Starting phenix.real_space_refine on Mon Mar 18 14:48:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkx_29260/03_2024/8fkx_29260_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkx_29260/03_2024/8fkx_29260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkx_29260/03_2024/8fkx_29260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkx_29260/03_2024/8fkx_29260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkx_29260/03_2024/8fkx_29260_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkx_29260/03_2024/8fkx_29260_neut_updated.pdb" } resolution = 2.59 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= 0.045 sd= 0.178 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 2477 5.49 5 Mg 61 5.21 5 S 354 5.16 5 C 77864 2.51 5 N 25659 2.21 5 O 32225 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 ASP 107": "OD1" <-> "OD2" Residue "BA GLU 131": "OE1" <-> "OE2" Residue "BA ASP 144": "OD1" <-> "OD2" Residue "BA ASP 153": "OD1" <-> "OD2" Residue "L6 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L6 GLU 79": "OE1" <-> "OE2" Residue "L6 GLU 108": "OE1" <-> "OE2" Residue "L6 GLU 119": "OE1" <-> "OE2" Residue "L7 ASP 106": "OD1" <-> "OD2" Residue "L7 GLU 144": "OE1" <-> "OE2" Residue "L7 TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 GLU 194": "OE1" <-> "OE2" Residue "L8 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ASP 39": "OD1" <-> "OD2" Residue "L8 ASP 59": "OD1" <-> "OD2" Residue "L8 GLU 96": "OE1" <-> "OE2" Residue "L8 ASP 106": "OD1" <-> "OD2" Residue "L8 GLU 126": "OE1" <-> "OE2" Residue "L9 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 ASP 17": "OD1" <-> "OD2" Residue "L9 PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 ASP 147": "OD1" <-> "OD2" Residue "LB ASP 4": "OD1" <-> "OD2" Residue "LB GLU 94": "OE1" <-> "OE2" Residue "LB ASP 124": "OD1" <-> "OD2" Residue "LC TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 85": "OD1" <-> "OD2" Residue "LC ASP 99": "OD1" <-> "OD2" Residue "LC PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE GLU 94": "OE1" <-> "OE2" Residue "LE ASP 103": "OD1" <-> "OD2" Residue "LE GLU 111": "OE1" <-> "OE2" Residue "LE GLU 147": "OE1" <-> "OE2" Residue "LE PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 99": "OE1" <-> "OE2" Residue "LH ASP 72": "OD1" <-> "OD2" Residue "LH TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI ASP 10": "OD1" <-> "OD2" Residue "LI GLU 54": "OE1" <-> "OE2" Residue "LI GLU 83": "OE1" <-> "OE2" Residue "LI GLU 120": "OE1" <-> "OE2" Residue "LK PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 140": "OE1" <-> "OE2" Residue "LN GLU 199": "OE1" <-> "OE2" Residue "LN TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 383": "OE1" <-> "OE2" Residue "LQ GLU 86": "OE1" <-> "OE2" Residue "LS ASP 22": "OD1" <-> "OD2" Residue "LS ASP 23": "OD1" <-> "OD2" Residue "LS GLU 27": "OE1" <-> "OE2" Residue "LS GLU 67": "OE1" <-> "OE2" Residue "LS TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT ASP 37": "OD1" <-> "OD2" Residue "LU GLU 46": "OE1" <-> "OE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 54": "OE1" <-> "OE2" Residue "LU ASP 66": "OD1" <-> "OD2" Residue "LW TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA GLU 426": "OE1" <-> "OE2" Residue "NA PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NB GLU 58": "OE1" <-> "OE2" Residue "NB GLU 63": "OE1" <-> "OE2" Residue "NB GLU 65": "OE1" <-> "OE2" Residue "NF TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF GLU 112": "OE1" <-> "OE2" Residue "NF ASP 158": "OD1" <-> "OD2" Residue "NF TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF GLU 249": "OE1" <-> "OE2" Residue "NH ASP 29": "OD1" <-> "OD2" Residue "NH ASP 87": "OD1" <-> "OD2" Residue "NH ASP 138": "OD1" <-> "OD2" Residue "NI PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NI TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 149": "OE1" <-> "OE2" Residue "SA ASP 288": "OD1" <-> "OD2" Residue "SC GLU 119": "OE1" <-> "OE2" Residue "SC PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC ASP 214": "OD1" <-> "OD2" Residue "SC GLU 244": "OE1" <-> "OE2" Residue "SD TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 188": "OE1" <-> "OE2" Residue "SD PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 203": "OE1" <-> "OE2" Residue "SD GLU 229": "OE1" <-> "OE2" Residue "SE GLU 105": "OE1" <-> "OE2" Residue "SE GLU 109": "OE1" <-> "OE2" Residue "SE ASP 211": "OD1" <-> "OD2" Residue "SE ASP 228": "OD1" <-> "OD2" Residue "SE TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG ASP 11": "OD1" <-> "OD2" Residue "SG ASP 37": "OD1" <-> "OD2" Residue "SH GLU 94": "OE1" <-> "OE2" Residue "SH ASP 97": "OD1" <-> "OD2" Residue "SH TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH GLU 124": "OE1" <-> "OE2" Residue "SH ASP 133": "OD1" <-> "OD2" Residue "SH GLU 163": "OE1" <-> "OE2" Residue "SI TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI ASP 178": "OD1" <-> "OD2" Residue "SI ASP 196": "OD1" <-> "OD2" Residue "SI GLU 210": "OE1" <-> "OE2" Residue "SI PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ GLU 547": "OE1" <-> "OE2" Residue "SJ TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ ASP 697": "OD1" <-> "OD2" Residue "SJ GLU 703": "OE1" <-> "OE2" Residue "SJ GLU 708": "OE1" <-> "OE2" Residue "SJ GLU 777": "OE1" <-> "OE2" Residue "SJ PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ ASP 825": "OD1" <-> "OD2" Residue "SJ ASP 831": "OD1" <-> "OD2" Residue "SK ASP 90": "OD1" <-> "OD2" Residue "SK GLU 168": "OE1" <-> "OE2" Residue "SL ASP 32": "OD1" <-> "OD2" Residue "SL GLU 34": "OE1" <-> "OE2" Residue "SL TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL ASP 91": "OD1" <-> "OD2" Residue "SL ASP 94": "OD1" <-> "OD2" Residue "SL PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM ASP 69": "OD1" <-> "OD2" Residue "SM PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM GLU 100": "OE1" <-> "OE2" Residue "SM TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM ASP 268": "OD1" <-> "OD2" Residue "SM GLU 270": "OE1" <-> "OE2" Residue "SM PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO GLU 183": "OE1" <-> "OE2" Residue "SO ASP 212": "OD1" <-> "OD2" Residue "SO GLU 224": "OE1" <-> "OE2" Residue "SO GLU 324": "OE1" <-> "OE2" Residue "SQ ASP 7": "OD1" <-> "OD2" Residue "SQ GLU 21": "OE1" <-> "OE2" Residue "SQ GLU 29": "OE1" <-> "OE2" Residue "SQ GLU 110": "OE1" <-> "OE2" Residue "SQ TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 138": "OD1" <-> "OD2" Residue "SQ GLU 178": "OE1" <-> "OE2" Residue "SQ ASP 180": "OD1" <-> "OD2" Residue "SQ TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 121": "OD1" <-> "OD2" Residue "SR TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 256": "OD1" <-> "OD2" Residue "SR PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS GLU 324": "OE1" <-> "OE2" Residue "ST PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU GLU 482": "OE1" <-> "OE2" Residue "SU PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 4": "OE1" <-> "OE2" Residue "SV GLU 62": "OE1" <-> "OE2" Residue "SV GLU 84": "OE1" <-> "OE2" Residue "SV GLU 117": "OE1" <-> "OE2" Residue "SW GLU 262": "OE1" <-> "OE2" Residue "SW GLU 334": "OE1" <-> "OE2" Residue "SW PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 493": "OE1" <-> "OE2" Residue "SW PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY ASP 252": "OD1" <-> "OD2" Residue "SY TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY ASP 480": "OD1" <-> "OD2" Residue "SY PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ ASP 61": "OD1" <-> "OD2" Residue "SZ GLU 105": "OE1" <-> "OE2" Residue "SZ TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ ASP 129": "OD1" <-> "OD2" Residue "SZ TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138643 Number of models: 1 Model: "" Number of chains: 67 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': 14, 'rna3p_pur': 60, 'rna3p_pyr': 63} Link IDs: {'rna2p': 28, 'rna3p': 123} 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: 48236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2250, 48236 Classifications: {'RNA': 2250} Modifications used: {'rna2p_pur': 213, 'rna2p_pyr': 130, 'rna3p_pur': 1020, 'rna3p_pyr': 887} Link IDs: {'rna2p': 343, 'rna3p': 1906} Chain breaks: 43 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: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1650 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 191} 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: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 926 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain breaks: 2 Chain: "LG" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "LH" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1071 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain breaks: 1 Chain: "LI" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LK" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 642 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "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: "LP" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 526 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 197 Chain: "LQ" Number of atoms: 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: "NA" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3389 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 22, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 529 Unresolved non-hydrogen angles: 673 Unresolved non-hydrogen dihedrals: 439 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 9, 'GLU:plan': 7, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 251 Chain: "NB" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 603 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain breaks: 1 Chain: "NF" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1696 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 200} 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: 4832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4832 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 29, 'TRANS': 582} Chain breaks: 5 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: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1721 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 200} 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: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1498 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 175} Chain: "SG" Number of atoms: 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: 1850 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1839 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 223, 1839 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 bond proxies already assigned to first conformer: 1861 Chain: "SJ" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1803 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} 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: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3646 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 420} Chain breaks: 4 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: 4073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 4073 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 19, 'TRANS': 473} Chain breaks: 1 Chain: "SS" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2150 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 26, 'TRANS': 232} Chain: "ST" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1091 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 139} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "SU" Number of atoms: 4360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4360 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 530} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "SV" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1171 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "SW" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3549 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 19, 'TRANS': 424} Chain breaks: 1 Chain: "SY" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2985 Classifications: {'peptide': 378} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 357} Chain: "SZ" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1338 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain breaks: 1 Chain: "L1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L3" Number of atoms: 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: "LB" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "SO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SR" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' K': 1, ' MG': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "SU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 77266 SG CYSLW 19 88.674 126.011 150.036 1.00 29.59 S ATOM 77294 SG CYSLW 22 89.341 123.349 152.732 1.00 26.88 S ATOM 77385 SG CYSLW 34 91.365 126.519 152.662 1.00 25.07 S ATOM 77404 SG CYSLW 37 91.873 124.013 149.912 1.00 26.32 S ATOM A0MSC SG CYSSV 6 57.127 182.558 235.131 1.00 24.88 S ATOM A0MT5 SG CYSSV 9 53.565 181.371 234.815 1.00 23.43 S ATOM A0MY9 SG CYSSV 32 56.329 178.855 235.534 1.00 22.69 S ATOM A0MZ3 SG CYSSV 36 56.075 180.410 232.124 1.00 24.43 S Time building chain proxies: 55.88, per 1000 atoms: 0.40 Number of scatterers: 138643 At special positions: 0 Unit cell: (237.984, 298.016, 334.464, 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 354 16.00 P 2477 15.00 Mg 61 11.99 O 32225 8.00 N 25659 7.00 C 77864 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: 48.52 Conformation dependent library (CDL) restraints added in 13.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 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 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20430 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: 420 helices and 86 sheets defined 53.1% alpha, 11.6% beta 806 base pairs and 1255 stacking pairs defined. Time for finding SS restraints: 79.74 Creating SS restraints... Processing helix chain 'BA' and resid 26 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: 3.625A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 5.026A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.539A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 Processing helix chain 'BB' and resid 6 through 25 Processing helix chain 'BB' and resid 70 through 81 Processing helix chain 'BB' and resid 86 through 97 removed outlier: 4.392A pdb=" N LYSBB 95 " --> pdb=" O LYSBB 91 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASNBB 96 " --> pdb=" O LYSBB 92 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYSBB 97 " --> pdb=" O LEUBB 93 " (cutoff:3.500A) Processing helix chain 'BB' and resid 98 through 108 removed outlier: 4.982A pdb=" N ASPBB 108 " --> pdb=" O ALABB 104 " (cutoff:3.500A) Processing helix chain 'BB' and resid 113 through 124 removed outlier: 4.325A pdb=" N LYSBB 118 " --> pdb=" O GLUBB 114 " (cutoff:3.500A) removed outlier: 4.981A 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: 3.543A 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: 5.272A pdb=" N LYSBB 195 " --> pdb=" O VALBB 191 " (cutoff:3.500A) Processing helix chain 'BB' and resid 197 through 202 removed outlier: 3.905A pdb=" N VALBB 201 " --> pdb=" O ASNBB 197 " (cutoff:3.500A) removed outlier: 5.413A 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: 4.740A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 4.127A 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: 4.099A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.745A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.552A pdb=" N GLYL7 30 " --> pdb=" O GLNL7 26 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 60 removed outlier: 3.746A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (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: 3.571A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.950A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.422A 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: 3.513A pdb=" N GLUL7 186 " --> pdb=" O GLUL7 182 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.939A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLNL8 56 " --> pdb=" O PHEL8 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'L8' and resid 51 through 56' Processing helix chain 'L8' and resid 69 through 81 removed outlier: 3.506A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.620A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.879A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 Processing helix chain 'L9' and resid 2 through 14 removed outlier: 4.008A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 4.840A 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: 3.845A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.814A 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: 6.270A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.849A 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: 3.531A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 4.066A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 4.129A 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 10 through 15 removed outlier: 3.529A pdb=" N SERLA 14 " --> pdb=" O ASNLA 10 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N CYSLA 15 " --> pdb=" O PROLA 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 10 through 15' Processing helix chain 'LA' and resid 25 through 37 removed outlier: 3.584A pdb=" N ALALA 35 " --> pdb=" O GLULA 31 " (cutoff:3.500A) Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 70 through 77 removed outlier: 4.229A pdb=" N LYSLA 74 " --> pdb=" O CYSLA 70 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLNLA 75 " --> pdb=" O ALALA 71 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLYLA 77 " --> pdb=" O ALALA 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 70 through 77' Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.189A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 