Starting phenix.real_space_refine on Sun Mar 17 04:51:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkt_29256/03_2024/8fkt_29256_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkt_29256/03_2024/8fkt_29256.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkt_29256/03_2024/8fkt_29256_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkt_29256/03_2024/8fkt_29256_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkt_29256/03_2024/8fkt_29256_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkt_29256/03_2024/8fkt_29256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkt_29256/03_2024/8fkt_29256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkt_29256/03_2024/8fkt_29256_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkt_29256/03_2024/8fkt_29256_neut_updated.pdb" } resolution = 2.81 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= 0.047 sd= 0.170 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 4 7.16 5 Zn 2 6.06 5 P 2352 5.49 5 Mg 64 5.21 5 S 346 5.16 5 C 75873 2.51 5 N 25076 2.21 5 O 31227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BA GLU 9": "OE1" <-> "OE2" Residue "BA TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA GLU 21": "OE1" <-> "OE2" Residue "BA GLU 72": "OE1" <-> "OE2" Residue "BA GLU 108": "OE1" <-> "OE2" Residue "BA GLU 124": "OE1" <-> "OE2" Residue "BA ASP 150": "OD1" <-> "OD2" Residue "BA GLU 161": "OE1" <-> "OE2" Residue "L6 GLU 79": "OE1" <-> "OE2" Residue "L6 GLU 119": "OE1" <-> "OE2" Residue "L7 GLU 39": "OE1" <-> "OE2" Residue "L7 GLU 162": "OE1" <-> "OE2" Residue "L7 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ASP 190": "OD1" <-> "OD2" Residue "L8 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ASP 29": "OD1" <-> "OD2" Residue "L8 ASP 32": "OD1" <-> "OD2" Residue "L8 ASP 81": "OD1" <-> "OD2" Residue "L8 GLU 96": "OE1" <-> "OE2" Residue "L8 GLU 99": "OE1" <-> "OE2" Residue "L9 GLU 9": "OE1" <-> "OE2" Residue "L9 PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 GLU 103": "OE1" <-> "OE2" Residue "L9 GLU 104": "OE1" <-> "OE2" Residue "L9 GLU 131": "OE1" <-> "OE2" Residue "L9 ASP 147": "OD1" <-> "OD2" Residue "LA GLU 9": "OE1" <-> "OE2" Residue "LA ASP 108": "OD1" <-> "OD2" Residue "LB GLU 17": "OE1" <-> "OE2" Residue "LB ASP 129": "OD1" <-> "OD2" Residue "LC TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC GLU 60": "OE1" <-> "OE2" Residue "LC ASP 85": "OD1" <-> "OD2" Residue "LC GLU 96": "OE1" <-> "OE2" Residue "LC GLU 130": "OE1" <-> "OE2" Residue "LE GLU 118": "OE1" <-> "OE2" Residue "LE GLU 147": "OE1" <-> "OE2" Residue "LE GLU 152": "OE1" <-> "OE2" Residue "LE GLU 157": "OE1" <-> "OE2" Residue "LG ASP 59": "OD1" <-> "OD2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG ASP 100": "OD1" <-> "OD2" Residue "LI GLU 88": "OE1" <-> "OE2" Residue "LI ASP 114": "OD1" <-> "OD2" Residue "LN TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 140": "OE1" <-> "OE2" Residue "LN GLU 147": "OE1" <-> "OE2" Residue "LN GLU 192": "OE1" <-> "OE2" Residue "LN GLU 199": "OE1" <-> "OE2" Residue "LN GLU 279": "OE1" <-> "OE2" Residue "LN PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 395": "OD1" <-> "OD2" Residue "LQ ASP 26": "OD1" <-> "OD2" Residue "LQ ASP 42": "OD1" <-> "OD2" Residue "LQ PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ GLU 86": "OE1" <-> "OE2" Residue "LQ GLU 132": "OE1" <-> "OE2" Residue "LQ GLU 133": "OE1" <-> "OE2" Residue "LS GLU 15": "OE1" <-> "OE2" Residue "LS ASP 22": "OD1" <-> "OD2" Residue "LS GLU 27": "OE1" <-> "OE2" Residue "LS GLU 67": "OE1" <-> "OE2" Residue "LS TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 89": "OE1" <-> "OE2" Residue "NB GLU 63": "OE1" <-> "OE2" Residue "NF GLU 31": "OE1" <-> "OE2" Residue "NF TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH ASP 42": "OD1" <-> "OD2" Residue "NH ASP 61": "OD1" <-> "OD2" Residue "NI ASP 321": "OD1" <-> "OD2" Residue "NI GLU 577": "OE1" <-> "OE2" Residue "NI ASP 677": "OD1" <-> "OD2" Residue "NK GLU 16": "OE1" <-> "OE2" Residue "NM ASP 9": "OD1" <-> "OD2" Residue "NM PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NM GLU 56": "OE1" <-> "OE2" Residue "NM TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NM ASP 159": "OD1" <-> "OD2" Residue "NO GLU 106": "OE1" <-> "OE2" Residue "NO PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NO GLU 341": "OE1" <-> "OE2" Residue "NQ ASP 105": "OD1" <-> "OD2" Residue "NQ TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NS ASP 150": "OD1" <-> "OD2" Residue "NS PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NS PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NS GLU 300": "OE1" <-> "OE2" Residue "NS GLU 339": "OE1" <-> "OE2" Residue "SA GLU 13": "OE1" <-> "OE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 155": "OE1" <-> "OE2" Residue "SA TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 297": "OE1" <-> "OE2" Residue "SA ASP 352": "OD1" <-> "OD2" Residue "SC TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 119": "OE1" <-> "OE2" Residue "SC TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 231": "OE1" <-> "OE2" Residue "SC GLU 238": "OE1" <-> "OE2" Residue "SD GLU 68": "OE1" <-> "OE2" Residue "SD ASP 171": "OD1" <-> "OD2" Residue "SD ASP 238": "OD1" <-> "OD2" Residue "SE GLU 