438 Dihedral : 20.351 178.345 67067 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.01 % Allowed : 0.14 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.03 (0.08), residues: 9279 helix: 1.40 (0.08), residues: 3859 sheet: 0.47 (0.14), residues: 1193 loop : 0.21 (0.09), residues: 4227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRPSV 86 HIS 0.014 0.002 HISLA 25 PHE 0.031 0.002 PHESR 18 TYR 0.039 0.002 TYRSR 176 ARG 0.015 0.001 ARGNH 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 949 time to evaluate : 7.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L8 104 MET cc_start: 0.8928 (mtm) cc_final: 0.8698 (mtp) REVERT: L8 118 MET cc_start: 0.8927 (tpt) cc_final: 0.8470 (tpt) REVERT: LN 19 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7221 (mtp180) REVERT: LN 299 ILE cc_start: 0.8254 (mt) cc_final: 0.7929 (mt) REVERT: LN 389 MET cc_start: 0.8501 (mmm) cc_final: 0.8178 (mmm) REVERT: NK 97 MET cc_start: 0.8827 (ttm) cc_final: 0.8620 (ttt) REVERT: SC 245 GLN cc_start: 0.7805 (tp-100) cc_final: 0.7126 (tp40) REVERT: SH 161 MET cc_start: 0.7477 (ttm) cc_final: 0.7103 (ttp) REVERT: SI 71 GLN cc_start: 0.7474 (tt0) cc_final: 0.7265 (tt0) REVERT: SI 253 GLN cc_start: 0.8029 (mt0) cc_final: 0.7688 (mt0) REVERT: SJ 708 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7428 (tm-30) REVERT: SQ 37 TYR cc_start: 0.8485 (m-80) cc_final: 0.8226 (m-80) REVERT: SR 238 MET cc_start: 0.8491 (mmm) cc_final: 0.8238 (mmm) REVERT: SS 341 SER cc_start: 0.8254 (p) cc_final: 0.8028 (t) REVERT: SW 275 MET cc_start: 0.7354 (mtp) cc_final: 0.7094 (mtp) REVERT: SW 339 LEU cc_start: 0.6987 (mm) cc_final: 0.6744 (pp) REVERT: SZ 122 MET cc_start: 0.7959 (mmt) cc_final: 0.7665 (mmt) outliers start: 1 outliers final: 1 residues processed: 949 average time/residue: 1.9765 time to fit residues: 2625.2895 Evaluate side-chains 760 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 759 time to evaluate : 7.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SZ residue 128 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1161 random chunks: chunk 980 optimal weight: 0.8980 chunk 879 optimal weight: 3.9990 chunk 488 optimal weight: 6.9990 chunk 300 optimal weight: 1.9990 chunk 593 optimal weight: 40.0000 chunk 470 optimal weight: 2.9990 chunk 909 optimal weight: 4.9990 chunk 352 optimal weight: 3.9990 chunk 553 optimal weight: 8.9990 chunk 677 optimal weight: 5.9990 chunk 1054 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L6 104 ASN ** L7 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L7 90 HIS L7 167 HIS L7 173 GLN ** LC 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LE 144 ASN LI 40 GLN LI 43 ASN LI 91 ASN LK 62 HIS LN 3 HIS LN 42 HIS LQ 23 HIS LS 65 GLN LS 96 ASN LU 26 HIS NB 16 HIS ** NF 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NF 33 HIS NF 255 ASN NH 105 GLN NH 124 ASN NH 175 HIS NI 349 HIS NI 409 ASN NI 454 HIS ** NI 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NK 92 GLN NK 98 ASN SC 136 HIS SC 190 HIS SD 24 ASN SD 131 ASN SE 85 GLN SG 42 ASN SG 140 GLN SH 60 GLN SI 225 HIS SJ 707 GLN SJ 712 HIS SJ 726 HIS SK 83 HIS SL 46 HIS SL 218 HIS SM 154 HIS SM 211 HIS SM 323 HIS SN 51 ASN SN 197 ASN SQ 25 ASN ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SQ 113 ASN SQ 186 GLN SQ 216 GLN SR 35 HIS SR 45 HIS SR 91 HIS SR 157 HIS SR 209 HIS SR 239 GLN SS 238 ASN SS 310 HIS SV 101 GLN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 296 GLN SW 300 ASN SW 593 HIS SY 404 GLN SY 430 HIS SZ 11 GLN SZ 164 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 133228 Z= 0.220 Angle : 0.538 12.426 191455 Z= 0.281 Chirality : 0.037 0.253 23236 Planarity : 0.004 0.058 15438 Dihedral : 21.759 177.762 48571 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.46 % Allowed : 6.22 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.08), residues: 9279 helix: 1.98 (0.08), residues: 3971 sheet: 0.48 (0.14), residues: 1247 loop : 0.27 (0.09), residues: 4061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPSV 86 HIS 0.009 0.001 HISLA 25 PHE 0.033 0.002 PHESY 579 TYR 0.023 0.001 TYRLK 61 ARG 0.009 0.001 ARGNH 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 829 time to evaluate : 7.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BA 57 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6488 (ttp80) REVERT: BA 124 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: L7 149 TYR cc_start: 0.8954 (m-80) cc_final: 0.8706 (m-80) REVERT: L8 118 MET cc_start: 0.9047 (tpt) cc_final: 0.8454 (tpt) REVERT: LN 389 MET cc_start: 0.8420 (mmm) cc_final: 0.8200 (mtm) REVERT: NF 250 ASN cc_start: 0.8262 (m-40) cc_final: 0.8054 (m-40) REVERT: SC 249 ASP cc_start: 0.7080 (m-30) cc_final: 0.6859 (m-30) REVERT: SE 105 GLU cc_start: 0.7294 (pt0) cc_final: 0.7068 (pt0) REVERT: SJ 674 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8720 (mt) REVERT: SJ 708 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7177 (tm-30) REVERT: SL 267 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: SM 220 MET cc_start: 0.8203 (mtm) cc_final: 0.7986 (mtm) REVERT: SO 334 LYS cc_start: 0.6399 (tptt) cc_final: 0.5710 (tttt) REVERT: SR 309 ASP cc_start: 0.6841 (m-30) cc_final: 0.6557 (m-30) REVERT: SS 199 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: SS 341 SER cc_start: 0.8219 (p) cc_final: 0.8003 (t) REVERT: SW 339 LEU cc_start: 0.7269 (mm) cc_final: 0.6905 (pp) REVERT: SW 372 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.5094 (tp30) outliers start: 111 outliers final: 38 residues processed: 869 average time/residue: 1.9693 time to fit residues: 2400.0375 Evaluate side-chains 782 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 738 time to evaluate : 7.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 57 ARG Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 62 LEU Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 106 SER Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L8 residue 136 LEU Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LI residue 93 THR Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 89 LEU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain NF residue 71 ARG Chi-restraints excluded: chain NF residue 101 VAL Chi-restraints excluded: chain NF residue 197 LEU Chi-restraints excluded: chain NH residue 124 ASN Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 87 LEU Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SN residue 199 ILE Chi-restraints excluded: chain SO residue 264 MET Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SQ residue 204 ILE Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 176 TYR Chi-restraints excluded: chain SS residue 199 GLU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 229 THR Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SW residue 225 THR Chi-restraints excluded: chain SW residue 372 GLU Chi-restraints excluded: chain SZ residue 165 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1161 random chunks: chunk 585 optimal weight: 1.9990 chunk 327 optimal weight: 10.0000 chunk 877 optimal weight: 0.8980 chunk 717 optimal weight: 