Processing helix chain 'LB' and resid 106 through 117 Processing helix chain 'LB' and resid 122 through 130 Processing helix chain 'LB' and resid 146 through 152 removed outlier: 4.370A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.513A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.354A 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: 4.580A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 4.946A 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: 3.698A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.406A 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: 3.561A pdb=" N SERLE 104 " --> pdb=" O LYSLE 100 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) Processing helix chain 'LG' and resid 122 through 130 Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 136 removed outlier: 3.537A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.524A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 93 Processing helix chain 'LH' and resid 105 through 118 Processing helix chain 'LH' and resid 145 through 154 Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 4.157A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.237A 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: 4.046A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VALLI 105 " --> pdb=" O PROLI 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 100 through 105' Processing helix chain 'LI' and resid 112 through 134 Processing helix chain 'LK' and resid 6 through 12 removed outlier: 3.919A pdb=" N LYSLK 10 " --> pdb=" O ARGLK 6 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARGLK 12 " --> pdb=" O THRLK 8 " (cutoff:3.500A) Processing helix chain 'LK' and resid 60 through 67 removed outlier: 5.495A pdb=" N GLNLK 67 " --> pdb=" O LEULK 63 " (cutoff:3.500A) Processing helix chain 'LK' and resid 74 through 83 removed outlier: 3.633A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 94 removed outlier: 4.753A pdb=" N LYSLK 94 " --> pdb=" O ALALK 90 " (cutoff:3.500A) Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.521A 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: 5.309A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.635A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 3.911A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LN' and resid 111 through 120 removed outlier: 3.987A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 4.274A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 157 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 3.986A 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: 3.610A pdb=" N GLULN 199 " --> pdb=" O ASPLN 195 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARGLN 200 " --> pdb=" O TRPLN 196 " (cutoff:3.500A) Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.826A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 3.801A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) Processing helix chain 'LN' and resid 381 through 390 Processing helix chain 'LN' and resid 392 through 403 Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.744A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) Processing helix chain 'LP' and resid 37 through 57 removed outlier: 4.972A pdb=" N ALALP 42 " --> pdb=" O PHELP 38 " (cutoff:3.500A) Proline residue: LP 43 - end of helix removed outlier: 3.536A pdb=" N LYSLP 47 " --> pdb=" O PROLP 43 " (cutoff:3.500A) Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.539A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 4.925A 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: 3.569A pdb=" N LEULQ 85 " --> pdb=" O ASNLQ 81 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLULQ 86 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.564A 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: 5.181A 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: 3.637A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.761A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 removed outlier: 3.964A pdb=" N GLYLS 38 " --> pdb=" O ALALS 34 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.502A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VALLS 49 " --> pdb=" O SERLS 45 " (cutoff:3.500A) Processing helix chain 'LS' and resid 80 through 85 Proline residue: LS 85 - end of helix Processing helix chain 'LS' and resid 88 through 95 removed outlier: 5.470A pdb=" N LEULS 95 " --> pdb=" O METLS 91 " (cutoff:3.500A) Processing helix chain 'LS' and resid 96 through 102 Processing helix chain 'LS' and resid 104 through 115 Proline residue: LS 115 - end of helix Processing helix chain 'LT' and resid 35 through 40 removed outlier: 3.603A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.398A 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: 4.169A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.293A 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 48 removed outlier: 3.965A pdb=" N GLULU 46 " --> pdb=" O ASPLU 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VALLU 47 " --> pdb=" O METLU 43 " (cutoff:3.500A) Processing helix chain 'LU' and resid 51 through 64 Processing helix chain 'LU' and resid 65 through 78 removed outlier: 3.520A pdb=" N LYSLU 75 " --> pdb=" O LYSLU 71 " (cutoff:3.500A) Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.631A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.051A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) Processing helix chain 'NA' and resid 150 through 164 Processing helix chain 'NA' and resid 166 through 186 removed outlier: 3.898A pdb=" N PHENA 177 " --> pdb=" O VALNA 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALANA 179 " --> pdb=" O GLNNA 175 " (cutoff:3.500A) Processing helix chain 'NA' and resid 187 through 195 removed outlier: 5.261A pdb=" N LYSNA 195 " --> pdb=" O ALANA 191 " (cutoff:3.500A) Processing helix chain 'NA' and resid 200 through 214 removed outlier: 3.524A pdb=" N PHENA 210 " --> pdb=" O ALANA 206 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYSNA 211 " --> pdb=" O LEUNA 207 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILENA 212 " --> pdb=" O VALNA 208 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARGNA 213 " --> pdb=" O THRNA 209 " (cutoff:3.500A) Processing helix chain 'NA' and resid 215 through 224 removed outlier: 3.813A pdb=" N LEUNA 222 " --> pdb=" O CYSNA 218 " (cutoff:3.500A) Processing helix chain 'NA' and resid 242 through 264 removed outlier: 4.283A pdb=" N VALNA 248 " --> pdb=" O GLYNA 244 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASPNA 249 " --> pdb=" O LYSNA 245 " (cutoff:3.500A) Processing helix chain 'NA' and resid 266 through 281 Processing helix chain 'NA' and resid 282 through 288 removed outlier: 3.625A pdb=" N PHENA 287 " --> pdb=" O CYSNA 283 " (cutoff:3.500A) Proline residue: NA 288 - end of helix Processing helix chain 'NA' and resid 289 through 305 removed outlier: 3.602A pdb=" N LYSNA 296 " --> pdb=" O ARGNA 292 " (cutoff:3.500A) Processing helix chain 'NA' and resid 306 through 325 Processing helix chain 'NA' and resid 328 through 345 removed outlier: 4.002A pdb=" N VALNA 332 " --> pdb=" O PHENA 328 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUNA 333 " --> pdb=" O LEUNA 329 " (cutoff:3.500A) Processing helix chain 'NA' and resid 349 through 370 Proline residue: NA 353 - end of helix removed outlier: 3.544A pdb=" N THRNA 363 " --> pdb=" O GLNNA 359 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUNA 369 " --> pdb=" O LEUNA 365 " (cutoff:3.500A) Proline residue: NA 370 - end of helix Processing helix chain 'NA' and resid 371 through 395 Processing helix chain 'NA' and resid 396 through 405 removed outlier: 3.750A pdb=" N TYRNA 400 " --> pdb=" O LYSNA 396 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLNNA 401 " --> pdb=" O LYSNA 397 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SERNA 402 " --> pdb=" O GLUNA 398 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VALNA 403 " --> pdb=" O THRNA 399 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASNNA 405 " --> pdb=" O GLNNA 401 " (cutoff:3.500A) Processing helix chain 'NA' and resid 406 through 421 Processing helix chain 'NA' and resid 422 through 429 removed outlier: 4.010A pdb=" N GLUNA 426 " --> pdb=" O ALANA 422 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALANA 427 " --> pdb=" O GLYNA 423 " (cutoff:3.500A) Processing helix chain 'NA' and resid 430 through 447 Proline residue: NA 434 - end of helix removed outlier: 4.952A pdb=" N ILENA 446 " --> pdb=" O CYSNA 442 " (cutoff:3.500A) Proline residue: NA 447 - end of helix Processing helix chain 'NA' and resid 448 through 469 removed outlier: 4.110A pdb=" N TYRNA 452 " --> pdb=" O THRNA 448 " (cutoff:3.500A) Proline residue: NA 453 - end of helix Processing helix chain 'NA' and resid 474 through 486 removed outlier: 4.774A pdb=" N PHENA 478 " --> pdb=" O PRONA 474 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N METNA 482 " --> pdb=" O PHENA 478 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHENA 483 " --> pdb=" O ILENA 479 " (cutoff:3.500A) Processing helix chain 'NA' and resid 509 through 516 removed outlier: 3.830A pdb=" N GLNNA 514 " --> pdb=" O ASNNA 510 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYSNA 516 " --> pdb=" O ASNNA 512 " (cutoff:3.500A) Processing helix chain 'NA' and resid 517 through 538 Processing helix chain 'NA' and resid 542 through 561 removed outlier: 3.536A pdb=" N LEUNA 548 " --> pdb=" O PRONA 544 " (cutoff:3.500A) Proline residue: NA 549 - end of helix Processing helix chain 'NA' and resid 564 through 592 removed outlier: 3.623A pdb=" N GLNNA 589 " --> pdb=" O CYSNA 585 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SERNA 592 " --> pdb=" O ARGNA 588 " (cutoff:3.500A) Processing helix chain 'NA' and resid 597 through 612 removed outlier: 3.715A pdb=" N VALNA 601 " --> pdb=" O GLUNA 597 " (cutoff:3.500A) Processing helix chain 'NA' and resid 613 through 634 removed outlier: 3.525A pdb=" N LEUNA 632 " --> pdb=" O ARGNA 628 " (cutoff:3.500A) Processing helix chain 'NB' and resid 14 through 36 Processing helix chain 'NB' and resid 56 through 81 Processing helix chain 'NF' and resid 5 through 14 removed outlier: 3.561A pdb=" N LEUNF 9 " --> pdb=" O GLUNF 5 " (cutoff:3.500A) Processing helix chain 'NF' and resid 21 through 34 removed outlier: 4.334A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.677A 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 116 Processing helix chain 'NF' and resid 173 through 178 removed outlier: 3.564A pdb=" N ARGNF 177 " --> pdb=" O PRONF 173 " (cutoff:3.500A) removed outlier: 5.807A 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: 4.234A pdb=" N TYRNH 19 " --> pdb=" O LYSNH 15 " (cutoff:3.500A) Processing helix chain 'NH' and resid 22 through 30 removed outlier: 4.611A pdb=" N LEUNH 26 " --> pdb=" O GLUNH 22 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARGNH 30 " --> pdb=" O LEUNH 26 " (cutoff:3.500A) Processing helix chain 'NH' and resid 48 through 59 removed outlier: 3.559A pdb=" N ALANH 56 " --> pdb=" O METNH 52 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASNNH 57 " --> pdb=" O LYSNH 53 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILENH 58 " --> pdb=" O LEUNH 54 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N SERNH 59 " --> pdb=" O ALANH 55 " (cutoff:3.500A) Processing helix chain 'NH' and resid 82 through 93 removed outlier: 4.478A pdb=" N LEUNH 86 " --> pdb=" O HISNH 82 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASPNH 87 " --> pdb=" O VALNH 83 " (cutoff:3.500A) removed outlier: 5.535A 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: 4.583A pdb=" N GLNNH 105 " --> pdb=" O PRONH 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SERNH 106 " --> pdb=" O GLYNH 102 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLYNH 110 " --> pdb=" O SERNH 106 " (cutoff:3.500A) Processing helix chain 'NH' and resid 114 through 119 removed outlier: 5.473A pdb=" N GLYNH 119 " --> pdb=" O LYSNH 115 " (cutoff:3.500A) Processing helix chain 'NH' and resid 149 through 157 removed outlier: 3.853A pdb=" N ARGNH 154 " --> pdb=" O THRNH 150 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYSNH 155 " --> pdb=" O GLNNH 151 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASPNH 157 " --> pdb=" O CYSNH 153 " (cutoff:3.500A) Processing helix chain 'NH' and resid 169 through 175 removed outlier: 4.630A pdb=" N VALNH 173 " --> pdb=" O ILENH 169 " (cutoff:3.500A) Processing helix chain 'NI' and resid 97 through 102 removed outlier: 3.607A pdb=" N GLYNI 102 " --> pdb=" O PHENI 98 " (cutoff:3.500A) Processing helix chain 'NI' and resid 104 through 115 removed outlier: 3.609A pdb=" N GLYNI 110 " --> pdb=" O PRONI 106 " (cutoff:3.500A) Processing helix chain 'NI' and resid 120 through 133 removed outlier: 3.521A pdb=" N LYSNI 125 " --> pdb=" O PRONI 121 " (cutoff:3.500A) Proline residue: NI 128 - end of helix Processing helix chain 'NI' and resid 145 through 159 removed outlier: 3.846A pdb=" N CYSNI 149 " --> pdb=" O GLYNI 145 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHENI 150 " --> pdb=" O LYSNI 146 " (cutoff:3.500A) Proline residue: NI 153 - end of helix Processing helix chain 'NI' and resid 175 through 190 Processing helix chain 'NI' and resid 205 through 216 removed outlier: 3.945A pdb=" N ASNNI 216 " --> pdb=" O ALANI 212 " (cutoff:3.500A) Processing helix chain 'NI' and resid 223 through 235 removed outlier: 3.507A pdb=" N HISNI 229 " --> pdb=" O GLYNI 225 " (cutoff:3.500A) Processing helix chain 'NI' and resid 248 through 256 removed outlier: 3.523A pdb=" N GLYNI 256 " --> pdb=" O LEUNI 252 " (cutoff:3.500A) Processing helix chain 'NI' and resid 257 through 269 removed outlier: 3.585A pdb=" N GLUNI 263 " --> pdb=" O GLUNI 259 " (cutoff:3.500A) Proline residue: NI 269 - end of helix Processing helix chain 'NI' and resid 282 through 293 Processing helix chain 'NI' and resid 301 through 307 removed outlier: 3.617A pdb=" N THRNI 305 " --> pdb=" O LEUNI 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYSNI 306 " --> pdb=" O ASPNI 302 " (cutoff:3.500A) removed outlier: 5.222A 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: 4.927A pdb=" N ALANI 324 " --> pdb=" O GLUNI 320 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALANI 325 " --> pdb=" O ASPNI 321 " (cutoff:3.500A) Processing helix chain 'NI' and resid 347 through 362 Processing helix chain 'NI' and resid 373 through 387 Processing helix chain 'NI' and resid 395 through 403 removed outlier: 5.077A pdb=" N GLYNI 401 " --> pdb=" O LEUNI 397 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEUNI 402 " --> pdb=" O ALANI 398 " (cutoff:3.500A) removed outlier: 5.376A 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 Proline residue: NI 448 - end of helix Processing helix chain 'NI' and resid 472 through 479 removed outlier: 5.283A pdb=" N GLYNI 478 " --> pdb=" O ALANI 474 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N METNI 479 " --> pdb=" O GLYNI 475 " (cutoff:3.500A) Processing helix chain 'NI' and resid 486 through 503 removed outlier: 4.100A pdb=" N GLYNI 494 " --> pdb=" O GLUNI 490 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SERNI 502 " --> pdb=" O THRNI 498 " (cutoff:3.500A) removed outlier: 4.849A 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: 3.560A pdb=" N LYSNI 532 " --> pdb=" O PRONI 528 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASPNI 538 " --> pdb=" O ALANI 534 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEUNI 539 " --> pdb=" O LYSNI 535 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N VALNI 540 " --> pdb=" O GLUNI 536 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLYNI 541 " --> pdb=" O METNI 537 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLYNI 543 " --> pdb=" O LEUNI 539 " (cutoff:3.500A) Processing helix chain 'NI' and resid 545 through 553 removed outlier: 4.304A pdb=" N ARGNI 551 " --> pdb=" O LEUNI 547 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHENI 552 " --> pdb=" O PHENI 548 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLUNI 553 " --> pdb=" O SERNI 549 " (cutoff:3.500A) Processing helix chain 'NI' and resid 554 through 569 removed outlier: 3.597A pdb=" N ILENI 566 " --> pdb=" O LEUNI 562 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYSNI 567 " --> pdb=" O VALNI 563 " (cutoff:3.500A) Processing helix chain 'NI' and resid 574 through 579 removed outlier: 4.989A pdb=" N ASNNI 579 " --> pdb=" O ILENI 575 " (cutoff:3.500A) Processing helix chain 'NI' and resid 584 through 598 Processing helix chain 'NI' and resid 599 through 618 Proline residue: NI 618 - end of helix Processing helix chain 'NI' and resid 703 through 712 removed outlier: 3.617A pdb=" N GLYNI 710 " --> pdb=" O GLNNI 706 " (cutoff:3.500A) Processing helix chain 'NI' and resid 719 through 739 removed outlier: 4.007A pdb=" N THRNI 724 " --> pdb=" O ALANI 720 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARGNI 725 " --> pdb=" O GLNNI 721 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLYNI 726 " --> pdb=" O ASNNI 722 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARGNI 727 " --> pdb=" O LEUNI 723 " (cutoff:3.500A) removed outlier: 3.956A 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 Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 98 through 112 Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.365A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.766A 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: 3.976A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.794A 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: 3.748A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.307A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.044A 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: 3.757A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.523A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.518A 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: 3.649A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.954A 