105": "OE1" <-> "OE2" Residue "SE GLU 119": "OE1" <-> "OE2" Residue "SE ASP 162": "OD1" <-> "OD2" Residue "SE GLU 165": "OE1" <-> "OE2" Residue "SE GLU 210": "OE1" <-> "OE2" Residue "SG ASP 11": "OD1" <-> "OD2" Residue "SG ASP 37": "OD1" <-> "OD2" Residue "SG ASP 58": "OD1" <-> "OD2" Residue "SG ASP 171": "OD1" <-> "OD2" Residue "SH PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH ASP 133": "OD1" <-> "OD2" Residue "SH ASP 182": "OD1" <-> "OD2" Residue "SH ASP 184": "OD1" <-> "OD2" Residue "SJ PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ GLU 696": "OE1" <-> "OE2" Residue "SJ GLU 698": "OE1" <-> "OE2" Residue "SJ GLU 700": "OE1" <-> "OE2" Residue "SJ GLU 725": "OE1" <-> "OE2" Residue "SJ GLU 839": "OE1" <-> "OE2" Residue "SK GLU 12": "OE1" <-> "OE2" Residue "SK TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 32": "OE1" <-> "OE2" Residue "SK ASP 171": "OD1" <-> "OD2" Residue "SL GLU 108": "OE1" <-> "OE2" Residue "SL ASP 153": "OD1" <-> "OD2" Residue "SL ASP 196": "OD1" <-> "OD2" Residue "SL PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM ASP 33": "OD1" <-> "OD2" Residue "SM GLU 100": "OE1" <-> "OE2" Residue "SN GLU 65": "OE1" <-> "OE2" Residue "SN GLU 162": "OE1" <-> "OE2" Residue "SN PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO ASP 212": "OD1" <-> "OD2" Residue "SO TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO GLU 324": "OE1" <-> "OE2" Residue "SQ TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 83": "OD1" <-> "OD2" Residue "SQ GLU 110": "OE1" <-> "OE2" Residue "SQ GLU 121": "OE1" <-> "OE2" Residue "SQ ASP 123": "OD1" <-> "OD2" Residue "SQ ASP 138": "OD1" <-> "OD2" Residue "SQ GLU 185": "OE1" <-> "OE2" Residue "SQ TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 209": "OD1" <-> "OD2" Residue "SR PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 68": "OD1" <-> "OD2" Residue "SR ASP 194": "OD1" <-> "OD2" Residue "SR GLU 270": "OE1" <-> "OE2" Residue "SR PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 298": "OE1" <-> "OE2" Residue "SR GLU 301": "OE1" <-> "OE2" Residue "SR ASP 302": "OD1" <-> "OD2" Residue "SR ASP 303": "OD1" <-> "OD2" Residue "SR GLU 334": "OE1" <-> "OE2" Residue "SR GLU 379": "OE1" <-> "OE2" Residue "SR ASP 412": "OD1" <-> "OD2" Residue "SR TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS ASP 230": "OD1" <-> "OD2" Residue "SS GLU 254": "OE1" <-> "OE2" Residue "SS GLU 319": "OE1" <-> "OE2" Residue "SS GLU 324": "OE1" <-> "OE2" Residue "SS PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY GLU 384": "OE1" <-> "OE2" Residue "SY PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ GLU 55": "OE1" <-> "OE2" Residue "SZ ASP 61": "OD1" <-> "OD2" Residue "SZ GLU 98": "OE1" <-> "OE2" Residue "SZ ASP 117": "OD1" <-> "OD2" Residue "SZ ASP 143": "OD1" <-> "OD2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 134945 Number of models: 1 Model: "" Number of chains: 65 Chain: "BA" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1208 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "BB" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1057 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 8, 'TRANS': 204} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 686 Unresolved non-hydrogen angles: 858 Unresolved non-hydrogen dihedrals: 573 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 320 Chain: "L1" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3234 Classifications: {'RNA': 152} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 12, 'rna3p_pur': 60, 'rna3p_pyr': 65} Link IDs: {'rna2p': 26, 'rna3p': 125} Chain breaks: 1 Chain: "L2" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1468 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 6, 'rna3p_pur': 21, 'rna3p_pyr': 31} Link IDs: {'rna2p': 16, 'rna3p': 52} Chain breaks: 3 Chain: "L3" Number of atoms: 45561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2125, 45561 Classifications: {'RNA': 2125} Modifications used: {'rna2p_pur': 206, 'rna2p_pyr': 125, 'rna3p_pur': 960, 'rna3p_pyr': 834} Link IDs: {'rna2p': 331, 'rna3p': 1793} Chain breaks: 35 Chain: "L6" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 998 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 110} Chain: "L7" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1634 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 189} Chain: "L8" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "L9" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1546 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "LA" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1286 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 1 Chain: "LB" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1223 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "LC" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1461 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain: "LE" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 747 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain breaks: 2 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 4, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "LG" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "LH" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 813 