0.9990 chunk 290 optimal weight: 0.0980 chunk 1056 optimal weight: 0.9980 chunk 1141 optimal weight: 4.9990 chunk 940 optimal weight: 1.9990 chunk 1047 optimal weight: 6.9990 chunk 360 optimal weight: 7.9990 chunk 847 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 115 GLN L7 173 GLN LA 72 GLN LA 93 HIS LA 101 ASN ** LA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 45 GLN LC 37 HIS LC 92 ASN ** LC 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LE 144 ASN LG 36 ASN LI 91 ASN LN 208 ASN LN 213 GLN NF 3 GLN NF 255 ASN NH 105 GLN ** NI 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NK 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NK 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 156 ASN SH 67 GLN SI 71 GLN SI 219 HIS SJ 707 GLN SJ 726 HIS ** SK 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 35 GLN SM 209 HIS SN 51 ASN SN 197 ASN ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SQ 216 GLN ** SR 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 277 HIS SW 525 HIS SZ 11 GLN SZ 153 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 133228 Z= 0.136 Angle : 0.470 14.154 191455 Z= 0.244 Chirality : 0.033 0.224 23236 Planarity : 0.003 0.048 15438 Dihedral : 21.655 179.169 48568 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.41 % Allowed : 8.33 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.80 (0.08), residues: 9279 helix: 2.36 (0.08), residues: 3982 sheet: 0.53 (0.14), residues: 1221 loop : 0.32 (0.09), residues: 4076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPL9 120 HIS 0.011 0.001 HISSJ 726 PHE 0.024 0.001 PHESY 579 TYR 0.026 0.001 TYRLK 61 ARG 0.006 0.000 ARGL9 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 804 time to evaluate : 7.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 57 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6626 (ttp80) REVERT: BA 114 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7688 (mtm110) REVERT: BA 124 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: L7 149 TYR cc_start: 0.8905 (m-80) cc_final: 0.8678 (m-80) REVERT: L8 118 MET cc_start: 0.8992 (tpt) cc_final: 0.8522 (tpt) REVERT: LA 23 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7046 (mtt-85) REVERT: LA 31 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7945 (mm-30) REVERT: LN 19 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7153 (mtp180) REVERT: LN 389 MET cc_start: 0.8426 (mmm) cc_final: 0.8185 (mmm) REVERT: LQ 98 GLU cc_start: 0.7740 (tt0) cc_final: 0.7081 (tp30) REVERT: NF 250 ASN cc_start: 0.8215 (m-40) cc_final: 0.8005 (m-40) REVERT: NI 424 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.7152 (t-170) REVERT: SA 14 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7604 (mtpm) REVERT: SC 245 GLN cc_start: 0.7444 (tp40) cc_final: 0.7188 (tp40) REVERT: SC 249 ASP cc_start: 0.6905 (m-30) cc_final: 0.6655 (m-30) REVERT: SE 105 GLU cc_start: 0.7286 (pt0) cc_final: 0.7053 (pt0) REVERT: SJ 674 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8569 (mt) REVERT: SJ 708 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7232 (tm-30) REVERT: SK 8 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6880 (mm-30) REVERT: SL 267 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: SM 220 MET cc_start: 0.8146 (mtm) cc_final: 0.7944 (mtm) REVERT: SO 334 LYS cc_start: 0.6341 (tptt) cc_final: 0.5935 (tttp) REVERT: SQ 47 ASN cc_start: 0.8087 (t0) cc_final: 0.7845 (t0) REVERT: SS 199 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6351 (tm-30) REVERT: ST 273 ARG cc_start: 0.6552 (ttp80) cc_final: 0.6268 (ttp80) REVERT: SV 62 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6578 (mm-30) REVERT: SW 265 MET cc_start: 0.6301 (tpt) cc_final: 0.5721 (ttt) REVERT: SW 275 MET cc_start: 0.7024 (mmm) cc_final: 0.6587 (mtp) REVERT: SW 323 MET cc_start: 0.7602 (ttm) cc_final: 0.7270 (ptp) outliers start: 107 outliers final: 37 residues processed: 853 average time/residue: 1.9609 time to fit residues: 2351.0051 Evaluate side-chains 787 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 741 time to evaluate : 7.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 57 ARG Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 114 ARG Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 106 SER Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 136 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LL residue 49 VAL Chi-restraints excluded: chain LN residue 300 LYS Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 89 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain NF residue 197 LEU Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NH residue 121 ILE Chi-restraints excluded: chain NI residue 332 HIS Chi-restraints excluded: chain NI residue 424 HIS Chi-restraints excluded: chain NK residue 19 LYS Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SN residue 100 ASP Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SN residue 199 ILE Chi-restraints excluded: chain SQ residue 50 ASN Chi-restraints excluded: chain SR residue 176 TYR Chi-restraints excluded: chain SS residue 199 GLU Chi-restraints excluded: chain ST residue 229 THR Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SY residue 540 VAL Chi-restraints excluded: chain SZ residue 165 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1161 random chunks: chunk 1043 optimal weight: 50.0000 chunk 794 optimal weight: 10.0000 chunk 548 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 504 optimal weight: 8.9990 chunk 709 optimal weight: 4.9990 chunk 1060 optimal weight: 9.9990 chunk 1122 optimal weight: 7.9990 chunk 553 optimal weight: 7.9990 chunk 1004 optimal weight: 6.9990 chunk 302 optimal weight: 0.6980 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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 173 GLN L9 8 GLN LA 28 ASN LA 34 GLN LA 93 HIS LB 45 GLN LB 93 GLN ** LC 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LE 144 ASN LG 36 ASN LI 14 ASN LI 91 ASN LN 302 ASN LQ 102 ASN LS 96 ASN LU 36 HIS NF 255 ASN NH 25 GLN NH 105 GLN NH 166 GLN NK 92 GLN SA 60 HIS SA 119 GLN SE 206 GLN SG 156 ASN SG 163 GLN SI 209 GLN SJ 707 GLN SJ 726 HIS SL 121 HIS SN 51 ASN ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SQ 216 GLN SR 56 GLN ** SS 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SS 296 HIS ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 122 GLN SW 277 HIS SY 404 GLN SZ 11 GLN SZ 153 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 133228 Z= 0.497 Angle : 0.665 14.712 191455 Z= 0.339 Chirality : 0.044 0.293 23236 Planarity : 0.006 0.082 15438 Dihedral : 21.663 177.607 48568 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.42 % Allowed : 9.23 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.28 (0.08), residues: 9279 helix: 1.88 (0.08), residues: 3977 sheet: 0.34 (0.14), residues: 1227 loop : 0.06 (0.09), residues: 4075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRPLT 6 HIS 0.014 0.002 HISL6 67 PHE 0.048 0.003 PHESR 18 TYR 0.026 0.002 TYRSN 109 ARG 0.009 0.001 ARGL9 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 772 time to evaluate : 7.