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: 3.801A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.657A 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: 4.422A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SC' and resid 58 through 67 Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.742A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.461A 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: 3.700A 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: 5.319A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.614A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.637A 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: 3.669A pdb=" N METSD 132 " --> pdb=" O ALASD 128 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VALSD 136 " --> pdb=" O METSD 132 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.055A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.745A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.193A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 238 through 248 removed outlier: 4.832A pdb=" N ARGSD 242 " --> pdb=" O ASPSD 238 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.569A pdb=" N ALASE 68 " --> pdb=" O GLNSE 64 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.408A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.569A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARGSE 103 " --> pdb=" O ALASE 99 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 124 Processing helix chain 'SE' and resid 139 through 150 removed outlier: 3.895A pdb=" N VALSE 143 " --> pdb=" O GLYSE 139 " (cutoff:3.500A) Processing helix chain 'SE' and resid 164 through 178 removed outlier: 4.963A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.811A 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: 3.616A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 231 removed outlier: 4.869A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASPSE 228 " --> pdb=" O THRSE 224 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARGSE 229 " --> pdb=" O ASNSE 225 " (cutoff:3.500A) Processing helix chain 'SE' and resid 232 through 237 removed outlier: 4.024A pdb=" N HISSE 236 " --> pdb=" O GLUSE 232 " (cutoff:3.500A) removed outlier: 5.342A 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: 3.528A pdb=" N ALASG 68 " --> pdb=" O ARGSG 64 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 4.086A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.891A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.787A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.585A 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: 6.032A 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 Processing helix chain 'SI' and resid 34 through 46 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.541A pdb=" N PHESI 64 " --> pdb=" O ARGSI 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VALSI 83 " --> pdb=" O ARGSI 79 " (cutoff:3.500A) Processing helix chain 'SI' and resid 109 through 120 Processing helix chain 'SI' and resid 133 through 144 Processing helix chain 'SI' and resid 153 through 164 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 3.644A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HISSI 185 " --> pdb=" O VALSI 181 " (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: 3.550A pdb=" N LEUSI 215 " --> pdb=" O ILESI 211 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.044A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ARGSI 230 " --> pdb=" O ALASI 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'SI' and resid 225 through 230' Processing helix chain 'SI' and resid 231 through 237 Processing helix chain 'SI' and resid 245 through 255 removed outlier: 4.446A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 519 through 532 removed outlier: 4.468A pdb=" N LYSSJ 532 " --> pdb=" O LEUSJ 528 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 539 through 561 removed outlier: 4.463A pdb=" N ALASJ 545 " --> pdb=" O ASPSJ 541 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEUSJ 546 " --> pdb=" O ALASJ 542 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILESJ 548 " --> pdb=" O GLUSJ 544 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SERSJ 549 " --> pdb=" O ALASJ 545 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLNSJ 550 " --> pdb=" O LEUSJ 546 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 664 through 677 Processing helix chain 'SJ' and resid 678 through 690 removed outlier: 3.800A pdb=" N PHESJ 689 " --> pdb=" O ILESJ 685 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASNSJ 690 " --> pdb=" O ASPSJ 686 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 702 through 713 removed outlier: 3.560A pdb=" N GLNSJ 711 " --> pdb=" O GLNSJ 707 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 720 through 733 removed outlier: 4.689A pdb=" N ARGSJ 730 " --> pdb=" O HISSJ 726 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRPSJ 731 " --> pdb=" O TYRSJ 727 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARGSJ 732 " --> pdb=" O ARGSJ 728 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLUSJ 733 " --> pdb=" O LYSSJ 729 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 738 through 767 Processing helix chain 'SJ' and resid 775 through 790 Processing helix chain 'SJ' and resid 825 through 843 removed outlier: 4.334A pdb=" N LYSSJ 829 " --> pdb=" O ASPSJ 825 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYSSJ 830 " --> pdb=" O SERSJ 826 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASPSJ 831 " --> pdb=" O ARGSJ 827 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 3.912A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.549A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLUSK 41 " --> pdb=" O VALSK 37 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 4.826A 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 removed outlier: 3.530A pdb=" N GLUSK 126 " --> pdb=" O ASPSK 122 " (cutoff:3.500A) Processing helix chain 'SK' and resid 147 through 152 removed outlier: 3.632A pdb=" N TYRSK 151 " --> pdb=" O LEUSK 147 " (cutoff:3.500A) Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.283A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 3.768A 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 50 Processing helix chain 'SL' and resid 106 through 122 Processing helix chain 'SL' and resid 131 through 138 Processing helix chain 'SL' and resid 141 through 153 removed outlier: 3.735A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 169 removed outlier: 5.041A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEUSL 165 " --> pdb=" O ILESL 161 " (cutoff:3.500A) Proline residue: SL 166 - end of helix Processing helix chain 'SL' and resid 170 through 177 removed outlier: 3.961A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 Processing helix chain 'SL' and resid 222 through 241 Processing helix chain 'SL' and resid 244 through 249 removed outlier: 6.717A pdb=" N VALSL 248 " --> pdb=" O LYSSL 244 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYSSL 249 " --> pdb=" O TRPSL 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 244 through 249' Processing helix chain 'SM' and resid 13 through 18 removed outlier: 3.833A pdb=" N TYRSM 17 " --> pdb=" O SERSM 13 " (cutoff:3.500A) removed outlier: 5.597A 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 removed outlier: 3.549A pdb=" N LYSSM 25 " --> pdb=" O ASNSM 21 " (cutoff:3.500A) Processing helix chain 'SM' and resid 30 through 42 Processing helix chain 'SM' and resid 66 through 77 removed outlier: 3.955A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 3.936A 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: 3.637A pdb=" N LYSSM 86 " --> pdb=" O PHESM 82 " (cutoff:3.500A) Processing helix chain 'SM' and resid 100 through 111 Processing helix chain 'SM' and resid 116 through 125 Proline residue: SM 125 - end of helix Processing helix chain 'SM' and resid 126 through 135 removed outlier: 4.653A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) Processing helix chain 'SM' and resid 136 through 148 removed outlier: 3.897A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 3.797A 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: 3.512A pdb=" N METSM 220 " --> pdb=" O ASPSM 216 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEUSM 242 " --> pdb=" O LEUSM 238 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 4.066A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.745A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.378A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.634A 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 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: 3.529A pdb=" N ARGSN 69 " --> pdb=" O GLUSN 65 " (cutoff:3.500A) Processing helix chain 'SN' and resid 100 through 127 Proline residue: SN 121 - end of helix Processing helix chain 'SN' and resid 143 through 177 Processing helix chain 'SN' and resid 178 through 205 Processing helix chain 'SO' and resid 71 through 86 Proline residue: SO 86 - end of helix Processing helix chain 'SO' and resid 99 through 111 removed outlier: 4.274A pdb=" N ILESO 103 " --> pdb=" O LYSSO 99 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNSO 104 " --> pdb=" O LEUSO 100 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLUSO 105 " --> pdb=" O PHESO 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYSSO 110 " --> pdb=" O VALSO 106 " (cutoff:3.500A) Processing helix chain 'SO' and resid 169 through 176 removed outlier: 4.544A pdb=" N ASPSO 173 " --> pdb=" O ASPSO 169 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLUSO 174 " --> pdb=" O PROSO 170 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEUSO 175 " --> pdb=" O ALASO 171 " (cutoff:3.500A) Proline residue: SO 176 - end of helix No H-bonds generated for 'chain 'SO' and resid 169 through 176' Processing helix chain 'SO' and resid 177 through 190 Processing helix chain 'SO' and resid 261 through 293 removed outlier: 3.716A pdb=" N HISSO 265 " --> pdb=" O SERSO 261 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLUSO 293 " --> pdb=" O LEUSO 289 " (cutoff:3.500A) Processing helix chain 'SO' and resid 337 through 353 Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.276A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 50 through 61 removed outlier: 4.723A pdb=" N LYSSQ 54 " --> pdb=" O ASNSQ 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASPSQ 55 " --> pdb=" O SERSQ 51 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 3.620A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.367A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 149 through 157 Processing helix chain 'SQ' and resid 183 through 194 Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 68 Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 120 removed outlier: 3.842A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 146 removed outlier: 3.770A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLNSR 146 " --> pdb=" O LYSSR 142 " (cutoff:3.500A) Processing helix chain 'SR' and resid 147 through 162 removed outlier: 3.545A pdb=" N GLNSR 153 " --> pdb=" O GLUSR 149 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEUSR 161 " --> pdb=" O HISSR 157 " (cutoff:3.500A) Proline residue: SR 162 - end of helix Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.517A pdb=" N ASNSR 186 " --> pdb=" O SERSR 182 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.626A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 229 through 234' Processing helix chain 'SR' and resid 235 through 247 removed outlier: 3.971A 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: 4.567A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 295 through 300 removed outlier: 5.494A pdb=" N SERSR 300 " --> pdb=" O ILESR 296 " (cutoff:3.500A) Processing helix chain 'SR' and resid 301 through 314 removed outlier: 3.576A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 4.622A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 4.059A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISSR 361 " --> pdb=" O LEUSR 357 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) Processing helix chain 'SR' and resid 378 through 391 removed outlier: 4.676A pdb=" N VALSR 382 " --> pdb=" O PROSR 378 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALASR 383 " --> pdb=" O GLUSR 379 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYSSR 386 " --> pdb=" O VALSR 382 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARGSR 387 " --> pdb=" O ALASR 383 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLUSR 389 " --> pdb=" O ARGSR 385 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THRSR 390 " --> pdb=" O LYSSR 386 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.261A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 418 removed outlier: 4.795A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASPSR 418 " --> pdb=" O GLNSR 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 418' Processing helix chain 'SR' and resid 421 through 426 removed outlier: 4.157A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.165A 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: 4.056A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 442' Processing helix chain 'SR' and resid 445 through 464 removed outlier: 3.712A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SR' and resid 475 through 501 Processing helix chain 'SS' and resid 140 through 146 removed outlier: 4.853A pdb=" N TYRSS 144 " --> pdb=" O PROSS 140 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASPSS 145 " --> pdb=" O LEUSS 141 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASPSS 146 " --> pdb=" O GLUSS 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 140 through 146' Processing helix chain 'SS' and resid 167 through 177 Processing helix chain 'SS' and resid 197 through 210 Processing helix chain 'SS' and resid 242 through 248 removed outlier: 4.021A pdb=" N PHESS 246 " --> pdb=" O ASPSS 242 " (cutoff:3.500A) removed outlier: 3.531A 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: 3.633A pdb=" N LYSSS 253 " --> pdb=" O SERSS 249 " (cutoff:3.500A) Processing helix chain 'SS' and resid 323 through 334 removed outlier: 5.473A pdb=" N GLUSS 334 " --> pdb=" O TRPSS 330 " (cutoff:3.500A) Processing helix chain 'SS' and resid 349 through 354 removed outlier: 3.627A pdb=" N VALSS 353 " --> pdb=" O SERSS 349 " (cutoff:3.500A) Proline residue: SS 354 - end of helix No H-bonds generated for 'chain 'SS' and resid 349 through 354' Processing helix chain 'SS' and resid 358 through 372 removed outlier: 3.689A pdb=" N TYRSS 371 " --> pdb=" O CYSSS 367 " (cutoff:3.500A) Processing helix chain 'ST' and resid 169 through 198 removed outlier: 4.621A pdb=" N ALAST 196 " --> pdb=" O ASNST 192 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HISST 197 " --> pdb=" O LEUST 193 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYSST 198 " --> pdb=" O ALAST 194 " (cutoff:3.500A) Processing helix chain 'ST' and resid 214 through 229 removed outlier: 3.515A pdb=" N GLNST 223 " --> pdb=" O GLYST 219 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THRST 229 " --> pdb=" O ALAST 225 " (cutoff:3.500A) Processing helix chain 'ST' and resid 260 through 277 removed outlier: 3.618A pdb=" N GLUST 264 " --> pdb=" O ASPST 260 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSST 265 " --> pdb=" O PHEST 261 " (cutoff:3.500A) Processing helix chain 'ST' and resid 283 through 303 Processing helix chain 'SU' and resid 200 through 229 removed outlier: 3.627A pdb=" N ALASU 219 " --> pdb=" O LYSSU 215 " (cutoff:3.500A) Proline residue: SU 229 - end of helix Processing helix chain 'SU' and resid 230 through 245 removed outlier: 5.888A pdb=" N LYSSU 234 " --> pdb=" O GLUSU 230 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LYSSU 235 " --> pdb=" O ASNSU 231 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N METSU 242 " --> pdb=" O GLUSU 238 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEUSU 243 " --> pdb=" O LEUSU 239 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N METSU 244 " --> pdb=" O ARGSU 240 " (cutoff:3.500A) Processing helix chain 'SU' and resid 251 through 270 removed outlier: 3.550A pdb=" N VALSU 260 " --> pdb=" O LYSSU 256 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYSSU 267 " --> pdb=" O METSU 263 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASPSU 268 " --> pdb=" O GLUSU 264 " (cutoff:3.500A) Processing helix chain 'SU' and resid 289 through 322 removed outlier: 3.655A pdb=" N TRPSU 319 " --> pdb=" O METSU 315 " (cutoff:3.500A) Processing helix chain 'SU' and resid 332 through 353 removed outlier: 4.372A pdb=" N LYSSU 336 " --> pdb=" O LEUSU 332 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLYSU 337 " --> pdb=" O LYSSU 333 " (cutoff:3.500A) Processing helix chain 'SU' and resid 358 through 372 removed outlier: 3.627A pdb=" N ILESU 362 " --> pdb=" O PHESU 358 " (cutoff:3.500A) Proline residue: SU 368 - end of helix removed outlier: 4.026A pdb=" N ASNSU 371 " --> pdb=" O VALSU 367 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASPSU 372 " --> pdb=" O PROSU 368 " (cutoff:3.500A) Processing helix chain 'SU' and resid 374 through 392 Processing helix chain 'SU' and resid 395 through 413 removed outlier: 3.658A pdb=" N ASNSU 413 " --> pdb=" O VALSU 409 " (cutoff:3.500A) Processing helix chain 'SU' and resid 417 through 427 removed outlier: 4.736A pdb=" N LEUSU 421 " --> pdb=" O ARGSU 417 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYSSU 422 " --> pdb=" O PROSU 418 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THRSU 423 " --> pdb=" O GLUSU 419 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHESU 424 " --> pdb=" O METSU 420 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEUSU 425 " --> pdb=" O LEUSU 421 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYSSU 426 " --> pdb=" O LYSSU 422 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEUSU 427 " --> pdb=" O THRSU 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 417 through 427' Processing helix chain 'SU' and resid 430 through 444 Proline residue: SU 444 - end of helix Processing helix chain 'SU' and resid 470 through 508 removed outlier: 3.552A pdb=" N GLUSU 485 " --> pdb=" O SERSU 481 " (cutoff:3.500A) Processing helix chain 'SU' and resid 514 through 526 Processing helix chain 'SU' and resid 531 through 548 removed outlier: 4.585A pdb=" N ASPSU 535 " --> pdb=" O VALSU 531 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASPSU 536 " --> pdb=" O GLUSU 532 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VALSU 539 " --> pdb=" O ASPSU 535 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLYSU 548 " --> pdb=" O LEUSU 544 " (cutoff:3.500A) Processing helix chain 'SU' and resid 551 through 568 removed outlier: 3.529A pdb=" N LEUSU 566 " --> pdb=" O ALASU 562 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLYSU 568 " --> pdb=" O HISSU 564 " (cutoff:3.500A) Processing helix chain 'SU' and resid 569 through 574 removed outlier: 4.867A pdb=" N LEUSU 573 " --> pdb=" O GLNSU 569 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASNSU 574 " --> pdb=" O GLYSU 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 569 through 574' Processing helix chain 'SU' and resid 577 through 588 Processing helix chain 'SU' and resid 596 through 611 removed outlier: 4.338A pdb=" N VALSU 600 " --> pdb=" O THRSU 596 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLUSU 601 " --> pdb=" O ASNSU 597 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILESU 602 " --> pdb=" O GLUSU 598 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VALSU 603 " --> pdb=" O GLYSU 599 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEUSU 604 " --> pdb=" O VALSU 600 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLNSU 605 " --> pdb=" O GLUSU 601 " (cutoff:3.500A) Processing helix chain 'SU' and resid 614 through 619 removed outlier: 5.776A pdb=" N SERSU 619 " --> pdb=" O ARGSU 615 " (cutoff:3.500A) Processing helix chain 'SU' and resid 620 through 637 removed outlier: 3.629A pdb=" N LEUSU 635 " --> pdb=" O CYSSU 631 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HISSU 636 " --> pdb=" O THRSU 632 " (cutoff:3.500A) Processing helix chain 'SU' and resid 638 through 656 removed outlier: 3.585A pdb=" N GLYSU 644 " --> pdb=" O ASNSU 640 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N HISSU 654 " --> pdb=" O ARGSU 650 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THRSU 655 " --> pdb=" O ILESU 651 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHESU 656 " --> pdb=" O LEUSU 652 " (cutoff:3.500A) Processing helix chain 'SU' and resid 659 through 665 removed outlier: 4.553A pdb=" N LEUSU 663 " --> pdb=" O THRSU 659 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASPSU 664 " --> pdb=" O ASPSU 660 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N SERSU 665 " --> pdb=" O LEUSU 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 659 through 665' Processing helix chain 'SU' and resid 679 through 684 removed outlier: 4.006A pdb=" N CYSSU 683 " --> pdb=" O GLUSU 679 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASNSU 684 " --> pdb=" O PROSU 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 679 through 684' Processing helix chain 'SU' and resid 690 through 699 removed outlier: 5.020A pdb=" N HISSU 694 " --> pdb=" O LEUSU 690 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALASU 695 " --> pdb=" O TRPSU 691 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARGSU 698 " --> pdb=" O HISSU 694 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HISSU 699 " --> pdb=" O ALASU 695 " (cutoff:3.500A) Processing helix chain 'SU' and resid 701 through 714 removed outlier: 3.872A pdb=" N ALASU 713 " --> pdb=" O ALASU 709 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLYSU 714 " --> pdb=" O HISSU 710 " (cutoff:3.500A) Processing helix chain 'SU' and resid 724 through 731 removed outlier: 3.616A pdb=" N ARGSU 730 " --> pdb=" O GLUSU 726 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SERSU 731 " --> pdb=" O LEUSU 727 " (cutoff:3.500A) Processing helix chain 'SU' and resid 732 through 740 removed outlier: 4.452A pdb=" N SERSU 740 " --> pdb=" O PHESU 736 " (cutoff:3.500A) Processing helix chain 'SU' and resid 769 through 784 removed outlier: 3.538A pdb=" N GLUSU 782 " --> pdb=" O ARGSU 778 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VALSU 783 " --> pdb=" O TYRSU 779 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALASU 784 " --> pdb=" O SERSU 780 " (cutoff:3.500A) Processing helix chain 'SV' and resid 33 through 43 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.156A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.199A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 71' Processing helix chain 'SV' and resid 82 through 136 removed outlier: 4.211A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASNSV 87 " --> pdb=" O ARGSV 83 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASPSV 91 " --> pdb=" O ASNSV 87 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARGSV 111 " --> pdb=" O PHESV 107 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILESV 131 " --> pdb=" O VALSV 127 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALASV 136 " --> pdb=" O HISSV 132 " (cutoff:3.500A) Processing helix chain 'SW' and resid 178 through 184 removed outlier: 3.869A pdb=" N LEUSW 182 " --> pdb=" O SERSW 178 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYSSW 183 " --> pdb=" O PHESW 179 " (cutoff:3.500A) removed outlier: 5.306A 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: 4.301A 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: 3.802A 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: 3.501A pdb=" N LEUSW 312 " --> pdb=" O THRSW 308 " (cutoff:3.500A) Processing helix chain 'SW' and resid 334 through 342 removed outlier: 3.767A pdb=" N ILESW 338 " --> pdb=" O GLUSW 334 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLYSW 342 " --> pdb=" O ILESW 338 " (cutoff:3.500A) Processing helix chain 'SW' and resid 343 through 355 removed outlier: 3.529A pdb=" N GLNSW 349 " --> pdb=" O GLUSW 345 " (cutoff:3.500A) Proline residue: SW 355 - end of helix Processing helix chain 'SW' and resid 368 through 379 removed outlier: 3.793A pdb=" N ILESW 377 " --> pdb=" O ASPSW 373 " (cutoff:3.500A) Processing helix chain 'SW' and resid 408 through 424 removed outlier: 5.074A pdb=" N PHESW 413 " --> pdb=" O SERSW 409 " (cutoff:3.500A) removed outlier: 5.123A 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 487 Processing helix chain 'SW' and resid 505 through 516 Processing helix chain 'SW' and resid 534 through 545 removed outlier: 4.685A pdb=" N LEUSW 538 " --> pdb=" O GLUSW 534 " (cutoff:3.500A) removed outlier: 4.024A 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: 3.516A 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 Processing helix chain 'SY' and resid 223 through 234 removed outlier: 3.607A pdb=" N GLUSY 228 " --> pdb=" O ALASY 224 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLNSY 229 " --> pdb=" O GLYSY 225 " (cutoff:3.500A) Proline residue: SY 234 - end of helix Processing helix chain 'SY' and resid 235 through 253 removed outlier: 3.538A 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 removed outlier: 3.538A pdb=" N ASPSY 290 " --> pdb=" O GLYSY 286 " (cutoff:3.500A) Proline residue: SY 293 - end of helix Processing helix chain 'SY' and resid 294 through 307 removed outlier: 4.205A pdb=" N VALSY 298 " --> pdb=" O LEUSY 294 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLUSY 299 " --> pdb=" O SERSY 295 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLUSY 305 " --> pdb=" O LEUSY 301 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VALSY 306 " --> pdb=" O GLUSY 302 " (cutoff:3.500A) Proline residue: SY 307 - end of helix Processing helix chain 'SY' and resid 320 through 332 Processing helix chain 'SY' and resid 358 through 364 Processing helix chain 'SY' and resid 370 through 381 Proline residue: SY 376 - end of helix Processing helix chain 'SY' and resid 396 through 407 Processing helix chain 'SY' and resid 418 through 433 removed outlier: 3.642A pdb=" N LEUSY 422 " --> pdb=" O ASNSY 418 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYSSY 423 " --> pdb=" O ALASY 419 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SERSY 424 " --> pdb=" O GLUSY 420 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VALSY 425 " --> pdb=" O ARGSY 421 " (cutoff:3.500A) Processing helix chain 'SY' and resid 468 through 473 Proline residue: SY 473 - end of helix Processing helix chain 'SY' and resid 480 through 503 removed outlier: 5.466A pdb=" N ASNSY 503 " --> pdb=" O ILESY 499 " (cutoff:3.500A) Processing helix chain 'SY' and resid 520 through 535 removed outlier: 4.325A pdb=" N TRPSY 526 " --> pdb=" O GLUSY 522 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VALSY 527 " --> pdb=" O GLUSY 523 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VALSY 528 " --> pdb=" O ASNSY 524 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 6 through 12 removed outlier: 3.610A pdb=" N ARGSZ 10 " --> pdb=" O GLYSZ 6 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYSSZ 12 " --> pdb=" O THRSZ 8 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 18 through 32 Proline residue: SZ 32 - end of helix Processing helix chain 'SZ' and resid 36 through 43 Processing helix chain 'SZ' and resid 48 through 57 Processing helix chain 'SZ' and resid 61 through 67 Proline residue: SZ 67 - end of helix Processing helix chain 'SZ' and resid 90 through 103 removed outlier: 4.523A pdb=" N LEUSZ 94 " --> pdb=" O LYSSZ 90 " (cutoff:3.500A) removed outlier: 3.653A 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: 5.548A pdb=" N GLUSZ 137 " --> pdb=" O METSZ 133 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 144 through 159 removed outlier: 3.649A pdb=" N TYRSZ 155 " --> pdb=" O LYSSZ 151 " (cutoff:3.500A) 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: 4.120A 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: 6.491A pdb=" N LEUBB 163 " --> pdb=" O LEUBB 38 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VALBB 32 " --> pdb=" O VALBB 169 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEUBB 204 " --> pdb=" O LEUBB 216 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 6, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 7, first strand: chain 'L8' and resid 11 through 15 removed outlier: 4.518A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEUL8 37 " --> pdb=" O VALL8 28 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.110A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.780A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LA' and resid 16 through 20 removed outlier: 5.393A pdb=" N SERLA 111 " --> pdb=" O LYSLA 153 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LA' and resid 116 through 122 removed outlier: 3.535A pdb=" N HISLA 116 " --> pdb=" O ILELA 149 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LB' and resid 118 through 121 removed outlier: 4.859A pdb=" N LYSLB 99 " --> pdb=" O LYSLB 78 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.656A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.115A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.636A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LE' and resid 39 through 43 removed outlier: 4.159A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 18, first strand: chain 'LG' and resid 24 through 27 removed outlier: 4.703A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LG' and resid 60 through 63 removed outlier: 6.900A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LG' and resid 87 through 90 removed outlier: 4.388A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.596A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.646A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LI' and resid 72 through 75 Processing sheet with id= 24, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.476A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.379A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSLL 65 " --> pdb=" O THRLL 48 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LN' and resid 41 through 44 removed outlier: 3.500A pdb=" N THRLN 44 " --> pdb=" O GLNLN 184 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLNLN 184 " --> pdb=" O THRLN 44 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LN' and resid 53 through 59 removed outlier: 6.648A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N HISLN 275 " --> pdb=" O THRLN 223 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.844A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LN' and resid 286 through 289 removed outlier: 3.552A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LN' and resid 77 through 80 Processing sheet with id= 31, first strand: chain 'LN' and resid 88 through 93 removed outlier: 3.704A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.809A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 34, first strand: chain 'LT' and resid 56 through 60 removed outlier: 5.894A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THRLT 59 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LT' and resid 8 through 12 removed outlier: 5.851A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LT' and resid 6 through 11 removed outlier: 4.583A pdb=" N HISLT 99 " --> pdb=" O PHELT 11 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LW' and resid 15 through 18 removed outlier: 8.577A pdb=" N THRLW 15 " --> pdb=" O HISLW 28 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N HISLW 28 " --> pdb=" O THRLW 15 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THRLW 17 " --> pdb=" O ALALW 26 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'NF' and resid 189 through 194 removed outlier: 3.609A pdb=" N ALANF 190 " --> pdb=" O HISNF 185 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASNNF 255 " --> pdb=" O THRNF 245 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYRNF 241 " --> pdb=" O LEUNF 259 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THRNF 218 " --> pdb=" O VALNF 244 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'NH' and resid 36 through 39 removed outlier: 7.042A pdb=" N VALNH 44 " --> pdb=" O PHENH 70 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'NH' and resid 71 through 74 removed outlier: 4.235A pdb=" N LYSNH 78 " --> pdb=" O THRNH 74 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'NH' and resid 95 through 99 removed outlier: 4.902A pdb=" N TYRNH 95 " --> pdb=" O GLYNH 130 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLYNH 142 " --> pdb=" O VALNH 133 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'NI' and resid 196 through 200 removed outlier: 3.704A pdb=" N VALNI 136 " --> pdb=" O THRNI 274 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALANI 140 " --> pdb=" O SERNI 278 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'NI' and resid 311 through 317 removed outlier: 3.506A pdb=" N ASNNI 409 " --> pdb=" O GLNNI 340 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'SA' and resid 7 through 10 removed outlier: 5.031A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'SA' and resid 77 through 80 removed outlier: 4.321A pdb=" N GLNSA 89 " --> pdb=" O VALSA 79 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.273A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'SC' and resid 90 through 95 removed outlier: 8.721A pdb=" N ALASC 90 " --> pdb=" O LEUSC 109 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'SC' and resid 149 through 153 removed outlier: 4.114A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 50, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.440A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 52, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.766A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SG' and resid 16 through 20 removed outlier: 3.543A pdb=" N GLYSG 32 " --> pdb=" O GLYSG 29 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.418A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.573A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SH' and resid 72 through 77 removed outlier: 3.623A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TYRSH 88 " --> pdb=" O SERSH 77 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SI' and resid 147 through 151 removed outlier: 4.264A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SJ' and resid 798 through 802 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'SK' and resid 1 through 5 Processing sheet with id= 60, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 61, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 62, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 63, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 64, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.077A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SL' and resid 127 through 130 Processing sheet with id= 66, first strand: chain 'SL' and resid 210 through 216 removed outlier: 6.147A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEUSL 251 " --> pdb=" O ILESL 263 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SM' and resid 179 through 184 removed outlier: 3.551A pdb=" N GLYSM 187 " --> pdb=" O SERSM 184 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 69, first strand: chain 'SO' and resid 87 through 91 removed outlier: 4.195A pdb=" N ASPSO 91 " --> pdb=" O ILESO 64 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N SERSO 66 " --> pdb=" O ASPSO 91 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALASO 120 " --> pdb=" O SERSO 67 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEUSO 126 " --> pdb=" O VALSO 143 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYSSO 140 " --> pdb=" O ILESO 241 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALASO 228 " --> pdb=" O ILESO 223 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASNSO 219 " --> pdb=" O ILESO 232 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHESO 217 " --> pdb=" O PROSO 234 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHESO 236 " --> pdb=" O ILESO 215 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILESO 215 " --> pdb=" O PHESO 236 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASPSO 203 " --> pdb=" O ILESO 222 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SO' and resid 137 through 140 removed outlier: 3.547A pdb=" N LYSSO 242 " --> pdb=" O LYSSO 140 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 5.205A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'SQ' and resid 135 through 139 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 74, first strand: chain 'SQ' and resid 213 through 217 Processing sheet with id= 75, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.138A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SR' and resid 205 through 211 removed outlier: 5.114A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'SS' and resid 183 through 188 removed outlier: 6.869A pdb=" N ARGSS 183 " --> pdb=" O LEUSS 196 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEUSS 196 " --> pdb=" O ARGSS 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARGSS 192 " --> pdb=" O ASPSS 187 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'SV' and resid 3 through 6 removed outlier: 6.521A pdb=" N GLUSV 4 " --> pdb=" O PROSV 12 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N CYSSV 6 " --> pdb=" O SERSV 10 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'SV' and resid 18 through 23 removed outlier: 3.763A pdb=" N LYSSV 27 " --> pdb=" O ARGSV 23 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'SW' and resid 281 through 285 removed outlier: 3.521A pdb=" N VALSW 388 " --> pdb=" O ALASW 222 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'SW' and resid 400 through 407 removed outlier: 3.571A pdb=" N GLUSW 401 " --> pdb=" O GLYSW 524 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'SW' and resid 452 through 455 Processing sheet with id= 83, first strand: chain 'SY' and resid 334 through 337 removed outlier: 6.869A pdb=" N ASNSY 334 " --> pdb=" O TYRSY 349 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THRSY 344 " --> pdb=" O THRSY 314 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VALSY 310 " --> pdb=" O VALSY 348 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HISSY 365 " --> pdb=" O ASNSY 315 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'SY' and resid 436 through 442 removed outlier: 5.535A pdb=" N ASNSY 436 " --> pdb=" O GLYSY 410 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYRSY 442 " --> pdb=" O ASPSY 416 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASPSY 460 " --> pdb=" O METSY 391 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N CYSSY 517 " --> pdb=" O ALASY 461 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLYSY 510 " --> pdb=" O LYSSY 586 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYSSY 583 " --> pdb=" O VALSY 540 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'SY' and resid 547 through 550 No H-bonds generated for sheet with id= 85 Processing sheet with id= 86, first strand: chain 'SY' and resid 566 through 571 removed outlier: 6.730A pdb=" N ASPSY 577 " --> pdb=" O PROSY 571 " (cutoff:3.500A) 4156 hydrogen bonds defined for protein. 12380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2114 hydrogen bonds 3672 hydrogen bond angles 0 basepair planarities 806 basepair parallelities 1255 stacking parallelities Total time for adding SS restraints: 132.89 Time building geometry restraints manager: 52.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 26676 1.33 - 1.45: 46523 1.45 - 1.57: 67693 1.57 - 1.70: 4906 1.70 - 1.82: 575 Bond restraints: 146373 Sorted by residual: bond pdb=" N7 GDPSR1001 " pdb=" C5 GDPSR1001 " ideal model delta sigma weight residual 1.350 1.518 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C6 GDPSR1001 " pdb=" O6 GDPSR1001 " ideal model delta sigma weight residual 1.250 1.398 -0.148 2.00e-02 2.50e+03 5.45e+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 2.19e+01 bond pdb=" N1 GDPSR1001 " pdb=" C2 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.402 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.277 0.060 2.00e-02 2.50e+03 8.92e+00 ... (remaining 146368 not shown) Histogram of bond angle deviations from ideal: 98.17 - 106.41: 16478 106.41 - 114.66: 90940 114.66 - 122.90: 83252 122.90 - 131.15: 17947 131.15 - 139.39: 819 Bond angle restraints: 209436 Sorted by residual: angle pdb=" N VALSE 140 " pdb=" CA VALSE 140 " pdb=" C VALSE 140 " ideal model delta sigma weight residual 111.90 107.78 4.12 8.10e-01 1.52e+00 2.58e+01 angle pdb=" C8 GDPSR1001 " pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 108.00 120.89 -12.89 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CB LYSLS 43 " pdb=" CG LYSLS 43 " pdb=" CD LYSLS 43 " ideal model delta sigma weight residual 111.30 119.41 -8.11 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CA VALSK 179 " pdb=" C VALSK 179 " pdb=" N PROSK 180 " ideal model delta sigma weight residual 116.57 119.77 -3.20 9.80e-01 1.04e+00 1.07e+01 angle pdb=" C3' GL34520 " pdb=" O3' GL34520 " pdb=" P UL34521 " ideal model delta sigma weight residual 120.20 124.57 -4.37 1.50e+00 4.44e-01 8.50e+00 ... (remaining 209431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 86198 35.86 - 71.72: 6054 71.72 - 107.57: 806 107.57 - 143.43: 6 143.43 - 179.29: 9 Dihedral angle restraints: 93073 sinusoidal: 61602 harmonic: 31471 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 32.98 167.02 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' CL2 61 " pdb=" C1' CL2 61 " pdb=" N1 CL2 61 " pdb=" C2 CL2 61 " ideal model delta sinusoidal sigma weight residual 200.00 54.80 145.20 1 1.50e+01 4.44e-03 7.77e+01 dihedral pdb=" O4' CL32091 " pdb=" C1' CL32091 " pdb=" N1 CL32091 " pdb=" C2 CL32091 " ideal model delta sinusoidal sigma weight residual -128.00 51.29 -179.29 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 93070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 21526 0.044 - 0.089: 2845 0.089 - 0.133: 846 0.133 - 0.177: 84 0.177 - 0.222: 5 Chirality restraints: 25306 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 2.24 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1' AL3 746 " pdb=" O4' AL3 746 " pdb=" C2' AL3 746 " pdb=" N9 AL3 746 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.02e+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 -2.54 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 25303 not shown) Planarity restraints: 17463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRPSV 86 " -0.030 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRPSV 86 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRPSV 86 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRPSV 86 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRPSV 86 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRPSV 86 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRPSV 86 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRPSV 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRPSV 86 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRPSV 86 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GL1 39 " -0.047 2.00e-02 2.50e+03 1.90e-02 1.08e+01 pdb=" N9 GL1 39 " 0.041 2.00e-02 2.50e+03 pdb=" C8 GL1 39 " 0.010 2.00e-02 2.50e+03 pdb=" N7 GL1 39 " 0.000 2.00e-02 2.50e+03 pdb=" C5 GL1 39 " 0.000 2.00e-02 2.50e+03 pdb=" C6 GL1 39 " -0.005 2.00e-02 2.50e+03 pdb=" O6 GL1 39 " -0.014 2.00e-02 2.50e+03 pdb=" N1 GL1 39 " -0.005 2.00e-02 2.50e+03 pdb=" C2 GL1 39 " 0.001 2.00e-02 2.50e+03 pdb=" N2 GL1 39 " 0.004 2.00e-02 2.50e+03 pdb=" N3 GL1 39 " 0.009 2.00e-02 2.50e+03 pdb=" C4 GL1 39 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYSSU 443 " -0.051 5.00e-02 4.00e+02 7.74e-02 9.58e+00 pdb=" N PROSU 444 " 0.134 5.00e-02 4.00e+02 pdb=" CA PROSU 444 " -0.038 5.00e-02 4.00e+02 pdb=" CD PROSU 444 " -0.044 5.00e-02 4.00e+02 ... (remaining 17460 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.60: 1402 2.60 - 3.23: 125749 3.23 - 3.87: 295508 3.87 - 4.50: 411392 4.50 - 5.14: 573262 Nonbonded interactions: 1407313 Sorted by model distance: nonbonded pdb=" OP2 GL1 75 " pdb=" OH TYRLI 74 " model vdw 1.961 2.440 nonbonded pdb=" OP2 GL3 356 " pdb="MG MGL36045 " model vdw 1.987 2.170 nonbonded pdb=" OG1 THRST 229 " pdb=" O SERST 231 " model vdw 1.987 2.440 nonbonded pdb=" OP2 AL31917 " pdb="MG MGL36025 " model vdw 2.003 2.170 nonbonded pdb=" OE1 GLUSK 99 " pdb=" OG1 THRSK 125 " model vdw 2.011 2.440 ... (remaining 1407308 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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 25.730 Check model and map are aligned: 1.490 Set scattering table: 0.910 Process input model: 445.640 Find NCS groups from input model: 3.910 Set up NCS constraints: 0.370 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:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 493.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 146373 Z= 0.209 Angle : 0.552 12.894 209436 Z= 0.289 Chirality : 0.035 0.222 25306 Planarity : 0.004 0.111 17463 Dihedral : 20.014 179.288 72643 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.01 % Allowed : 0.10 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % 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: 1.69 (0.08), residues: 10623 helix: 1.96 (0.07), residues: 4746 sheet: 0.84 (0.14), residues: 1289 loop : 0.43 (0.09), residues: 4588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRPSV 86 HIS 0.007 0.001 HISSK 118 PHE 0.022 0.001 PHENA 346 TYR 0.030 0.001 TYRSY 401 ARG 0.017 0.001 ARGSL 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1141 time to evaluate : 9.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: LA 34 GLN cc_start: 0.8418 (mm110) cc_final: 0.8139 (mm110) REVERT: LA 64 ASN cc_start: 0.8316 (p0) cc_final: 0.8098 (p0) REVERT: SC 62 MET cc_start: 0.7500 (mmm) cc_final: 0.7213 (mmm) REVERT: SC 245 GLN cc_start: 0.7476 (tp40) cc_final: 0.7216 (tm-30) REVERT: SC 249 ASP cc_start: 0.7063 (m-30) cc_final: 0.6625 (m-30) REVERT: SD 43 ARG cc_start: 0.7263 (mtm-85) cc_final: 0.7054 (mtm-85) REVERT: SJ 821 PHE cc_start: 0.7366 (p90) cc_final: 0.7140 (p90) REVERT: SQ 122 MET cc_start: 0.8219 (mmm) cc_final: 0.7846 (mmt) REVERT: SZ 168 ASP cc_start: 0.7013 (m-30) cc_final: 0.6769 (m-30) outliers start: 1 outliers final: 1 residues processed: 1142 average time/residue: 2.1687 time to fit residues: 3506.6615 Evaluate side-chains 933 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 932 time to evaluate : 9.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LB residue 67 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1304 random chunks: chunk 1101 optimal weight: 9.9990 chunk 988 optimal weight: 10.0000 chunk 548 optimal weight: 7.9990 chunk 337 optimal weight: 0.9980 chunk 666 optimal weight: 6.9990 chunk 528 optimal weight: 5.9990 chunk 1022 optimal weight: 0.0040 chunk 395 optimal weight: 4.9990 chunk 621 optimal weight: 9.9990 chunk 760 optimal weight: 10.0000 chunk 1184 optimal weight: 1.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 19 GLN ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L7 5 GLN L7 90 HIS L8 48 GLN L8 69 HIS LA 93 HIS LC 36 ASN LC 125 GLN LE 144 ASN LG 36 ASN LI 14 ASN LK 62 HIS LL 100 ASN LN 42 HIS NA 376 HIS NA 457 HIS NA 484 GLN NA 501 ASN NA 565 ASN NA 621 HIS NB 22 GLN NF 72 ASN NH 127 GLN NH 175 HIS NI 332 HIS NI 333 ASN NI 412 ASN SA 61 GLN SC 136 HIS SC 190 HIS ** SC 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 211 HIS SD 131 ASN SE 64 GLN SE 94 GLN SE 112 GLN SE 206 GLN SG 39 ASN SG 42 ASN SG 138 GLN SI 71 GLN SI 94 HIS SI 225 HIS ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 68 HIS SK 79 GLN SK 83 HIS SL 112 GLN SL 218 HIS SM 154 HIS SM 211 HIS SQ 152 GLN SQ 217 GLN SR 35 HIS SR 157 HIS SR 209 HIS SR 239 GLN SS 310 HIS ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 203 HIS ** SU 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SU 361 ASN SU 491 HIS SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 636 HIS SU 699 HIS SU 701 HIS SU 774 GLN SV 17 HIS SV 24 ASN SV 129 GLN SW 402 GLN SW 525 HIS SW 593 HIS ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 109 ASN SZ 125 ASN SZ 147 GLN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 146373 Z= 0.292 Angle : 0.556 12.043 209436 Z= 0.290 Chirality : 0.038 0.286 25306 Planarity : 0.004 0.084 17463 Dihedral : 21.515 179.124 51025 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.57 % Allowed : 6.01 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.08), residues: 10623 helix: 2.30 (0.07), residues: 4881 sheet: 0.75 (0.14), residues: 1283 loop : 0.29 (0.09), residues: 4459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPSV 86 HIS 0.013 0.001 HISL6 67 PHE 0.029 0.002 PHESW 233 TYR 0.029 0.002 TYRLK 61 ARG 0.008 0.001 ARGLN 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 959 time to evaluate : 8.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L9 161 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7185 (mpp) REVERT: LE 127 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: LE 149 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6745 (tm-30) REVERT: LE 158 PHE cc_start: 0.8424 (m-80) cc_final: 0.7889 (m-80) REVERT: LG 73 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8047 (mtm-85) REVERT: LL 102 TYR cc_start: 0.8722 (t80) cc_final: 0.8496 (t80) REVERT: LN 394 LYS cc_start: 0.7749 (ptpp) cc_final: 0.7428 (pttm) REVERT: SA 95 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7981 (pmm) REVERT: SA 291 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6601 (ttp-170) REVERT: SC 245 GLN cc_start: 0.7421 (tp40) cc_final: 0.6944 (tm-30) REVERT: SC 249 ASP cc_start: 0.7349 (m-30) cc_final: 0.6529 (m-30) REVERT: SJ 821 PHE cc_start: 0.7430 (p90) cc_final: 0.7186 (p90) REVERT: SQ 218 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6494 (mtm) REVERT: SS 304 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7779 (mtmm) REVERT: SV 19 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7516 (ttp) outliers start: 140 outliers final: 48 residues processed: 1002 average time/residue: 2.1462 time to fit residues: 3036.8498 Evaluate side-chains 958 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 901 time to evaluate : 9.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L7 residue 183 LYS Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L9 residue 100 SER Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain L9 residue 197 THR Chi-restraints excluded: chain LB residue 111 SER Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 99 SER Chi-restraints excluded: chain LE residue 127 GLN Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LE residue 149 GLU Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 73 ARG Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LN residue 59 GLU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 311 ASP Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 88 GLU Chi-restraints excluded: chain NA residue 416 CYS Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 53 SER Chi-restraints excluded: chain NF residue 171 ILE Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 126 SER Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 291 ARG Chi-restraints excluded: chain SD residue 42 LEU Chi-restraints excluded: chain SH residue 181 ILE Chi-restraints excluded: chain SI residue 68 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 440 LEU Chi-restraints excluded: chain SN residue 135 ASP Chi-restraints excluded: chain SN residue 208 ASP Chi-restraints excluded: chain SQ residue 216 GLN Chi-restraints excluded: chain SQ residue 218 MET Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 342 HIS Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 285 THR Chi-restraints excluded: chain SU residue 254 VAL Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 19 MET Chi-restraints excluded: chain SV residue 24 ASN Chi-restraints excluded: chain SV residue 98 GLU Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SY residue 291 LEU Chi-restraints excluded: chain SY residue 451 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1304 random chunks: chunk 658 optimal weight: 9.9990 chunk 367 optimal weight: 6.9990 chunk 985 optimal weight: 50.0000 chunk 806 optimal weight: 5.9990 chunk 326 optimal weight: 0.8980 chunk 1186 optimal weight: 3.9990 chunk 1281 optimal weight: 0.8980 chunk 1056 optimal weight: 4.9990 chunk 1176 optimal weight: 0.6980 chunk 404 optimal weight: 8.9990 chunk 951 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L6 19 GLN L7 167 HIS L8 44 GLN LA 25 HIS LA 93 HIS LE 144 ASN LG 36 ASN LI 14 ASN LI 127 GLN LQ 92 ASN LU 26 HIS LW 66 HIS NA 484 GLN NA 501 ASN NA 565 ASN NA 572 GLN NA 621 HIS NF 72 ASN NH 23 ASN NH 124 ASN NH 151 GLN NI 412 ASN SA 61 GLN ** SC 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SE 112 GLN SE 206 GLN SE 225 ASN SG 42 ASN SI 71 GLN SI 209 GLN ** SJ 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 178 GLN SL 46 HIS SL 112 GLN SM 572 HIS SN 169 GLN SN 194 HIS SQ 217 GLN SR 351 ASN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 527 HIS SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 402 GLN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 146373 Z= 0.206 Angle : 0.495 12.066 209436 Z= 0.259 Chirality : 0.036 0.246 25306 Planarity : 0.004 0.077 17463 Dihedral : 21.449 179.020 51023 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.50 % Allowed : 8.07 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % 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: 1.95 (0.08), residues: 10623 helix: 2.45 (0.07), residues: 4887 sheet: 0.60 (0.14), residues: 1292 loop : 0.26 (0.09), residues: 4444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL9 120 HIS 0.011 0.001 HISSN 194 PHE 0.023 0.001 PHESW 233 TYR 0.024 0.001 TYRLK 61 ARG 0.011 0.000 ARGSI 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 942 time to evaluate : 9.