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "LI" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LK" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 642 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "LN" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2884 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 345} Chain breaks: 2 Chain: "LQ" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1096 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "LS" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "LT" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "LU" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} Chain: "LW" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 612 Classifications: {'peptide': 74} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 70} Chain: "NB" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2424 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 22, 'TRANS': 364} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 642 Unresolved non-hydrogen angles: 814 Unresolved non-hydrogen dihedrals: 526 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 3, 'ASN:plan1': 13, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 18, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 296 Chain: "NF" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1661 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 3 Chain: "NH" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1441 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "NI" Number of atoms: 3866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 3866 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 240} Link IDs: {'PTRANS': 27, 'TRANS': 570} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 895 Unresolved non-hydrogen angles: 1126 Unresolved non-hydrogen dihedrals: 744 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 18, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 463 Chain: "NK" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 581 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "NM" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1550 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "NO" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2487 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain breaks: 1 Chain: "NQ" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2502 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 305} Chain breaks: 1 Chain: "NS" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2529 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 284} Chain: "SA" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2864 Classifications: {'peptide': 360} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 341} Chain: "SC" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1627 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 187} Chain breaks: 2 Chain: "SD" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1985 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 229} Chain: "SE" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1491 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 174} Chain: "SG" Number of atoms: 1526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Conformer: "B" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} bond proxies already assigned to first conformer: 1528 Chain: "SH" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1267 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "SI" Number of atoms: 1887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 228, 1876 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 228, 1876 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain breaks: 1 bond proxies already assigned to first conformer: 1900 Chain: "SJ" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 855 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain breaks: 2 Chain: "SK" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1852 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "SL" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1960 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "SM" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3735 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 432} Chain breaks: 3 Chain: "SN" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1350 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "SO" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2544 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 284} Chain: "SQ" Number of atoms: 1778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Conformer: "B" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} bond proxies already assigned to first conformer: 1797 Chain: "SR" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3695 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 19, 'TRANS': 429} Chain breaks: 1 Chain: "SS" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2116 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 28, 'TRANS': 227} Chain breaks: 1 Chain: "ST" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 787 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 87 Chain: "SV" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1171 