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 57 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6461 (ttp80) REVERT: BA 124 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: L8 118 MET cc_start: 0.9020 (tpt) cc_final: 0.8341 (tpt) REVERT: LA 23 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7275 (mtt-85) REVERT: LN 19 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7245 (mtp180) REVERT: LN 162 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8471 (p) REVERT: LN 174 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6933 (mmt90) REVERT: LN 389 MET cc_start: 0.8504 (mmm) cc_final: 0.8148 (mmm) REVERT: NI 424 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.7252 (t-170) REVERT: NK 100 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7030 (ptm160) REVERT: SA 348 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8216 (ttpt) REVERT: SC 245 GLN cc_start: 0.7510 (tp40) cc_final: 0.7208 (tp40) REVERT: SE 105 GLU cc_start: 0.7487 (pt0) cc_final: 0.7264 (pt0) REVERT: SG 1 MET cc_start: 0.8338 (ttp) cc_final: 0.7946 (ttm) REVERT: SG 152 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: SJ 674 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8750 (mt) REVERT: SK 8 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6932 (mm-30) REVERT: SO 334 LYS cc_start: 0.6905 (tptt) cc_final: 0.6665 (tttp) REVERT: SQ 88 ASN cc_start: 0.8007 (t0) cc_final: 0.7621 (t0) REVERT: SQ 217 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: SW 220 LEU cc_start: 0.6530 (tm) cc_final: 0.6285 (tp) REVERT: SW 265 MET cc_start: 0.6368 (tpt) cc_final: 0.5755 (ttt) REVERT: SW 275 MET cc_start: 0.7409 (mmm) cc_final: 0.6838 (mtp) outliers start: 184 outliers final: 73 residues processed: 862 average time/residue: 1.9518 time to fit residues: 2370.5105 Evaluate side-chains 807 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 723 time to evaluate : 7.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 57 ARG Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 62 LEU Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 106 SER Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 136 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 146 ILE Chi-restraints excluded: chain LB residue 66 MET Chi-restraints excluded: chain LG residue 32 THR Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LH residue 34 SER Chi-restraints excluded: chain LI residue 93 THR Chi-restraints excluded: chain LK residue 61 TYR Chi-restraints excluded: chain LL residue 49 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 300 LYS Chi-restraints excluded: chain LN residue 301 ASN Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 89 LEU Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 37 THR Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 30 GLN Chi-restraints excluded: chain NF residue 53 GLN Chi-restraints excluded: chain NF residue 66 LYS Chi-restraints excluded: chain NF residue 197 LEU Chi-restraints excluded: chain NF residue 204 SER Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NI residue 424 HIS Chi-restraints excluded: chain NK residue 95 ILE Chi-restraints excluded: chain NK residue 100 ARG Chi-restraints excluded: chain SA residue 27 VAL Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 202 ASP Chi-restraints excluded: chain SC residue 205 ASN Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SC residue 278 THR Chi-restraints excluded: chain SE residue 179 VAL Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 152 GLU Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SI residue 153 ASN Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SL residue 120 LYS Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SN residue 128 VAL Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SN residue 199 ILE Chi-restraints excluded: chain SQ residue 217 GLN Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 176 TYR Chi-restraints excluded: chain SR residue 329 ILE Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 209 SER Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SW residue 225 THR Chi-restraints excluded: chain SY residue 540 VAL Chi-restraints excluded: chain SZ residue 165 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1161 random chunks: chunk 934 optimal weight: 0.9990 chunk 637 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 835 optimal weight: 3.9990 chunk 463 optimal weight: 0.9990 chunk 957 optimal weight: 10.0000 chunk 775 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 573 optimal weight: 1.9990 chunk 1007 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 115 GLN L7 173 GLN LA 34 GLN ** LA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 45 GLN LB 93 GLN LC 108 GLN ** LC 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LE 144 ASN LI 14 ASN LI 91 ASN NF 255 ASN NH 166 GLN NI 367 HIS NK 92 GLN SA 119 GLN SE 206 GLN SJ 707 GLN SJ 726 HIS ** SK 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 51 ASN ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 50 ASN SQ 91 GLN SQ 216 GLN SR 218 GLN SR 274 ASN SS 149 HIS ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 349 GLN SZ 11 GLN SZ 153 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 133228 Z= 0.228 Angle : 0.522 14.521 191455 Z= 0.270 Chirality : 0.036 0.260 23236 Planarity : 0.004 0.049 15438 Dihedral : 21.638 178.240 48568 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.96 % Allowed : 10.47 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.08), residues: 9279 helix: 2.14 (0.08), residues: 3963 sheet: 0.34 (0.14), residues: 1237 loop : 0.09 (0.09), residues: 4079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLT 6 HIS 0.010 0.001 HISSJ 726 PHE 0.034 0.001 PHESY 579 TYR 0.023 0.001 TYRSN 109 ARG 0.006 0.000 ARGSY 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 747 time to evaluate : 7.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 57 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6627 (ttp80) REVERT: BA 124 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: L7 149 TYR cc_start: 0.8926 (m-80) cc_final: 0.8651 (m-80) REVERT: L8 118 MET cc_start: 0.9005 (tpt) cc_final: 0.8429 (tpt) REVERT: L9 161 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7344 (mmm) REVERT: LA 23 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7390 (mtt-85) REVERT: LN 19 ARG cc_start: 0.7655 (mtt180) cc_final: 0.7179 (mtp180) REVERT: LN 162 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8353 (p) REVERT: LN 174 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6958 (mmt90) REVERT: LN 389 MET cc_start: 0.8488 (mmm) cc_final: 0.8151 (mmm) REVERT: LQ 98 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: NF 250 ASN cc_start: 0.8198 (m-40) cc_final: 0.7997 (m-40) REVERT: NI 424 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.7182 (t-170) REVERT: NK 100 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7122 (ptm160) REVERT: SA 348 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8175 (ttpt) REVERT: SG 1 MET cc_start: 0.8317 (ttp) cc_final: 0.7988 (ttm) REVERT: SJ 674 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8674 (mt) REVERT: SK 8 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6842 (mm-30) REVERT: SO 281 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: SQ 47 ASN cc_start: 0.8173 (t0) cc_final: 0.7923 (t0) REVERT: SQ 88 ASN cc_start: 0.7975 (t0) cc_final: 0.7629 (t0) REVERT: SW 265 MET cc_start: 0.6299 (tpt) cc_final: 0.5680 (ttt) outliers start: 149 outliers final: 73 residues processed: 828 average time/residue: 1.9475 time to fit residues: 2267.2522 Evaluate side-chains 802 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 717 time to evaluate : 7.