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 34 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8511 (p) REVERT: L8 44 GLN cc_start: 0.8156 (mm110) cc_final: 0.7908 (mt0) REVERT: LE 63 ARG cc_start: 0.7457 (ttm110) cc_final: 0.7115 (mtt-85) REVERT: LE 149 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: LL 28 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6794 (pm20) REVERT: LL 102 TYR cc_start: 0.8711 (t80) cc_final: 0.8495 (t80) REVERT: LQ 86 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: SA 95 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7962 (pmm) REVERT: SC 245 GLN cc_start: 0.7360 (tp40) cc_final: 0.6793 (tm-30) REVERT: SC 249 ASP cc_start: 0.7379 (m-30) cc_final: 0.6608 (m-30) REVERT: SD 220 MET cc_start: 0.7570 (ptm) cc_final: 0.7363 (ptp) REVERT: SM 440 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7912 (mp) REVERT: SR 388 MET cc_start: 0.3261 (mtp) cc_final: 0.2862 (ttt) REVERT: SS 304 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7760 (mtmm) outliers start: 134 outliers final: 60 residues processed: 1000 average time/residue: 2.1403 time to fit residues: 3041.7945 Evaluate side-chains 955 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 888 time to evaluate : 9.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 64 THR Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L9 residue 100 SER Chi-restraints excluded: chain L9 residue 197 THR Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 111 SER Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 99 SER Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LE residue 149 GLU Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 93 THR Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 114 ASP Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 59 GLU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain NA residue 329 LEU Chi-restraints excluded: chain NA residue 416 CYS Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 53 SER Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 126 SER Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 289 LEU Chi-restraints excluded: chain SD residue 42 LEU Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SH residue 181 ILE Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SJ residue 799 THR Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 70 ILE Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 440 LEU Chi-restraints excluded: chain SN residue 135 ASP Chi-restraints excluded: chain SO residue 180 LEU Chi-restraints excluded: chain SO residue 265 HIS Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SQ residue 216 GLN Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 342 HIS Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain ST residue 201 LEU Chi-restraints excluded: chain SU residue 242 MET Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SU residue 578 LEU Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SY residue 451 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1304 random chunks: chunk 1172 optimal weight: 0.9980 chunk 891 optimal weight: 10.0000 chunk 615 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 566 optimal weight: 4.9990 chunk 796 optimal weight: 0.9980 chunk 1190 optimal weight: 2.9990 chunk 1260 optimal weight: 0.6980 chunk 622 optimal weight: 8.9990 chunk 1128 optimal weight: 10.0000 chunk 339 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L6 19 GLN L9 32 GLN LA 93 HIS LA 116 HIS LC 117 HIS LE 144 ASN LG 36 ASN LI 127 GLN LQ 92 ASN NA 484 GLN NA 501 ASN NA 572 GLN ** NA 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS NH 124 ASN SA 61 GLN SC 135 GLN ** SC 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 112 GLN SE 206 GLN SE 225 ASN SG 42 ASN SI 71 GLN ** SJ 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN SM 572 HIS SN 169 GLN SN 194 HIS SQ 129 ASN SQ 217 GLN SR 351 ASN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SU 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 774 GLN SW 402 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 146373 Z= 0.228 Angle : 0.500 11.657 209436 Z= 0.260 Chirality : 0.036 0.247 25306 Planarity : 0.004 0.067 17463 Dihedral : 21.384 178.256 51023 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.88 % Allowed : 9.23 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.08), residues: 10623 helix: 2.44 (0.07), residues: 4897 sheet: 0.52 (0.14), residues: 1289 loop : 0.17 (0.09), residues: 4437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPSL 271 HIS 0.012 0.001 HISL6 67 PHE 0.023 0.001 PHESW 233 TYR 0.023 0.001 TYRSC 216 ARG 0.010 0.000 ARGL7 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 918 time to evaluate : 9.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 34 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (p) REVERT: L9 161 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7679 (mpp) REVERT: LE 63 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7187 (mtt-85) REVERT: LL 28 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6797 (pm20) REVERT: LL 102 TYR cc_start: 0.8711 (t80) cc_final: 0.8494 (t80) REVERT: LQ 86 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: SA 291 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6672 (ttp-170) REVERT: SC 245 GLN cc_start: 0.7405 (tp40) cc_final: 0.6810 (tm-30) REVERT: SC 249 ASP cc_start: 0.7353 (m-30) cc_final: 0.6673 (m-30) REVERT: SH 191 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5728 (mm110) REVERT: SL 272 ASP cc_start: 0.5956 (OUTLIER) cc_final: 0.5382 (t70) REVERT: SM 273 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7233 (mmm) REVERT: SM 440 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7906 (mp) REVERT: SQ 218 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6472 (mtm) REVERT: SR 388 MET cc_start: 0.3474 (mtp) cc_final: 0.2799 (ttt) REVERT: SS 304 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7754 (mtmm) REVERT: SU 308 TYR cc_start: 0.7197 (t80) cc_final: 0.6829 (t80) REVERT: SW 491 ILE cc_start: 0.8075 (mm) cc_final: 0.7863 (mm) REVERT: SY 402 MET cc_start: 0.7410 (mtp) cc_final: 0.7164 (mtp) outliers start: 168 outliers final: 68 residues processed: 1000 average time/residue: 2.1160 time to fit residues: 3002.6578 Evaluate side-chains 967 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 888 time to evaluate : 9.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L9 residue 100 SER Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain L9 residue 197 THR Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 103 GLU Chi-restraints excluded: chain LB residue 111 SER Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 99 SER Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LG residue 72 LEU Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 93 THR Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 59 GLU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NA residue 329 LEU Chi-restraints excluded: chain NA residue 352 LEU Chi-restraints excluded: chain NA residue 416 CYS Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 53 SER Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 126 SER Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain SA residue 289 LEU Chi-restraints excluded: chain SA residue 291 ARG Chi-restraints excluded: chain SC residue 96 VAL Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SE residue 222 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SH residue 181 ILE Chi-restraints excluded: chain SH residue 191 GLN Chi-restraints excluded: chain SI residue 68 SER Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SJ residue 799 THR Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SL residue 116 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 70 ILE Chi-restraints excluded: chain SM residue 273 MET Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 440 LEU Chi-restraints excluded: chain SN residue 135 ASP Chi-restraints excluded: chain SO residue 180 LEU Chi-restraints excluded: chain SQ residue 216 GLN Chi-restraints excluded: chain SQ residue 218 MET Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 342 HIS Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 343 LEU Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 285 THR Chi-restraints excluded: chain SU residue 254 VAL Chi-restraints excluded: chain SU residue 432 VAL Chi-restraints excluded: chain SU residue 441 ILE Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SV residue 68 SER Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SY residue 451 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1304 random chunks: chunk 1049 optimal weight: 4.9990 chunk 715 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 938 optimal weight: 2.9990 chunk 520 optimal weight: 10.0000 chunk 1075 optimal weight: 10.0000 chunk 871 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 643 optimal weight: 4.9990 chunk 1131 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN ** L6 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 10 ASN LA 93 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 144 ASN ** LH 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 14 ASN LI 127 GLN LQ 92 ASN NA 343 ASN NA 484 GLN NA 539 HIS ** NA 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS NH 124 ASN SA 61 GLN SA 317 ASN SC 135 GLN ** SC 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SE 112 GLN SE 206 GLN SE 208 ASN SE 225 ASN SG 42 ASN SH 108 ASN SI 71 GLN ** SJ 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 10 ASN SK 162 HIS SL 112 GLN SM 572 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 217 GLN SR 342 HIS SR 351 ASN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 402 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 146373 Z= 0.390 Angle : 0.584 11.604 209436 Z= 0.301 Chirality : 0.040 0.287 25306 Planarity : 0.005 0.067 17463 Dihedral : 21.398 178.251 51023 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.23 % Allowed : 10.09 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.08), residues: 10623 helix: 2.21 (0.07), residues: 4893 sheet: 0.35 (0.14), residues: 1284 loop : -0.01 (0.09), residues: 4446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPLT 6 HIS 0.015 0.002 HISL6 67 PHE 0.030 0.002 PHESR 18 TYR 0.026 0.002 TYRLK 61 ARG 0.009 0.001 ARGSH 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 902 time to evaluate : 9.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 34 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8532 (p) REVERT: L9 161 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7428 (mpp) REVERT: LE 63 ARG cc_start: 0.7536 (ttm110) cc_final: 0.7259 (mtt-85) REVERT: LE 149 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: LG 15 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6899 (ttp-170) REVERT: LG 71 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: LL 28 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6880 (pm20) REVERT: LL 102 TYR cc_start: 0.8766 (t80) cc_final: 0.8552 (t80) REVERT: LQ 86 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: NF 98 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5518 (mpp-170) REVERT: NI 101 MET cc_start: 0.5415 (OUTLIER) cc_final: 0.4977 (mtt) REVERT: SA 95 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.7913 (pmm) REVERT: SA 291 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6645 (ttp-170) REVERT: SC 245 GLN cc_start: 0.7552 (tp40) cc_final: 0.6900 (tm-30) REVERT: SC 249 ASP cc_start: 0.7368 (m-30) cc_final: 0.6738 (m-30) REVERT: SH 191 GLN cc_start: 0.6028 (OUTLIER) cc_final: 0.5724 (mm110) REVERT: SK 134 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8440 (mmtp) REVERT: SL 78 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7984 (tp) REVERT: SL 271 TRP cc_start: 0.6386 (OUTLIER) cc_final: 0.6046 (t-100) REVERT: SM 440 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7870 (OUTLIER) REVERT: SQ 218 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.6498 (mtm) REVERT: SS 304 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7816 (mtmm) REVERT: ST 246 ARG cc_start: 0.6372 (mmm160) cc_final: 0.6138 (mmm160) REVERT: SW 491 ILE cc_start: 0.8079 (mm) cc_final: 0.7827 (mm) outliers start: 199 outliers final: 101 residues processed: 1004 average time/residue: 2.1554 time to fit residues: 3070.2414 Evaluate side-chains 993 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 875 time to evaluate : 9.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L9 residue 100 SER Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain L9 residue 197 THR Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LA residue 103 GLU Chi-restraints excluded: chain LB residue 7 HIS Chi-restraints excluded: chain LB residue 64 SER Chi-restraints excluded: chain LB residue 111 SER Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 99 SER Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LE residue 149 GLU Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 71 GLU Chi-restraints excluded: chain LG residue 72 LEU Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 93 THR Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 58 MET Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 59 GLU Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 306 ASP Chi-restraints excluded: chain LN residue 309 LEU Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain NA residue 329 LEU Chi-restraints excluded: chain NA residue 352 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 416 CYS Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 53 SER Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NF residue 103 SER Chi-restraints excluded: chain NF residue 171 ILE Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 126 SER Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 101 MET Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 289 LEU Chi-restraints excluded: chain SA residue 291 ARG Chi-restraints excluded: chain SC residue 96 VAL Chi-restraints excluded: chain SD residue 42 LEU Chi-restraints excluded: chain SE residue 222 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SH residue 181 ILE Chi-restraints excluded: chain SH residue 191 GLN Chi-restraints excluded: chain SI residue 68 SER Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SJ residue 538 ILE Chi-restraints excluded: chain SJ residue 548 ILE Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SJ residue 799 THR Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 134 LYS Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SL residue 78 LEU Chi-restraints excluded: chain SL residue 116 LYS Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 66 LEU Chi-restraints excluded: chain SM residue 70 ILE Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 273 MET Chi-restraints excluded: chain SM residue 440 LEU Chi-restraints excluded: chain SN residue 51 ASN Chi-restraints excluded: chain SN residue 134 THR Chi-restraints excluded: chain SN residue 135 ASP Chi-restraints excluded: chain SN residue 208 ASP Chi-restraints excluded: chain SO residue 180 LEU Chi-restraints excluded: chain SQ residue 87 ASP Chi-restraints excluded: chain SQ residue 216 GLN Chi-restraints excluded: chain SQ residue 218 MET Chi-restraints excluded: chain SR residue 32 THR Chi-restraints excluded: chain SR residue 33 VAL Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 342 HIS Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 343 LEU Chi-restraints excluded: chain ST residue 201 LEU Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain SU residue 230 GLU Chi-restraints excluded: chain SU residue 254 VAL Chi-restraints excluded: chain SU residue 329 VAL Chi-restraints excluded: chain SU residue 432 VAL Chi-restraints excluded: chain SU residue 441 ILE Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SU residue 578 LEU Chi-restraints excluded: chain SV residue 68 SER Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SW residue 554 SER Chi-restraints excluded: chain SY residue 451 VAL Chi-restraints excluded: chain SY residue 576 MET Chi-restraints excluded: chain SZ residue 22 LEU Chi-restraints excluded: chain SZ residue 144 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1304 random chunks: chunk 424 optimal weight: 0.0370 chunk 1135 optimal weight: 3.9990 chunk 249 optimal weight: 20.0000 chunk 740 optimal weight: 0.9980 chunk 311 optimal weight: 0.8980 chunk 1261 optimal weight: 2.9990 chunk 1047 optimal weight: 3.9990 chunk 584 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 417 optimal weight: 0.0470 chunk 662 optimal weight: 7.9990 overall best weight: 0.9958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN BA 118 HIS L8 44 GLN LA 93 HIS LC 37 HIS LE 144 ASN ** LH 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 14 ASN LI 43 ASN LI 127 GLN LQ 92 ASN LS 30 GLN NA 484 GLN ** NA 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS NH 124 ASN ** NK 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SA 61 GLN SA 317 ASN SC 135 GLN ** SC 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SE 112 GLN SE 206 GLN SE 225 ASN SG 42 ASN SI 71 GLN ** SJ 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 769 ASN ** SK 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN SM 572 HIS SQ 217 GLN ** SR 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 351 ASN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 687 ASN SU 774 GLN SW 402 GLN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 146373 Z= 0.142 Angle : 0.471 11.761 209436 Z= 0.245 Chirality : 0.034 0.235 25306 Planarity : 0.004 0.056 17463 Dihedral : 21.368 178.626 51023 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.74 % Allowed : 11.09 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % 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: 1.85 (0.08), residues: 10623 helix: 2.48 (0.07), residues: 4903 sheet: 0.43 (0.14), residues: 1286 loop : 0.10 (0.09), residues: 4434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPLN 122 HIS 0.033 0.001 HISSR 342 PHE 0.022 0.001 PHESW 233 TYR 0.024 0.001 TYRSC 216 ARG 0.011 0.000 ARGL7 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 910 time to evaluate : 9.