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "SW" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3549 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 19, 'TRANS': 424} Chain breaks: 1 Chain: "SY" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2985 Classifications: {'peptide': 378} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 357} Chain: "SZ" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1338 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain breaks: 1 Chain: "L1" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Unusual residues: {' MG': 52} Classifications: {'undetermined': 52} Link IDs: {None: 51} Chain: "L9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "NI" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "NM" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "SA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SR" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' K': 1, ' MG': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "SV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 72847 SG CYSLW 19 88.428 146.351 149.457 1.00 28.75 S ATOM 72875 SG CYSLW 22 89.060 143.606 152.019 1.00 26.89 S ATOM 72966 SG CYSLW 34 91.120 146.815 152.153 1.00 30.94 S ATOM 72985 SG CYSLW 37 91.608 144.471 149.277 1.00 27.85 S ATOM 83626 SG CYSNM 29 105.975 76.787 193.810 1.00 24.17 S ATOM 83742 SG CYSNM 44 111.744 75.191 192.332 1.00 26.70 S ATOM 83705 SG CYSNM 39 110.557 80.794 195.204 1.00 25.64 S ATOM 83526 SG CYSNM 17 108.375 79.704 189.006 1.00 24.05 S ATOM A0JXB SG CYSSV 6 57.471 203.173 236.031 1.00 26.64 S ATOM A0JY4 SG CYSSV 9 53.972 201.993 235.507 1.00 24.99 S ATOM A0K38 SG CYSSV 32 56.670 199.367 236.013 1.00 26.57 S ATOM A0K42 SG CYSSV 36 56.509 201.235 232.809 1.00 25.70 S Time building chain proxies: 51.67, per 1000 atoms: 0.38 Number of scatterers: 134945 At special positions: 0 Unit cell: (239.056, 254.064, 336.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 Fe 4 26.01 K 1 19.00 S 346 16.00 P 2352 15.00 Mg 64 11.99 O 31227 8.00 N 25076 7.00 C 75873 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: 44.70 Conformation dependent library (CDL) restraints added in 12.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4NM 401 " pdb="FE1 SF4NM 401 " - pdb=" SG CYSNM 29 " pdb="FE2 SF4NM 401 " - pdb=" SG CYSNM 44 " pdb="FE3 SF4NM 401 " - pdb=" SG CYSNM 39 " pdb="FE4 SF4NM 401 " - pdb=" SG CYSNM 17 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " 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 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 12 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20382 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: 402 helices and 89 sheets defined 49.4% alpha, 12.8% beta 755 base pairs and 1185 stacking pairs defined. Time for finding SS restraints: 77.80 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 removed outlier: 4.075A pdb=" N GLYBA 51 " --> pdb=" O ALABA 47 " (cutoff:3.500A) Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.547A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 91 through 96 removed outlier: 5.025A pdb=" N LYSBA 96 " --> pdb=" O ARGBA 92 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 5.186A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.607A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 removed outlier: 3.512A pdb=" N ILEBA 151 " --> pdb=" O HISBA 147 " (cutoff:3.500A) Processing helix chain 'BB' and resid 6 through 25 Processing helix chain 'BB' and resid 70 through 81 Processing helix chain 'BB' and resid 86 through 95 removed outlier: 4.366A pdb=" N LYSBB 95 " --> pdb=" O LYSBB 91 " (cutoff:3.500A) Processing helix chain 'BB' and resid 96 through 108 removed outlier: 4.878A pdb=" N ASPBB 108 " --> pdb=" O ALABB 104 " (cutoff:3.500A) Processing helix chain 'BB' and resid 113 through 124 removed outlier: 4.306A pdb=" N LYSBB 118 " --> pdb=" O GLUBB 114 " (cutoff:3.500A) removed outlier: 4.773A 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: 3.532A 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: 5.248A pdb=" N LYSBB 195 " --> pdb=" O VALBB 191 " (cutoff:3.500A) Processing helix chain 'BB' and resid 197 through 202 removed outlier: 3.927A pdb=" N VALBB 201 " --> pdb=" O ASNBB 197 " (cutoff:3.500A) removed outlier: 5.431A 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: 4.517A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 4.284A 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: 4.153A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.921A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.894A pdb=" N ILEL7 22 " --> pdb=" O ARGL7 18 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 61 removed outlier: 3.594A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ARGL7 61 " --> pdb=" O PHEL7 57 " (cutoff:3.500A) Processing helix chain 'L7' and resid 75 through 89 removed outlier: 3.537A pdb=" N LEUL7 88 " --> pdb=" O VALL7 84 " (cutoff:3.500A) Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 3.735A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.885A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYSL7 116 " --> pdb=" O TYRL7 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L7' and resid 110 through 116' Processing helix chain 'L7' and resid 124 