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 57 ARG Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 62 LEU Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 106 SER Chi-restraints excluded: chain L7 residue 46 ASN Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 132 LYS Chi-restraints excluded: chain L8 residue 136 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 146 ILE Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LH residue 34 SER Chi-restraints excluded: chain LI residue 93 THR Chi-restraints excluded: chain LL residue 49 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 300 LYS Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 89 LEU Chi-restraints excluded: chain LQ residue 98 GLU Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 37 THR Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NF residue 197 LEU Chi-restraints excluded: chain NI residue 424 HIS Chi-restraints excluded: chain NK residue 19 LYS Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 87 LEU Chi-restraints excluded: chain NK residue 100 ARG Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 205 ASN Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SC residue 268 GLN Chi-restraints excluded: chain SD residue 33 LEU Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SD residue 134 ARG Chi-restraints excluded: chain SE residue 179 VAL Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 190 LEU Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 127 GLU Chi-restraints excluded: chain SK residue 172 GLU Chi-restraints excluded: chain SL residue 193 GLU Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SO residue 281 GLN Chi-restraints excluded: chain SQ residue 27 ILE Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 176 TYR Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 254 PHE Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SW residue 191 LEU Chi-restraints excluded: chain SW residue 225 THR Chi-restraints excluded: chain SW residue 339 LEU Chi-restraints excluded: chain SY residue 539 LEU Chi-restraints excluded: chain SY residue 540 VAL Chi-restraints excluded: chain SZ residue 37 SER Chi-restraints excluded: chain SZ residue 165 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1161 random chunks: chunk 377 optimal weight: 6.9990 chunk 1010 optimal weight: 2.9990 chunk 221 optimal weight: 20.0000 chunk 658 optimal weight: 10.0000 chunk 277 optimal weight: 0.9990 chunk 1123 optimal weight: 3.9990 chunk 932 optimal weight: 7.9990 chunk 520 optimal weight: 0.2980 chunk 93 optimal weight: 7.9990 chunk 371 optimal weight: 10.0000 chunk 589 optimal weight: 40.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 173 GLN LA 34 GLN ** LA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 45 GLN LB 93 GLN ** LC 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LE 144 ASN LG 36 ASN LI 14 ASN LI 91 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NF 255 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 92 GLN SA 119 GLN SE 206 GLN SG 156 ASN SJ 707 GLN SJ 726 HIS ** SK 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 375 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SQ 216 GLN SR 218 GLN SR 274 ASN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 133228 Z= 0.279 Angle : 0.533 15.105 191455 Z= 0.275 Chirality : 0.037 0.260 23236 Planarity : 0.004 0.053 15438 Dihedral : 21.607 178.552 48568 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.26 % Allowed : 10.83 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.43 (0.09), residues: 9279 helix: 2.14 (0.08), residues: 3950 sheet: 0.32 (0.14), residues: 1230 loop : 0.04 (0.09), residues: 4099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPNH 98 HIS 0.011 0.001 HISSJ 726 PHE 0.033 0.002 PHESY 579 TYR 0.026 0.002 TYRSN 109 ARG 0.011 0.000 ARGLS 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 742 time to evaluate : 7.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 57 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6623 (ttp80) REVERT: BA 124 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: L7 149 TYR cc_start: 0.8932 (m-80) cc_final: 0.8684 (m-80) REVERT: L8 118 MET cc_start: 0.9011 (tpt) cc_final: 0.8808 (tpt) REVERT: L9 161 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7357 (mmm) REVERT: LA 23 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7222 (mtt-85) REVERT: LA 148 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7715 (pmm) REVERT: LN 19 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7179 (mtp180) REVERT: LN 162 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8346 (p) REVERT: LN 174 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7019 (mmt90) REVERT: LN 332 MET cc_start: 0.8218 (ttm) cc_final: 0.7869 (ttp) REVERT: LN 389 MET cc_start: 0.8501 (mmm) cc_final: 0.8129 (mmm) REVERT: NF 250 ASN cc_start: 0.8204 (m-40) cc_final: 0.7998 (m-40) REVERT: NH 25 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6446 (tm-30) REVERT: NH 29 ASP cc_start: 0.5817 (p0) cc_final: 0.5583 (p0) REVERT: NI 424 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.7220 (t-170) REVERT: NK 100 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7055 (ptm160) REVERT: NK 105 LEU cc_start: 0.8353 (mp) cc_final: 0.8089 (mt) REVERT: SA 348 LYS cc_start: 0.8387 (ttmm) cc_final: 0.8148 (ttpt) REVERT: SG 1 MET cc_start: 0.8336 (ttp) cc_final: 0.8044 (ttm) REVERT: SI 92 ASP cc_start: 0.6862 (m-30) cc_final: 0.6630 (m-30) REVERT: SJ 674 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8688 (mt) REVERT: SK 8 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6820 (mm-30) REVERT: SQ 88 ASN cc_start: 0.7967 (t0) cc_final: 0.7568 (t0) REVERT: SQ 217 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: SR 176 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7361 (t80) REVERT: SS 189 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6936 (mtp) REVERT: SS 199 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6418 (tm-30) REVERT: SW 220 LEU cc_start: 0.6700 (tm) cc_final: 0.6445 (tp) REVERT: SW 265 MET cc_start: 0.6295 (tpt) cc_final: 0.5669 (ttt) REVERT: SY 227 MET cc_start: 0.2381 (mtt) cc_final: 0.0922 (mmp) outliers start: 172 outliers final: 88 residues processed: 839 average time/residue: 1.9596 time to fit residues: 2315.1602 Evaluate side-chains 820 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 716 time to evaluate : 7.