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 34 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8433 (t) REVERT: L9 161 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7685 (mpp) REVERT: LE 63 ARG cc_start: 0.7517 (ttm110) cc_final: 0.7254 (mtt-85) REVERT: LG 15 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6967 (ttp-170) REVERT: LL 28 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: NB 66 LEU cc_start: 0.8698 (mm) cc_final: 0.8433 (mm) REVERT: NH 175 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.6512 (m90) REVERT: SA 95 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7905 (pmm) REVERT: SC 245 GLN cc_start: 0.7432 (tp40) cc_final: 0.6887 (tm-30) REVERT: SC 249 ASP cc_start: 0.7397 (m-30) cc_final: 0.6807 (m-30) REVERT: SH 108 ASN cc_start: 0.8288 (m-40) cc_final: 0.8072 (m110) REVERT: SI 171 ASN cc_start: 0.6322 (p0) cc_final: 0.6044 (p0) REVERT: SL 271 TRP cc_start: 0.6036 (OUTLIER) cc_final: 0.5788 (t-100) REVERT: SM 273 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7215 (mmm) REVERT: SS 304 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7692 (mtmm) REVERT: SU 308 TYR cc_start: 0.7268 (t80) cc_final: 0.6935 (t80) REVERT: SW 219 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7659 (tp) REVERT: SW 491 ILE cc_start: 0.8087 (mm) cc_final: 0.7857 (mm) outliers start: 155 outliers final: 68 residues processed: 989 average time/residue: 2.1596 time to fit residues: 3033.7071 Evaluate side-chains 967 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 889 time to evaluate : 8.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L8 residue 55 MET Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LE residue 99 SER Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 108 GLN Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NA residue 329 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 416 CYS Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 53 SER Chi-restraints excluded: chain NH residue 32 ASP Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 126 SER Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NK residue 105 LEU Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 289 LEU Chi-restraints excluded: chain SC residue 96 VAL Chi-restraints excluded: chain SD residue 63 GLN Chi-restraints excluded: chain SE residue 222 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SH residue 181 ILE Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SJ residue 548 ILE Chi-restraints excluded: chain SJ residue 799 THR Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 273 MET Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SN residue 51 ASN Chi-restraints excluded: chain SN residue 135 ASP Chi-restraints excluded: chain SO residue 180 LEU Chi-restraints excluded: chain SQ residue 216 GLN Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 343 LEU Chi-restraints excluded: chain ST residue 285 THR Chi-restraints excluded: chain SU residue 254 VAL Chi-restraints excluded: chain SU residue 432 VAL Chi-restraints excluded: chain SU residue 441 ILE Chi-restraints excluded: chain SU residue 515 LEU Chi-restraints excluded: chain SU residue 578 LEU Chi-restraints excluded: chain SV residue 68 SER Chi-restraints excluded: chain SV residue 82 GLN Chi-restraints excluded: chain SW residue 219 LEU Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SW residue 554 SER Chi-restraints excluded: chain SZ residue 105 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1304 random chunks: chunk 1216 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 718 optimal weight: 8.9990 chunk 921 optimal weight: 1.9990 chunk 713 optimal weight: 5.9990 chunk 1062 optimal weight: 0.7980 chunk 704 optimal weight: 9.9990 chunk 1256 optimal weight: 1.9990 chunk 786 optimal weight: 0.9980 chunk 766 optimal weight: 5.9990 chunk 580 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 97 ASN BA 115 GLN L6 19 GLN L9 196 ASN ** LA 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 93 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 95 HIS LE 144 ASN ** LH 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 127 GLN LS 30 GLN NA 484 GLN ** NA 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS NH 124 ASN ** NK 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SC 135 GLN ** SC 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SE 112 GLN SE 206 GLN SE 225 ASN SG 42 ASN SI 71 GLN ** SJ 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 10 ASN SL 112 GLN SQ 217 GLN SR 351 ASN SR 426 HIS ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS SU 597 ASN SV 110 ASN SW 402 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 146373 Z= 0.247 Angle : 0.501 11.610 209436 Z= 0.260 Chirality : 0.036 0.250 25306 Planarity : 0.004 0.062 17463 Dihedral : 21.314 178.175 51023 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.78 % Allowed : 11.53 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.08), residues: 10623 helix: 2.44 (0.07), residues: 4894 sheet: 0.38 (0.14), residues: 1286 loop : 0.06 (0.09), residues: 4443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPLT 6 HIS 0.011 0.001 HISNA 621 PHE 0.023 0.001 PHESW 233 TYR 0.023 0.001 TYRLK 61 ARG 0.015 0.000 ARGSC 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 897 time to evaluate : 9.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 34 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8508 (p) REVERT: L9 161 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7686 (mmm) REVERT: LE 63 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7270 (mtt-85) REVERT: LG 15 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6959 (ttp-170) REVERT: LG 71 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: LL 28 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6769 (pm20) REVERT: LW 85 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7284 (tptt) REVERT: NA 358 MET cc_start: 0.6352 (ttp) cc_final: 0.6113 (ttp) REVERT: NA 362 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7709 (tt) REVERT: NH 175 HIS cc_start: 0.6827 (OUTLIER) cc_final: 0.6598 (m90) REVERT: NI 101 MET cc_start: 0.5336 (OUTLIER) cc_final: 0.4934 (mtt) REVERT: SA 95 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7888 (pmm) REVERT: SA 291 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6712 (ttp-170) REVERT: SC 245 GLN cc_start: 0.7506 (tp40) cc_final: 0.6947 (tm-30) REVERT: SC 249 ASP cc_start: 0.7408 (m-30) cc_final: 0.6834 (m-30) REVERT: SH 108 ASN cc_start: 0.8296 (m-40) cc_final: 0.8077 (m110) REVERT: SI 171 ASN cc_start: 0.6409 (p0) cc_final: 0.6130 (p0) REVERT: SK 134 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8388 (mmtp) REVERT: SL 271 TRP cc_start: 0.6132 (OUTLIER) cc_final: 0.5832 (t-100) REVERT: SM 273 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7244 (mmm) REVERT: SQ 20 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7927 (tm) REVERT: SR 477 MET cc_start: 0.4594 (mmp) cc_final: 0.3866 (ptt) REVERT: SS 304 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7708 (mtmm) REVERT: ST 246 ARG cc_start: 0.6465 (mmm160) cc_final: 0.6246 (mmm160) REVERT: ST 283 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6200 (m-30) REVERT: SU 308 TYR cc_start: 0.7207 (t80) cc_final: 0.6854 (t80) REVERT: SW 219 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7670 (tp) REVERT: SW 491 ILE cc_start: 0.8141 (mm) cc_final: 0.7915 (mm) outliers start: 159 outliers final: 85 residues processed: 979 average time/residue: 2.1620 time to fit residues: 3005.1360 Evaluate side-chains 990 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 887 time to evaluate : 10.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L9 residue 100 SER Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 7 ASP Chi-restraints excluded: chain LB residue 111 SER Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LE residue 99 SER Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 71 GLU Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 108 GLN Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 58 MET Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 59 GLU Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 309 LEU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 85 LYS Chi-restraints excluded: chain NA residue 352 LEU Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 416 CYS Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 53 SER Chi-restraints excluded: chain NH residue 32 ASP Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 126 SER Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 101 MET Chi-restraints excluded: chain NK residue 105 LEU Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 289 LEU Chi-restraints excluded: chain SA residue 291 ARG Chi-restraints excluded: chain SC residue 96 VAL Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SE residue 201 THR Chi-restraints excluded: chain SE residue 222 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SH residue 181 ILE Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SJ residue 548 ILE Chi-restraints excluded: chain SJ residue 799 THR Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 134 LYS Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 70 ILE Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 273 MET Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SN residue 51 ASN Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 135 ASP Chi-restraints excluded: chain SO residue 180 LEU Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SQ residue 216 GLN Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 328 LEU Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 343 LEU Chi-restraints excluded: chain ST residue 201 LEU Chi-restraints excluded: chain ST residue 283 ASP Chi-restraints excluded: chain SU residue 254 VAL Chi-restraints excluded: chain SU residue 297 PHE Chi-restraints excluded: chain SU residue 432 VAL Chi-restraints excluded: chain SU residue 441 ILE Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SU residue 578 LEU Chi-restraints excluded: chain SU residue 637 VAL Chi-restraints excluded: chain SU residue 668 GLN Chi-restraints excluded: chain SW residue 217 ARG Chi-restraints excluded: chain SW residue 219 LEU Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SW residue 554 SER Chi-restraints excluded: chain SY residue 451 VAL Chi-restraints excluded: chain SY residue 576 MET Chi-restraints excluded: chain SZ residue 22 LEU Chi-restraints excluded: chain SZ residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1304 random chunks: chunk 777 optimal weight: 2.9990 chunk 501 optimal weight: 50.0000 chunk 750 optimal weight: 8.9990 chunk 378 optimal weight: 0.9990 chunk 246 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 799 optimal weight: 1.9990 chunk 856 optimal weight: 0.0970 chunk 621 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 987 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L6 19 GLN L8 44 GLN LA 80 GLN LA 93 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 144 ASN ** LH 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 92 ASN LS 30 GLN NA 484 GLN ** NA 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS NH 124 ASN ** NK 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SC 135 GLN ** SC 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 63 GLN SE 64 GLN SE 112 GLN SE 206 GLN SE 225 ASN SG 42 ASN SI 71 GLN ** SJ 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 712 HIS SK 10 ASN SL 112 GLN SQ 217 GLN SR 351 ASN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS SU 774 GLN SW 402 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 146373 Z= 0.231 Angle : 0.497 11.604 209436 Z= 0.257 Chirality : 0.036 0.280 25306 Planarity : 0.004 0.056 17463 Dihedral : 21.308 177.959 51023 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.80 % Allowed : 11.87 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % 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: 1.77 (0.08), residues: 10623 helix: 2.43 (0.07), residues: 4888 sheet: 0.38 (0.14), residues: 1286 loop : 0.03 (0.09), residues: 4449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPL9 120 HIS 0.012 0.001 HISNA 621 PHE 0.039 0.001 PHESU 297 TYR 0.024 0.001 TYRSC 216 ARG 0.015 0.000 ARGSC 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 887 time to evaluate : 9.542 Fit side-chains revert: symmetry clash REVERT: L7 34 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8493 (p) REVERT: L9 161 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7643 (mpp) REVERT: LB 146 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7474 (mtp85) REVERT: LE 63 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7302 (mtt-85) REVERT: LE 127 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: LE 149 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: LG 15 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6993 (ttp-170) REVERT: LL 28 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6771 (pm20) REVERT: LW 85 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7288 (tptt) REVERT: NA 352 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6116 (mt) REVERT: NA 358 MET cc_start: 0.6554 (ttp) cc_final: 0.6332 (ttp) REVERT: NA 362 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7663 (tt) REVERT: NH 175 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6659 (m90) REVERT: SA 95 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7888 (pmm) REVERT: SA 291 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6702 (ttp-170) REVERT: SA 312 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7289 (ttp-110) REVERT: SC 245 GLN cc_start: 0.7534 (tp40) cc_final: 0.6983 (tm-30) REVERT: SC 249 ASP cc_start: 0.7383 (m-30) cc_final: 0.6796 (m-30) REVERT: SI 171 ASN cc_start: 0.6457 (p0) cc_final: 0.6179 (p0) REVERT: SK 134 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8411 (mmtp) REVERT: SL 271 TRP cc_start: 0.6244 (OUTLIER) cc_final: 0.5799 (t-100) REVERT: SM 273 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7244 (mmm) REVERT: SQ 20 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7915 (tm) REVERT: SR 477 MET cc_start: 0.4681 (mmp) cc_final: 0.3966 (ptt) REVERT: SS 304 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7725 (mtmm) REVERT: ST 246 ARG cc_start: 0.6496 (mmm160) cc_final: 0.6238 (mmm160) REVERT: ST 283 ASP cc_start: 0.6540 (OUTLIER) cc_final: 0.6211 (m-30) REVERT: SU 308 TYR cc_start: 0.7215 (t80) cc_final: 0.6864 (t80) REVERT: SW 219 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7666 (tp) REVERT: SW 491 ILE cc_start: 0.8130 (mm) cc_final: 0.7890 (mm) REVERT: SY 314 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7841 (m) outliers start: 161 outliers final: 96 residues processed: 968 average time/residue: 2.1660 time to fit residues: 2975.3620 Evaluate side-chains 996 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 879 time to evaluate : 9.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L9 residue 100 SER Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain L9 residue 197 THR Chi-restraints excluded: chain LA residue 7 ASP Chi-restraints excluded: chain LB residue 111 SER Chi-restraints excluded: chain LB residue 146 ARG Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LE residue 99 SER Chi-restraints excluded: chain LE residue 127 GLN Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LE residue 149 GLU Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 108 GLN Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 58 MET Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 59 GLU Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 309 LEU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 85 LYS Chi-restraints excluded: chain NA residue 329 LEU Chi-restraints excluded: chain NA residue 352 LEU Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 416 CYS Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 53 SER Chi-restraints excluded: chain NH residue 32 ASP Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 126 SER Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NK residue 105 LEU Chi-restraints excluded: chain SA residue 80 ARG Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 289 LEU Chi-restraints excluded: chain SA residue 291 ARG Chi-restraints excluded: chain SC residue 96 VAL Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SE residue 201 THR Chi-restraints excluded: chain SE residue 222 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SH residue 181 ILE Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SJ residue 538 ILE Chi-restraints excluded: chain SJ residue 548 ILE Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SJ residue 799 THR Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 134 LYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 70 ILE Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 273 MET Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 440 LEU Chi-restraints excluded: chain SN residue 51 ASN Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 135 ASP Chi-restraints excluded: chain SO residue 180 LEU Chi-restraints excluded: chain SQ residue 20 LEU Chi-restraints excluded: chain SQ residue 207 MET Chi-restraints excluded: chain SQ residue 216 GLN Chi-restraints excluded: chain SR residue 32 THR Chi-restraints excluded: chain SR residue 54 THR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 328 LEU Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 343 LEU Chi-restraints excluded: chain ST residue 283 ASP Chi-restraints excluded: chain ST residue 285 THR Chi-restraints excluded: chain SU residue 254 VAL Chi-restraints excluded: chain SU residue 329 VAL Chi-restraints excluded: chain SU residue 377 ILE Chi-restraints excluded: chain SU residue 432 VAL Chi-restraints excluded: chain SU residue 441 ILE Chi-restraints excluded: chain SU residue 515 LEU Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SU residue 564 HIS Chi-restraints excluded: chain SU residue 578 LEU Chi-restraints excluded: chain SU residue 596 THR Chi-restraints excluded: chain SU residue 668 GLN Chi-restraints excluded: chain SW residue 219 LEU Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SW residue 554 SER Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 451 VAL Chi-restraints excluded: chain SY residue 576 MET Chi-restraints excluded: chain SZ residue 22 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1304 random chunks: chunk 1143 optimal weight: 8.9990 chunk 1204 optimal weight: 5.9990 chunk 1098 optimal weight: 50.0000 chunk 1171 optimal weight: 3.9990 chunk 1203 optimal weight: 0.8980 chunk 704 optimal weight: 10.0000 chunk 510 optimal weight: 2.9990 chunk 919 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 1058 optimal weight: 2.9990 chunk 1107 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L6 19 GLN L8 44 GLN LA 80 GLN LA 93 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 144 ASN ** LH 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 127 GLN NA 484 GLN ** NA 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS NH 41 ASN NH 124 ASN ** NK 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SA 317 ASN SC 135 GLN ** SC 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SE 112 GLN SE 206 GLN SE 225 ASN SG 42 ASN SH 108 ASN SI 71 GLN ** SJ 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 10 ASN SL 112 GLN SM 16 ASN SQ 217 GLN SR 351 ASN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 402 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 146373 Z= 0.333 Angle : 0.550 11.775 209436 Z= 0.283 Chirality : 0.038 0.394 25306 Planarity : 0.005 0.081 17463 Dihedral : 21.316 177.645 51023 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.91 % Allowed : 11.96 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % 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: 1.62 (0.08), residues: 10623 helix: 2.30 (0.07), residues: 4893 sheet: 0.29 (0.14), residues: 1297 loop : -0.03 (0.09), residues: 4433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPLT 6 HIS 0.012 0.001 HISNA 621 PHE 0.026 0.002 PHESU 297 TYR 0.023 0.002 TYRLK 61 ARG 0.016 0.001 ARGSW 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 886 time to evaluate : 9.