through 129 Processing helix chain 'L7' and resid 137 through 146 Processing helix chain 'L7' and resid 149 through 190 removed outlier: 5.699A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.571A pdb=" N HISL7 199 " --> pdb=" O VALL7 195 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLYL7 200 " --> pdb=" O LEUL7 196 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.863A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLNL8 56 " --> pdb=" O PHEL8 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'L8' and resid 51 through 56' Processing helix chain 'L8' and resid 69 through 81 Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.579A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 4.127A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 removed outlier: 3.584A pdb=" N LEUL8 136 " --> pdb=" O LYSL8 132 " (cutoff:3.500A) Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.907A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 4.910A 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: 3.772A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.685A 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: 6.180A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.867A 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: 3.645A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 4.156A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLYL9 173 " --> pdb=" O ARGL9 169 " (cutoff:3.500A) Processing helix chain 'L9' and resid 187 through 197 Processing helix chain 'LA' and resid 25 through 37 Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 70 through 77 removed outlier: 4.366A pdb=" N LYSLA 74 " --> pdb=" O CYSLA 70 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLNLA 75 " --> pdb=" O ALALA 71 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLYLA 77 " --> pdb=" O ALALA 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 70 through 77' Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LA' and resid 159 through 176 Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.444A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.623A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.547A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 Processing helix chain 'LB' and resid 146 through 152 removed outlier: 4.085A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 3.547A 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: 5.309A pdb=" N GLNLC 125 " --> pdb=" O ALALC 121 " (cutoff:3.500A) Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.478A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.138A 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: 3.828A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.204A 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: 3.978A 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: 3.515A 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: 3.646A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 92 Processing helix chain 'LH' and resid 105 through 118 Processing helix chain 'LH' and resid 145 through 154 removed outlier: 3.563A pdb=" N VALLH 149 " --> pdb=" O ASPLH 145 " (cutoff:3.500A) Processing helix chain 'LI' and resid 10 through 21 removed outlier: 3.562A pdb=" N ALALI 21 " --> pdb=" O ARGLI 17 " (cutoff:3.500A) Processing helix chain 'LI' and resid 22 through 31 removed outlier: 3.886A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.396A 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: 4.179A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.583A 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: 3.930A pdb=" N LYSLK 10 " --> pdb=" O ARGLK 6 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARGLK 12 " --> pdb=" O THRLK 8 " (cutoff:3.500A) Processing helix chain 'LK' and resid 60 through 67 removed outlier: 5.520A pdb=" N GLNLK 67 " --> pdb=" O LEULK 63 " (cutoff:3.500A) Processing helix chain 'LK' and resid 74 through 83 removed outlier: 4.760A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 94 removed outlier: 4.721A pdb=" N LYSLK 94 " --> pdb=" O ALALK 90 " (cutoff:3.500A) Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.545A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 Processing helix chain 'LN' and resid 111 through 120 removed outlier: 3.952A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 4.275A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 157 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 4.066A 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: 3.577A pdb=" N ARGLN 200 " --> pdb=" O TRPLN 196 " (cutoff:3.500A) Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.870A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 4.044A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) Processing helix chain 'LN' and resid 381 through 390 Processing helix chain 'LN' and resid 392 through 403 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.532A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 5.021A 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: 3.567A pdb=" N GLULQ 86 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.614A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LS' and resid 5 through 11 removed outlier: 3.521A pdb=" N LEULS 9 " --> pdb=" O