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 57 ARG Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 62 LEU Chi-restraints excluded: chain BA residue 85 LEU Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 106 SER Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 132 LYS Chi-restraints excluded: chain L8 residue 136 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 146 ILE Chi-restraints excluded: chain LA residue 148 MET Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LH residue 34 SER Chi-restraints excluded: chain LI residue 93 THR Chi-restraints excluded: chain LL residue 49 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 300 LYS Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 89 LEU Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 37 THR Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NF residue 66 LYS Chi-restraints excluded: chain NF residue 197 LEU Chi-restraints excluded: chain NH residue 25 GLN Chi-restraints excluded: chain NI residue 424 HIS Chi-restraints excluded: chain NK residue 19 LYS Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 95 ILE Chi-restraints excluded: chain NK residue 100 ARG Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 205 ASN Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 33 LEU Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SD residue 134 ARG Chi-restraints excluded: chain SE residue 179 VAL Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 85 THR Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 190 LEU Chi-restraints excluded: chain SI residue 153 ASN Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 127 GLU Chi-restraints excluded: chain SK residue 172 GLU Chi-restraints excluded: chain SL residue 30 GLN Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 193 GLU Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SN residue 128 VAL Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SN residue 199 ILE Chi-restraints excluded: chain SQ residue 27 ILE Chi-restraints excluded: chain SQ residue 217 GLN Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 176 TYR Chi-restraints excluded: chain SR residue 179 VAL Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SR residue 329 ILE Chi-restraints excluded: chain SS residue 189 MET Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 199 GLU Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 229 THR Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SW residue 191 LEU Chi-restraints excluded: chain SW residue 225 THR Chi-restraints excluded: chain SW residue 231 LEU Chi-restraints excluded: chain SW residue 339 LEU Chi-restraints excluded: chain SY residue 539 LEU Chi-restraints excluded: chain SY residue 540 VAL Chi-restraints excluded: chain SY residue 545 ASP Chi-restraints excluded: chain SZ residue 165 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1161 random chunks: chunk 1083 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 640 optimal weight: 50.0000 chunk 820 optimal weight: 6.9990 chunk 635 optimal weight: 10.0000 chunk 945 optimal weight: 5.9990 chunk 627 optimal weight: 5.9990 chunk 1119 optimal weight: 4.9990 chunk 700 optimal weight: 10.0000 chunk 682 optimal weight: 0.5980 chunk 516 optimal weight: 3.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 173 GLN LA 34 GLN LB 45 GLN LB 93 GLN ** LC 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 127 GLN LE 144 ASN LI 91 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NF 255 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 92 GLN SA 119 GLN SJ 707 GLN SJ 726 HIS ** SK 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 197 ASN ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SQ 216 GLN SR 274 ASN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 277 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 133228 Z= 0.380 Angle : 0.589 18.039 191455 Z= 0.302 Chirality : 0.040 0.281 23236 Planarity : 0.005 0.068 15438 Dihedral : 21.622 178.352 48568 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.29 % Allowed : 11.63 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.22 (0.08), residues: 9279 helix: 1.94 (0.08), residues: 3958 sheet: 0.19 (0.14), residues: 1235 loop : -0.05 (0.09), residues: 4086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPLT 6 HIS 0.010 0.001 HISSJ 726 PHE 0.045 0.002 PHESY 579 TYR 0.027 0.002 TYRSN 109 ARG 0.012 0.001 ARGNH 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 736 time to evaluate : 7.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 57 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6634 (ttp80) REVERT: BA 124 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: L8 118 MET cc_start: 0.9001 (tpt) cc_final: 0.8738 (tpt) REVERT: LA 23 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7156 (mtt-85) REVERT: LA 148 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7912 (pmm) REVERT: LN 19 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7279 (mtp180) REVERT: LN 162 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8371 (p) REVERT: LN 174 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7084 (mmt90) REVERT: LN 389 MET cc_start: 0.8537 (mmm) cc_final: 0.8267 (mtm) REVERT: LS 97 LYS cc_start: 0.7192 (mptm) cc_final: 0.6952 (mptm) REVERT: LW 14 LYS cc_start: 0.7756 (mmtt) cc_final: 0.7319 (mmmt) REVERT: NH 129 GLN cc_start: 0.6646 (tp-100) cc_final: 0.6229 (tp-100) REVERT: NI 424 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.7291 (t-170) REVERT: NK 100 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7130 (ptm160) REVERT: SA 348 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8187 (ttpt) REVERT: SG 1 MET cc_start: 0.8310 (ttp) cc_final: 0.8031 (ttm) REVERT: SJ 670 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8471 (mt) REVERT: SJ 674 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8720 (mt) REVERT: SK 8 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6892 (mm-30) REVERT: SQ 88 ASN cc_start: 0.7958 (t0) cc_final: 0.7554 (t0) REVERT: SQ 217 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: SR 176 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7404 (t80) REVERT: SS 189 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6975 (mtp) REVERT: SS 199 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: SW 220 LEU cc_start: 0.6689 (tm) cc_final: 0.6415 (tp) REVERT: SW 265 MET cc_start: 0.6297 (tpt) cc_final: 0.5708 (ttt) REVERT: SY 227 MET cc_start: 0.2272 (mtt) cc_final: 0.0888 (mmp) REVERT: SZ 11 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6801 (tp40) REVERT: SZ 175 MET cc_start: 0.4840 (mmt) cc_final: 0.4310 (tmm) outliers start: 174 outliers final: 97 residues processed: 835 average time/residue: 1.9497 time to fit residues: 2286.1070 Evaluate side-chains 824 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 711 time to evaluate : 7.