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 34 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8537 (p) REVERT: L9 161 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7447 (mpp) REVERT: LB 146 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7460 (mtp85) REVERT: LE 63 ARG cc_start: 0.7561 (ttm110) cc_final: 0.7295 (mtt-85) REVERT: LE 127 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: LE 149 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6735 (tm-30) REVERT: LG 15 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7006 (ttp-170) REVERT: LL 28 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6863 (pm20) REVERT: LW 85 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7298 (tptt) REVERT: NA 358 MET cc_start: 0.6559 (ttp) cc_final: 0.6318 (ttp) REVERT: NA 362 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7761 (tt) REVERT: NI 101 MET cc_start: 0.5340 (OUTLIER) cc_final: 0.4999 (mtt) REVERT: SA 95 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7871 (pmm) REVERT: SA 291 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6759 (ttp-170) REVERT: SA 312 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7395 (ttp-110) REVERT: SC 245 GLN cc_start: 0.7568 (tp40) cc_final: 0.7199 (tp40) REVERT: SC 249 ASP cc_start: 0.7396 (m-30) cc_final: 0.7024 (m-30) REVERT: SI 171 ASN cc_start: 0.6422 (p0) cc_final: 0.6142 (p0) REVERT: SK 134 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8423 (mmtp) REVERT: SL 271 TRP cc_start: 0.6157 (OUTLIER) cc_final: 0.5942 (t-100) REVERT: SR 477 MET cc_start: 0.4684 (mmp) cc_final: 0.3974 (ptt) REVERT: SS 304 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7740 (mtmm) REVERT: ST 246 ARG cc_start: 0.6488 (mmm160) cc_final: 0.6175 (mmm160) REVERT: ST 283 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6254 (m-30) REVERT: SU 308 TYR cc_start: 0.7278 (t80) cc_final: 0.6958 (t80) REVERT: SU 692 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6583 (pm20) REVERT: SW 491 ILE cc_start: 0.8155 (mm) cc_final: 0.7917 (mm) REVERT: SY 314 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7842 (m) outliers start: 170 outliers final: 106 residues processed: 975 average time/residue: 2.2045 time to fit residues: 3061.1713 Evaluate side-chains 999 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 875 time to evaluate : 9.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 64 THR Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L9 residue 100 SER Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain L9 residue 197 THR Chi-restraints excluded: chain LA residue 2 VAL Chi-restraints excluded: chain LA residue 7 ASP Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LB residue 111 SER Chi-restraints excluded: chain LB residue 146 ARG Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LE residue 99 SER Chi-restraints excluded: chain LE residue 127 GLN Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LE residue 149 GLU Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 72 LEU Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 87 MET Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 58 MET Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LN residue 59 GLU Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 309 LEU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 85 LYS Chi-restraints excluded: chain NA residue 352 LEU Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 416 CYS Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 53 SER Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 126 SER Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 101 MET Chi-restraints excluded: chain NK residue 105 LEU Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 289 LEU Chi-restraints excluded: chain SA residue 291 ARG Chi-restraints excluded: chain SC residue 96 VAL Chi-restraints excluded: chain SC residue 258 LEU Chi-restraints excluded: chain SD residue 42 LEU Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SE residue 201 THR Chi-restraints excluded: chain SE residue 222 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SH residue 181 ILE Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SI residue 239 THR Chi-restraints excluded: chain SJ residue 538 ILE Chi-restraints excluded: chain SJ residue 677 SER Chi-restraints excluded: chain SJ residue 799 THR Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 134 LYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 70 ILE Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 440 LEU Chi-restraints excluded: chain SN residue 51 ASN Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 135 ASP Chi-restraints excluded: chain SO residue 180 LEU Chi-restraints excluded: chain SQ residue 216 GLN Chi-restraints excluded: chain SR residue 32 THR Chi-restraints excluded: chain SR residue 54 THR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 328 LEU Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 343 LEU Chi-restraints excluded: chain ST residue 222 MET Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 283 ASP Chi-restraints excluded: chain SU residue 230 GLU Chi-restraints excluded: chain SU residue 254 VAL Chi-restraints excluded: chain SU residue 329 VAL Chi-restraints excluded: chain SU residue 377 ILE Chi-restraints excluded: chain SU residue 515 LEU Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SU residue 564 HIS Chi-restraints excluded: chain SU residue 578 LEU Chi-restraints excluded: chain SU residue 596 THR Chi-restraints excluded: chain SU residue 637 VAL Chi-restraints excluded: chain SU residue 668 GLN Chi-restraints excluded: chain SU residue 692 GLU Chi-restraints excluded: chain SW residue 219 LEU Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SW residue 480 LEU Chi-restraints excluded: chain SW residue 554 SER Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 451 VAL Chi-restraints excluded: chain SY residue 576 MET Chi-restraints excluded: chain SZ residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1304 random chunks: chunk 1167 optimal weight: 0.8980 chunk 769 optimal weight: 0.5980 chunk 1238 optimal weight: 4.9990 chunk 755 optimal weight: 9.9990 chunk 587 optimal weight: 0.8980 chunk 860 optimal weight: 3.9990 chunk 1299 optimal weight: 7.9990 chunk 1195 optimal weight: 6.9990 chunk 1034 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 799 optimal weight: 0.8980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L6 19 GLN L8 44 GLN LA 93 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 144 ASN ** LH 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 30 GLN NA 484 GLN ** NA 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS NB 22 GLN NH 124 ASN ** NK 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SA 317 ASN SC 135 GLN ** SC 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SE 112 GLN SE 206 GLN SG 42 ASN SH 108 ASN SI 71 GLN ** SJ 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 10 ASN SL 112 GLN SQ 217 GLN SR 351 ASN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 774 GLN SW 402 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 146373 Z= 0.173 Angle : 0.498 11.988 209436 Z= 0.259 Chirality : 0.035 0.411 25306 Planarity : 0.004 0.069 17463 Dihedral : 21.343 177.791 51023 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.49 % Allowed : 12.39 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % 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: 1.75 (0.08), residues: 10623 helix: 2.43 (0.07), residues: 4876 sheet: 0.35 (0.14), residues: 1295 loop : 0.02 (0.09), residues: 4452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPSU 319 HIS 0.012 0.001 HISNA 621 PHE 0.032 0.001 PHESY 579 TYR 0.026 0.001 TYRSC 216 ARG 0.015 0.000 ARGSK 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21246 Ramachandran restraints generated. 10623 Oldfield, 0 Emsley, 10623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 893 time to evaluate : 9.454 Fit side-chains revert: symmetry clash REVERT: L7 34 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8464 (t) REVERT: L9 161 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7688 (mmm) REVERT: LC 92 ASN cc_start: 0.7835 (m-40) cc_final: 0.7623 (m-40) REVERT: LE 63 ARG cc_start: 0.7541 (ttm110) cc_final: 0.7279 (mtt-85) REVERT: LE 127 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: LE 149 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6737 (tm-30) REVERT: LG 15 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7290 (ttp-170) REVERT: LL 28 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: LW 85 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7292 (tptt) REVERT: NA 352 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6180 (mt) REVERT: NA 358 MET cc_start: 0.6549 (ttp) cc_final: 0.6313 (ttp) REVERT: NA 362 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7637 (tt) REVERT: NB 66 LEU cc_start: 0.8728 (mm) cc_final: 0.8423 (mm) REVERT: NF 42 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8119 (mtp) REVERT: SA 95 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7873 (pmm) REVERT: SA 291 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6719 (ttp-170) REVERT: SA 312 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7331 (ttp-110) REVERT: SC 245 GLN cc_start: 0.7505 (tp40) cc_final: 0.7147 (tp40) REVERT: SC 249 ASP cc_start: 0.7374 (m-30) cc_final: 0.7002 (m-30) REVERT: SI 171 ASN cc_start: 0.6405 (p0) cc_final: 0.6123 (p0) REVERT: SK 134 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8410 (mmtp) REVERT: SL 271 TRP cc_start: 0.6244 (OUTLIER) cc_final: 0.5843 (t-100) REVERT: SR 477 MET cc_start: 0.4660 (mmp) cc_final: 0.3964 (ptt) REVERT: SS 304 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7724 (mtmm) REVERT: ST 246 ARG cc_start: 0.6557 (mmm160) cc_final: 0.6240 (mmm160) REVERT: SU 308 TYR cc_start: 0.7157 (t80) cc_final: 0.6846 (t80) REVERT: SU 692 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6515 (pm20) REVERT: SW 219 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7698 (tp) REVERT: SW 491 ILE cc_start: 0.8126 (mm) cc_final: 0.7889 (mm) outliers start: 133 outliers final: 84 residues processed: 968 average time/residue: 2.1905 time to fit residues: 3010.2605 Evaluate side-chains 991 residues out of total 9477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 890 time to evaluate : 8.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 116 MET Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 64 THR Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L8 residue 55 MET Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 161 MET Chi-restraints excluded: chain LA residue 7 ASP Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LB residue 7 HIS Chi-restraints excluded: chain LB residue 111 SER Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LE residue 99 SER Chi-restraints excluded: chain LE residue 127 GLN Chi-restraints excluded: chain LE residue 149 GLU Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 45 ILE Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 87 MET Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 57 VAL Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 160 ILE Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LS residue 30 GLN Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 85 LYS Chi-restraints excluded: chain NA residue 352 LEU Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 416 CYS Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 53 SER Chi-restraints excluded: chain NB residue 58 GLU Chi-restraints excluded: chain NF residue 42 MET Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 126 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 289 LEU Chi-restraints excluded: chain SA residue 291 ARG Chi-restraints excluded: chain SC residue 96 VAL Chi-restraints excluded: chain SC residue 258 LEU Chi-restraints excluded: chain SD residue 121 THR Chi-restraints excluded: chain SE residue 201 THR Chi-restraints excluded: chain SE residue 222 ILE Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SH residue 181 ILE Chi-restraints excluded: chain SI residue 227 THR Chi-restraints excluded: chain SJ residue 799 THR Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 134 LYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 440 LEU Chi-restraints excluded: chain SN residue 135 ASP Chi-restraints excluded: chain SO residue 180 LEU Chi-restraints excluded: chain SQ residue 216 GLN Chi-restraints excluded: chain SR residue 32 THR Chi-restraints excluded: chain SR residue 54 THR Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 328 LEU Chi-restraints excluded: chain SS residue 341 SER Chi-restraints excluded: chain SS residue 343 LEU Chi-restraints excluded: chain ST residue 222 MET Chi-restraints excluded: chain SU residue 230 GLU Chi-restraints excluded: chain SU residue 254 VAL Chi-restraints excluded: chain SU residue 515 LEU Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SU residue 564 HIS Chi-restraints excluded: chain SU residue 578 LEU Chi-restraints excluded: chain SU residue 596 THR Chi-restraints excluded: chain SU residue 668 GLN Chi-restraints excluded: chain SU residue 692 GLU Chi-restraints excluded: chain SW residue 219 LEU Chi-restraints excluded: chain SW residue 435 CYS Chi-restraints excluded: chain SW residue 480 LEU Chi-restraints excluded: chain SW residue 554 SER Chi-restraints excluded: chain SY residue 451 VAL Chi-restraints excluded: chain SY residue 576 MET Chi-restraints excluded: chain SZ residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1304 random chunks: chunk 634 optimal weight: 4.9990 chunk 821 optimal weight: 3.9990 chunk 1101 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 953 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 287 optimal weight: 0.5980 chunk 1036 optimal weight: 9.9990 chunk 433 optimal weight: 5.9990 chunk 1063 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L6 19 GLN L6 104 ASN L8 44 GLN LA 93 HIS ** LE 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 30 GLN NA 343 ASN NA 484 GLN ** NA 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS NH 124 ASN ** NK 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SA 317 ASN ** SC 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SE 112 GLN SE 206 GLN SG 42 ASN SI 71 GLN ** SJ 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 10 ASN SL 112 GLN ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 217 GLN SR 351 ASN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 402 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.096904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.067388 restraints weight = 336755.461| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.82 r_work: 0.2917 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 146373 Z= 0.346 Angle : 0.558 12.173 209436 Z= 0.287 Chirality : 0.039 0.410 25306 Planarity : 0.005 0.085 17463 Dihedral : 21.311 177.604 51023 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.56 % Allowed : 12.38 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.08), residues: 10623 helix: 2.27 (0.07), residues: 4893 sheet: 0.28 (0.14), residues: 1289 loop : -0.07 (0.09), residues: 4441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPSU 319 HIS 0.012 0.001 HISNA 621 PHE 0.036 0.002 PHESY 579 TYR 0.028 0.002 TYRSN 202 ARG 0.016 0.001 ARGSK 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48439.16 seconds wall clock time: 838 minutes 45.50 seconds (50325.50 seconds total)