LYSLS 5 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 removed outlier: 4.118A pdb=" N GLYLS 38 " --> pdb=" O ALALS 34 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 4.139A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 3.831A 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: 5.797A 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: 3.701A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.527A 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: 4.176A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARGLU 30 " --> pdb=" O HISLU 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 25 through 30' Processing helix chain 'LU' and resid 34 through 49 removed outlier: 3.779A pdb=" N GLYLU 49 " --> pdb=" O ARGLU 45 " (cutoff:3.500A) Processing helix chain 'LU' and resid 51 through 64 Processing helix chain 'LU' and resid 65 through 78 removed outlier: 3.663A pdb=" N LYSLU 75 " --> pdb=" O LYSLU 71 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARGLU 76 " --> pdb=" O PHELU 72 " (cutoff:3.500A) Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.733A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 3.528A pdb=" N LYSLW 68 " --> pdb=" O METLW 64 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLYLW 77 " --> pdb=" O ARGLW 73 " (cutoff:3.500A) Processing helix chain 'NB' and resid 14 through 36 Processing helix chain 'NB' and resid 56 through 77 removed outlier: 3.592A pdb=" N LEUNB 60 " --> pdb=" O PHENB 56 " (cutoff:3.500A) Processing helix chain 'NB' and resid 125 through 141 Processing helix chain 'NB' and resid 152 through 158 removed outlier: 3.677A pdb=" N CYSNB 156 " --> pdb=" O ASPNB 152 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N CYSNB 158 " --> pdb=" O LEUNB 154 " (cutoff:3.500A) Processing helix chain 'NB' and resid 159 through 169 Processing helix chain 'NB' and resid 179 through 184 removed outlier: 3.842A pdb=" N VALNB 183 " --> pdb=" O LYSNB 179 " (cutoff:3.500A) Proline residue: NB 184 - end of helix No H-bonds generated for 'chain 'NB' and resid 179 through 184' Processing helix chain 'NB' and resid 185 through 199 removed outlier: 3.642A pdb=" N LYSNB 197 " --> pdb=" O ASNNB 193 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLUNB 198 " --> pdb=" O TYRNB 194 " (cutoff:3.500A) Processing helix chain 'NB' and resid 236 through 252 Processing helix chain 'NB' and resid 266 through 276 Processing helix chain 'NB' and resid 316 through 324 Processing helix chain 'NB' and resid 332 through 345 removed outlier: 3.682A pdb=" N GLNNB 343 " --> pdb=" O ALANB 339 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASPNB 345 " --> pdb=" O LEUNB 341 " (cutoff:3.500A) Processing helix chain 'NB' and resid 346 through 354 Processing helix chain 'NB' and resid 360 through 373 Processing helix chain 'NB' and resid 382 through 396 Processing helix chain 'NB' and resid 416 through 426 removed outlier: 5.047A pdb=" N GLYNB 426 " --> pdb=" O ASPNB 422 " (cutoff:3.500A) Processing helix chain 'NB' and resid 428 through 444 removed outlier: 3.554A pdb=" N LEUNB 432 " --> pdb=" O ASNNB 428 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LYSNB 444 " --> pdb=" O ILENB 440 " (cutoff:3.500A) Processing helix chain 'NB' and resid 447 through 452 removed outlier: 4.962A pdb=" N ILENB 452 " --> pdb=" O LEUNB 448 " (cutoff:3.500A) Processing helix chain 'NF' and resid 5 through 14 Processing helix chain 'NF' and resid 21 through 34 removed outlier: 4.220A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N HISNF 33 " --> pdb=" O SERNF 29 " (cutoff:3.500A) Processing helix chain 'NF' and resid 44 through 72 Processing helix chain 'NF' and resid 97 through 117 Processing helix chain 'NF' and resid 164 through 169 removed outlier: 3.703A pdb=" N GLUNF 168 " --> pdb=" O PRONF 164 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ARGNF 169 " --> pdb=" O PRONF 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'NF' and resid 164 through 169' Processing helix chain 'NF' and resid 205 through 212 Processing helix chain 'NF' and resid 247 through 252 Processing helix chain 'NH' and resid 5 through 20 removed outlier: 3.962A pdb=" N TYRNH 19 " --> pdb=" O LYSNH 15 " (cutoff:3.500A) Processing helix chain 'NH' and resid 22 through 30 removed outlier: 4.528A pdb=" N LEUNH 26 " --> pdb=" O GLUNH 22 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARGNH 30 " --> pdb=" O LEUNH 26 " (cutoff:3.500A) Processing helix chain 'NH' and resid 48 through 59 removed outlier: 4.297A pdb=" N ASNNH 57 " --> pdb=" O LYSNH 53 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILENH 58 " --> pdb=" O LEUNH 54 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SERNH 59 " --> pdb=" O ALANH 55 " (cutoff:3.500A) Processing helix chain 'NH' and resid 82 through 93 removed outlier: 4.476A pdb=" N LEUNH 86 " --> pdb=" O HISNH 82 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASPNH 87 " --> pdb=" O VALNH 83 " (cutoff:3.500A) removed outlier: 5.772A 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: 4.375A pdb=" N GLNNH 105 " --> pdb=" O PRONH 101 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SERNH 106 " --> pdb=" O GLYNH 102 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLYNH 110 " --> pdb=" O SERNH 106 " (cutoff:3.500A) Processing helix chain 'NH' and resid 114 through 119 removed outlier: 5.717A pdb=" N GLYNH 119 " --> pdb=" O LYSNH 115 " (cutoff:3.500A) Processing helix chain 'NH' and resid 149 through 156 removed outlier: 4.121A pdb=" N LYSNH 155 " --> pdb=" O GLNNH 151 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VALNH 156 " --> pdb=" O ASPNH 152 " (cutoff:3.500A) Processing helix chain 'NH' and resid 170 through 175 Processing helix chain 'NI' and resid 97 through 102 removed outlier: 3.993A pdb=" N GLYNI 102 " --> pdb=" O PHENI 98 " (cutoff:3.500A) Processing helix chain 'NI' and resid 104 through 115 Processing helix chain 'NI' and resid 120 through 133 removed outlier: 3.534A pdb=" N LYSNI 125 " --> pdb=" O PRONI 121 " (cutoff:3.500A) Proline residue: NI 128 - end of helix removed outlier: 3.644A pdb=" N GLYNI 133 " --> pdb=" O VALNI 129 " (cutoff:3.500A) Processing helix chain 'NI' and resid 145 through 159 removed outlier: 4.025A pdb=" N CYSNI 149 " --> pdb=" O GLYNI 145 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHENI 150 " --> pdb=" O LYSNI 146 " (cutoff:3.500A) Proline residue: NI 153 - end of helix removed outlier: 3.976A pdb=" N LYSNI 159 " --> pdb=" O PHENI 155 " (cutoff:3.500A) Processing helix chain 'NI' and resid 175 through 191 Processing helix chain 'NI' and resid 205 through 216 removed outlier: 4.131A pdb=" N ASNNI 216 " --> pdb=" O ALANI 212 " (cutoff:3.500A) Processing helix chain 'NI' and resid 223 through 235 Processing helix chain 'NI' and resid 248 through 256 removed outlier: 3.611A pdb=" N GLYNI 256 " --> pdb=" O LEUNI 252 " (cutoff:3.500A) Processing helix chain 'NI' and resid 257 through 269 removed outlier: 3.545A pdb=" N LEUNI 268 " --> pdb=" O ILENI 264 " (cutoff:3.500A) Proline residue: NI 269 - end of helix Processing helix chain 'NI' and resid 282 through 292 Processing helix chain 'NI' and resid 301 through 307 removed outlier: 3.719A pdb=" N THRNI 305 " --> pdb=" O LEUNI 301 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYSNI 306 " --> pdb=" O ASPNI 302 " (cutoff:3.500A) removed outlier: 5.213A 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: 4.735A pdb=" N ALANI 324 " --> pdb=" O GLUNI 320 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALANI 325 " --> pdb=" O ASPNI 321 " (cutoff:3.500A) Processing helix chain 'NI' and resid 347 through 362 removed outlier: 4.278A pdb=" N ARGNI 362 " --> pdb=" O LEUNI 358 " (cutoff:3.500A) Processing helix chain 'NI' and resid 373 through 387 Processing helix chain 'NI' and resid 395 through 403 removed outlier: 5.016A pdb=" N GLYNI 401 " --> pdb=" O LEUNI 397 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEUNI 402 " --> pdb=" O ALANI 398 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASPNI 403 " --> pdb=" O ALANI 399 " (cutoff:3.500A) Processing helix chain 'NI' and resid 418 through 427 removed outlier: 3.619A pdb=" N PHENI 422 " --> pdb=" O LYSNI 418 " (cutoff:3.500A) Processing helix chain 'NI' and resid 443 through 458 removed outlier: 3.554A pdb=" N ILENI 447 " --> pdb=" O ALANI 443 " (cutoff:3.500A) Proline residue: NI 448 - end of helix Processing helix chain 'NI' and resid 472 through 478 removed outlier: 5.494A pdb=" N GLYNI 478 " --> pdb=" O ALANI 474 " (cutoff:3.500A) Processing helix chain 'NI' and resid 486 through 503 removed outlier: 3.537A pdb=" N GLUNI 491 " --> pdb=" O VALNI 487 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLYNI 494 " --> pdb=" O GLUNI 490 " (cutoff:3.500A) removed outlier: 4.806A 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 538 removed outlier: 5.593A pdb=" N ASPNI 538 " --> pdb=" O ALANI 534 " (cutoff:3.500A) Processing helix chain 'NI' and resid 545 through 553 removed outlier: 4.325A pdb=" N ARGNI 551 " --> pdb=" O LEUNI 547 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHENI 552 " --> pdb=" O PHENI 548 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLUNI 553 " --> pdb=" O SERNI 549 " (cutoff:3.500A) Processing helix chain 'NI' and resid 554 through 569 removed outlier: 3.543A pdb=" N LYSNI 567 " --> pdb=" O VALNI 563 " (cutoff:3.500A) Processing helix chain 'NI' and resid 574 through 579 removed outlier: 4.988A 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: 3.790A pdb=" N GLYNI 710 " --> pdb=" O GLNNI 706 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALANI 711 " --> pdb=" O GLNNI 707 " (cutoff:3.500A) Processing helix chain 'NI' and resid 719 through 739 removed outlier: 4.029A pdb=" N THRNI 724 " --> pdb=" O ALANI 720 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARGNI 725 " --> pdb=" O GLNNI 721 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLYNI 726 " --> pdb=" O ASNNI 722 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARGNI 727 " --> pdb=" O LEUNI 723 " (cutoff:3.500A) removed outlier: 4.265A 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 'NM' and resid 3 through 12 Processing helix chain 'NM' and resid 44 through 49 removed outlier: 5.199A pdb=" N SERNM 49 " --> pdb=" O PRONM 45 " (cutoff:3.500A) Processing helix chain 'NM' and resid 67 through 72 removed outlier: 4.426A pdb=" N ALANM 72 " --> pdb=" O ILENM 68 " (cutoff:3.500A) Processing helix chain 'NM' and resid 86 through 99 Processing helix chain 'NM' and resid 102 through 