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 57 ARG Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 62 LEU Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 106 SER Chi-restraints excluded: chain L7 residue 46 ASN Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 132 LYS Chi-restraints excluded: chain L8 residue 136 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 94 MET Chi-restraints excluded: chain LA residue 146 ILE Chi-restraints excluded: chain LA residue 148 MET Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LH residue 34 SER Chi-restraints excluded: chain LI residue 93 THR Chi-restraints excluded: chain LL residue 49 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 300 LYS Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 89 LEU Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 37 THR Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NF residue 53 GLN Chi-restraints excluded: chain NF residue 66 LYS Chi-restraints excluded: chain NF residue 192 PHE Chi-restraints excluded: chain NF residue 197 LEU Chi-restraints excluded: chain NI residue 424 HIS Chi-restraints excluded: chain NK residue 19 LYS Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 95 ILE Chi-restraints excluded: chain NK residue 100 ARG Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 205 ASN Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SC residue 278 THR Chi-restraints excluded: chain SD residue 33 LEU Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SD residue 134 ARG Chi-restraints excluded: chain SE residue 135 VAL Chi-restraints excluded: chain SE residue 179 VAL Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 85 THR Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 161 MET Chi-restraints excluded: chain SI residue 153 ASN Chi-restraints excluded: chain SJ residue 670 LEU Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 127 GLU Chi-restraints excluded: chain SK residue 172 GLU Chi-restraints excluded: chain SK residue 238 ASP Chi-restraints excluded: chain SL residue 30 GLN Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 193 GLU Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SN residue 100 ASP Chi-restraints excluded: chain SN residue 128 VAL Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SN residue 199 ILE Chi-restraints excluded: chain SQ residue 217 GLN Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 176 TYR Chi-restraints excluded: chain SR residue 179 VAL Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SR residue 329 ILE Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain SS residue 189 MET Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 199 GLU Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 229 THR Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SW residue 191 LEU Chi-restraints excluded: chain SW residue 225 THR Chi-restraints excluded: chain SW residue 231 LEU Chi-restraints excluded: chain SW residue 339 LEU Chi-restraints excluded: chain SY residue 539 LEU Chi-restraints excluded: chain SY residue 540 VAL Chi-restraints excluded: chain SZ residue 11 GLN Chi-restraints excluded: chain SZ residue 165 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1161 random chunks: chunk 692 optimal weight: 6.9990 chunk 446 optimal weight: 0.9990 chunk 668 optimal weight: 0.6980 chunk 337 optimal weight: 4.9990 chunk 219 optimal weight: 30.0000 chunk 216 optimal weight: 10.0000 chunk 711 optimal weight: 3.9990 chunk 762 optimal weight: 2.9990 chunk 553 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 879 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 173 GLN LA 34 GLN ** LA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 45 GLN LB 93 GLN LC 92 ASN ** LC 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 144 ASN LG 36 ASN LI 14 ASN LI 91 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NF 255 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 92 GLN SA 119 GLN ** SI 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 166 GLN ** SI 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 707 GLN SJ 726 HIS ** SK 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SQ 216 GLN SR 100 ASN SR 274 ASN ST 200 GLN SV 115 ASN SW 300 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 133228 Z= 0.160 Angle : 0.487 15.361 191455 Z= 0.252 Chirality : 0.034 0.240 23236 Planarity : 0.004 0.068 15438 Dihedral : 21.602 179.627 48568 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.63 % Allowed : 12.67 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.54 (0.09), residues: 9279 helix: 2.26 (0.08), residues: 3965 sheet: 0.33 (0.14), residues: 1241 loop : 0.07 (0.09), residues: 4073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPL9 120 HIS 0.012 0.001 HISSJ 726 PHE 0.035 0.001 PHEST 254 TYR 0.025 0.001 TYRLK 61 ARG 0.019 0.000 ARGL7 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 728 time to evaluate : 7.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BA 57 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6597 (ttp80) REVERT: BA 124 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: L7 149 TYR cc_start: 0.8892 (m-80) cc_final: 0.8655 (m-80) REVERT: LA 23 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7205 (mtt-85) REVERT: LG 112 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6329 (mtp) REVERT: LN 19 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7178 (mtp180) REVERT: LN 162 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8274 (p) REVERT: LN 389 MET cc_start: 0.8507 (mmm) cc_final: 0.8125 (mmm) REVERT: LS 97 LYS cc_start: 0.7030 (mptm) cc_final: 0.6809 (mptm) REVERT: NF 71 ARG cc_start: 0.7715 (tpm170) cc_final: 0.7477 (tpm170) REVERT: NI 424 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.7207 (t-170) REVERT: NI 479 MET cc_start: 0.6109 (tmt) cc_final: 0.5597 (tmt) REVERT: NK 100 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7271 (ptm160) REVERT: SA 348 LYS cc_start: 0.8398 (ttmm) cc_final: 0.8166 (ttpt) REVERT: SJ 674 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8627 (mt) REVERT: SJ 730 ARG cc_start: 0.6296 (ptp-110) cc_final: 0.5926 (ptp-170) REVERT: SK 8 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6840 (mm-30) REVERT: SQ 88 ASN cc_start: 0.7898 (t0) cc_final: 0.7533 (t0) REVERT: SR 176 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7396 (t80) REVERT: SS 199 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6319 (tm-30) REVERT: SW 220 LEU cc_start: 0.6609 (tm) cc_final: 0.6385 (tp) REVERT: SW 265 MET cc_start: 0.6226 (tpt) cc_final: 0.5624 (ttt) REVERT: SY 227 MET cc_start: 0.2319 (mtt) cc_final: 0.0914 (mmp) outliers start: 124 outliers final: 60 residues processed: 799 average time/residue: 1.9668 time to fit residues: 2203.7354 Evaluate side-chains 771 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 700 time to evaluate : 7.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 57 ARG Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 62 LEU Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 106 SER Chi-restraints excluded: chain L7 residue 46 ASN Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 132 LYS Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 148 MET Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LH residue 34 SER Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 300 LYS Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 89 LEU Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 37 THR Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain NF residue 66 LYS Chi-restraints excluded: chain NF residue 197 LEU Chi-restraints excluded: chain NH residue 124 ASN Chi-restraints excluded: chain NI residue 424 HIS Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 100 ARG Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SD residue 134 ARG Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SJ residue 668 LEU Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SN residue 128 VAL Chi-restraints excluded: chain SO residue 326 LYS Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 176 TYR Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 199 GLU Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain ST residue 229 THR Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SW residue 191 LEU Chi-restraints excluded: chain SW residue 225 THR Chi-restraints excluded: chain SY residue 540 VAL Chi-restraints excluded: chain SY residue 552 THR Chi-restraints excluded: chain SZ residue 165 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1161 random chunks: chunk 1017 optimal weight: 3.9990 chunk 1072 optimal weight: 30.0000 chunk 978 optimal weight: 3.9990 chunk 1042 optimal weight: 50.0000 chunk 1071 optimal weight: 10.0000 chunk 627 optimal weight: 2.9990 chunk 454 optimal weight: 0.9980 chunk 818 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 942 optimal weight: 0.0670 chunk 986 optimal weight: 3.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 173 GLN LA 34 GLN LB 45 GLN LB 93 GLN LC 50 GLN ** LC 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 144 ASN LG 36 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NF 255 ASN NH 124 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 92 GLN SA 119 GLN SJ 726 HIS ** SK 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SQ 216 GLN SR 274 ASN SR 289 ASN SW 277 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 133228 Z= 0.229 Angle : 0.508 18.449 191455 Z= 0.261 Chirality : 0.035 0.241 23236 Planarity : 0.004 0.073 15438 Dihedral : 21.554 179.706 48568 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.42 % Allowed : 13.38 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.51 (0.09), residues: 9279 helix: 2.24 (0.08), residues: 3957 sheet: 0.31 (0.14), residues: 1245 loop : 0.05 (0.09), residues: 4077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLT 6 HIS 0.012 0.001 HISSJ 726 PHE 0.038 0.001 PHEST 254 TYR 0.027 0.001 TYRSN 109 ARG 0.017 0.000 ARGL7 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 711 time to evaluate : 7.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BA 57 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6586 (ttp80) REVERT: BA 124 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: L7 149 TYR cc_start: 0.8906 (m-80) cc_final: 0.8666 (m-80) REVERT: LA 23 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7174 (mtt-85) REVERT: LA 148 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8019 (pmm) REVERT: LN 19 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7193 (mtp180) REVERT: LN 162 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8289 (p) REVERT: LN 332 MET cc_start: 0.8135 (ttm) cc_final: 0.7879 (ttp) REVERT: LN 389 MET cc_start: 0.8513 (mmm) cc_final: 0.8118 (mmm) REVERT: LS 97 LYS cc_start: 0.7079 (mptm) cc_final: 0.6868 (mptm) REVERT: NF 71 ARG cc_start: 0.7742 (tpm170) cc_final: 0.7502 (tpm170) REVERT: NI 479 MET cc_start: 0.6097 (tmt) cc_final: 0.5590 (tmt) REVERT: NK 100 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7466 (ptm160) REVERT: SA 348 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8168 (ttpt) REVERT: SJ 670 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8435 (mt) REVERT: SJ 674 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8660 (mt) REVERT: SJ 730 ARG cc_start: 0.6260 (ptp-110) cc_final: 0.5913 (ptp-170) REVERT: SK 8 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6855 (mm-30) REVERT: SQ 88 ASN cc_start: 0.7936 (t0) cc_final: 0.7665 (t160) REVERT: SR 176 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7465 (t80) REVERT: SS 199 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6411 (tm-30) REVERT: SW 220 LEU cc_start: 0.6614 (tm) cc_final: 0.6386 (tp) REVERT: SW 265 MET cc_start: 0.6256 (tpt) cc_final: 0.5648 (ttt) REVERT: SY 227 MET cc_start: 0.2339 (mtt) cc_final: 0.0930 (mmp) outliers start: 108 outliers final: 71 residues processed: 778 average time/residue: 1.9967 time to fit residues: 2179.1666 Evaluate side-chains 784 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 702 time to evaluate : 7.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 57 ARG Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 62 LEU Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 106 SER Chi-restraints excluded: chain L7 residue 46 ASN Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 132 LYS Chi-restraints excluded: chain L8 residue 136 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 146 ILE Chi-restraints excluded: chain LA residue 148 MET Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 34 SER Chi-restraints excluded: chain LL residue 49 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 300 LYS Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 89 LEU Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 37 THR Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain NF residue 66 LYS Chi-restraints excluded: chain NF residue 197 LEU Chi-restraints excluded: chain NH residue 124 ASN Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 100 ARG Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SD residue 134 ARG Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SJ residue 668 LEU Chi-restraints excluded: chain SJ residue 670 LEU Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 193 GLU Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SN residue 128 VAL Chi-restraints excluded: chain SN residue 199 ILE Chi-restraints excluded: chain SO residue 326 LYS Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 176 TYR Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 199 GLU Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 229 THR Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SW residue 191 LEU Chi-restraints excluded: chain SW residue 225 THR Chi-restraints excluded: chain SY residue 247 VAL Chi-restraints excluded: chain SY residue 540 VAL Chi-restraints excluded: chain SY residue 552 THR Chi-restraints excluded: chain SZ residue 165 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1161 random chunks: chunk 1039 optimal weight: 7.9990 chunk 684 optimal weight: 2.9990 chunk 1102 optimal weight: 5.9990 chunk 673 optimal weight: 0.5980 chunk 523 optimal weight: 2.9990 chunk 766 optimal weight: 4.9990 chunk 1156 optimal weight: 6.9990 chunk 1064 optimal weight: 30.0000 chunk 921 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 711 optimal weight: 0.0770 overall best weight: 2.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 173 GLN LA 34 GLN LB 45 GLN LB 93 GLN ** LC 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 144 ASN LI 91 ASN NF 255 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 92 GLN SA 119 GLN SJ 726 HIS ** SK 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 216 GLN SR 274 ASN SR 289 ASN SW 511 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 133228 Z= 0.222 Angle : 0.506 15.492 191455 Z= 0.260 Chirality : 0.035 0.238 23236 Planarity : 0.004 0.084 15438 Dihedral : 21.549 179.898 48568 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.46 % Allowed : 13.39 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.09), residues: 9279 helix: 2.23 (0.08), residues: 3974 sheet: 0.33 (0.14), residues: 1248 loop : 0.05 (0.09), residues: 4057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLT 6 HIS 0.012 0.001 HISSJ 726 PHE 0.035 0.001 PHEST 254 TYR 0.027 0.001 TYRSN 109 ARG 0.020 0.000 ARGL7 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18558 Ramachandran restraints generated. 9279 Oldfield, 0 Emsley, 9279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 710 time to evaluate : 7.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BA 57 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6586 (ttp80) REVERT: BA 124 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: L7 149 TYR cc_start: 0.8896 (m-80) cc_final: 0.8663 (m-80) REVERT: LA 23 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7168 (mtt-85) REVERT: LA 148 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7942 (pmm) REVERT: LN 19 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7196 (mtp180) REVERT: LN 162 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8289 (p) REVERT: LN 332 MET cc_start: 0.8153 (ttm) cc_final: 0.7903 (ttp) REVERT: LN 389 MET cc_start: 0.8517 (mmm) cc_final: 0.8117 (mmm) REVERT: LS 97 LYS cc_start: 0.7067 (mptm) cc_final: 0.6853 (mptm) REVERT: NF 71 ARG cc_start: 0.7735 (tpm170) cc_final: 0.7492 (tpm170) REVERT: NI 479 MET cc_start: 0.6036 (tmt) cc_final: 0.5560 (tmt) REVERT: NK 100 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7451 (ptm160) REVERT: SJ 670 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8440 (mt) REVERT: SJ 674 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8666 (mt) REVERT: SJ 730 ARG cc_start: 0.6222 (ptp-110) cc_final: 0.5875 (ptp-170) REVERT: SK 8 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6856 (mm-30) REVERT: SQ 88 ASN cc_start: 0.7946 (t0) cc_final: 0.7568 (t160) REVERT: SQ 91 GLN cc_start: 0.8012 (mp10) cc_final: 0.7741 (mp10) REVERT: SR 176 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7493 (t80) REVERT: SS 199 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6372 (tm-30) REVERT: SW 265 MET cc_start: 0.6299 (tpt) cc_final: 0.5647 (ttt) REVERT: SY 227 MET cc_start: 0.2061 (mtt) cc_final: 0.0971 (mmp) REVERT: SZ 11 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.6760 (tp40) outliers start: 111 outliers final: 72 residues processed: 779 average time/residue: 1.9262 time to fit residues: 2112.5647 Evaluate side-chains 785 residues out of total 8269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 701 time to evaluate : 6.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 57 ARG Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 62 LEU Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 106 SER Chi-restraints excluded: chain L7 residue 46 ASN Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 175 MET Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 132 LYS Chi-restraints excluded: chain L8 residue 136 LEU Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 146 ILE Chi-restraints excluded: chain LA residue 148 MET Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LH residue 34 SER Chi-restraints excluded: chain LL residue 49 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 300 LYS Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LQ residue 89 LEU Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LS residue 37 THR Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain NF residue 66 LYS Chi-restraints excluded: chain NF residue 197 LEU Chi-restraints excluded: chain NH residue 124 ASN Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 100 ARG Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 102 SER Chi-restraints excluded: chain SD residue 134 ARG Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SJ residue 668 LEU Chi-restraints excluded: chain SJ residue 670 LEU Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 193 GLU Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SN residue 128 VAL Chi-restraints excluded: chain SN residue 199 ILE Chi-restraints excluded: chain SO residue 326 LYS Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 176 TYR Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 199 GLU Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 229 THR Chi-restraints excluded: chain ST residue 232 VAL Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SW residue 191 LEU Chi-restraints excluded: chain SW residue 225 THR Chi-restraints excluded: chain SY residue 247 VAL Chi-restraints excluded: chain SY residue 540 VAL Chi-restraints excluded: chain SY residue 552 THR Chi-restraints excluded: chain SZ residue 11 GLN Chi-restraints excluded: chain SZ residue 165 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1161 random chunks: chunk 564 optimal weight: 9.9990 chunk 731 optimal weight: 0.7980 chunk 981 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 849 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 922 optimal weight: 5.9990 chunk 386 optimal weight: 50.0000 chunk 947 optimal weight: 0.4980 chunk 116 optimal weight: 10.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 173 GLN LA 97 ASN LB 45 GLN LB 93 GLN LC 50 GLN ** LC 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 144 ASN LI 91 ASN NF 255 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 92 GLN SA 119 GLN SJ 707 GLN SJ 726 HIS ** SK 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 51 ASN ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 216 GLN SR 274 ASN SR 289 ASN SW 277 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.094341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.066687 restraints weight = 334358.113| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.55 r_work: 0.3002 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 133228 Z= 0.215 Angle : 0.503 17.606 191455 Z= 0.258 Chirality : 0.035 0.235 23236 Planarity : 0.004 0.060 15438 Dihedral : 21.535 179.898 48568 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.30 % Allowed : 13.59 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.54 (0.09), residues: 9279 helix: 2.27 (0.08), residues: 3966 sheet: 0.33 (0.14), residues: 1229 loop : 0.06 (0.09), residues: 4084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLT 6 HIS 0.013 0.001 HISSJ 726 PHE 0.050 0.001 PHESY 579 TYR 0.026 0.001 TYRSN 109 ARG 0.021 0.000 ARGSD 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37118.03 seconds wall clock time: 645 minutes 49.83 seconds (38749.83 seconds total)