129 Processing helix chain 'NM' and resid 138 through 173 removed outlier: 6.107A pdb=" N LEUNM 158 " --> pdb=" O ILENM 154 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASPNM 159 " --> pdb=" O ALANM 155 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASNNM 160 " --> pdb=" O ALANM 156 " (cutoff:3.500A) Processing helix chain 'NO' and resid 8 through 19 Processing helix chain 'NO' and resid 21 through 43 removed outlier: 5.317A pdb=" N ALANO 43 " --> pdb=" O ARGNO 39 " (cutoff:3.500A) Processing helix chain 'NO' and resid 48 through 66 removed outlier: 3.785A pdb=" N GLNNO 66 " --> pdb=" O CYSNO 62 " (cutoff:3.500A) Processing helix chain 'NO' and resid 68 through 86 removed outlier: 4.648A pdb=" N VALNO 83 " --> pdb=" O ILENO 79 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N HISNO 84 " --> pdb=" O SERNO 80 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALANO 85 " --> pdb=" O GLNNO 81 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHENO 86 " --> pdb=" O LEUNO 82 " (cutoff:3.500A) Processing helix chain 'NO' and resid 88 through 107 Processing helix chain 'NO' and resid 111 through 137 removed outlier: 4.246A pdb=" N ASPNO 116 " --> pdb=" O ARGNO 112 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LYSNO 117 " --> pdb=" O LEUNO 113 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHENO 118 " --> pdb=" O ARGNO 114 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N METNO 124 " --> pdb=" O METNO 120 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEUNO 133 " --> pdb=" O SERNO 129 " (cutoff:3.500A) Processing helix chain 'NO' and resid 139 through 154 Processing helix chain 'NO' and resid 162 through 181 removed outlier: 4.847A pdb=" N LEUNO 174 " --> pdb=" O ILENO 170 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLUNO 175 " --> pdb=" O GLUNO 171 " (cutoff:3.500A) Processing helix chain 'NO' and resid 186 through 204 Proline residue: NO 196 - end of helix removed outlier: 3.550A pdb=" N ARGNO 199 " --> pdb=" O ASPNO 195 " (cutoff:3.500A) Processing helix chain 'NO' and resid 206 through 248 removed outlier: 4.365A pdb=" N GLUNO 219 " --> pdb=" O ARGNO 215 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THRNO 220 " --> pdb=" O GLYNO 216 " (cutoff:3.500A) Proline residue: NO 226 - end of helix Processing helix chain 'NO' and resid 299 through 313 removed outlier: 3.877A pdb=" N ARGNO 313 " --> pdb=" O GLUNO 309 " (cutoff:3.500A) Processing helix chain 'NO' and resid 317 through 337 removed outlier: 3.504A pdb=" N VALNO 327 " --> pdb=" O ARGNO 323 " (cutoff:3.500A) Processing helix chain 'NO' and resid 345 through 353 removed outlier: 3.543A pdb=" N LEUNO 352 " --> pdb=" O ALANO 348 " (cutoff:3.500A) Processing helix chain 'NQ' and resid 1 through 7 removed outlier: 4.381A pdb=" N ARGNQ 7 " --> pdb=" O ALANQ 3 " (cutoff:3.500A) Processing helix chain 'NS' and resid 59 through 93 Processing helix chain 'NS' and resid 104 through 109 Processing helix chain 'NS' and resid 120 through 130 Processing helix chain 'NS' and resid 132 through 138 Processing helix chain 'NS' and resid 153 through 168 Proline residue: NS 168 - end of helix Processing helix chain 'NS' and resid 179 through 191 Proline residue: NS 185 - end of helix Processing helix chain 'NS' and resid 228 through 233 removed outlier: 5.511A pdb=" N LYSNS 233 " --> pdb=" O ARGNS 229 " (cutoff:3.500A) Processing helix chain 'NS' and resid 253 through 268 removed outlier: 3.525A pdb=" N LEUNS 266 " --> pdb=" O METNS 262 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHENS 267 " --> pdb=" O PHENS 263 " (cutoff:3.500A) Proline residue: NS 268 - end of helix Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.443A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALASA 30 " --> pdb=" O ALASA 26 " (cutoff:3.500A) Proline residue: SA 31 - end of helix No H-bonds generated for 'chain 'SA' and resid 25 through 31' Processing helix chain 'SA' and resid 33 through 49 removed outlier: 4.051A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.577A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.759A 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: 3.914A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.382A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 3.912A 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: 3.783A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLNSA 187 " --> pdb=" O VALSA 183 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.576A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.511A pdb=" N LYSSA 259 " --> pdb=" O SERSA 255 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 Processing helix chain 'SA' and resid 296 through 303 removed outlier: 4.406A pdb=" N ARGSA 300 " --> pdb=" O PROSA 296 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEUSA 302 " --> pdb=" O ILESA 298 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 296 through 303' Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.497A 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: 4.475A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SC' and resid 47 through 54 removed outlier: 3.754A pdb=" N VALSC 51 " --> pdb=" O ASNSC 47 " (cutoff:3.500A) Processing helix chain 'SC' and resid 58 through 74 removed outlier: 3.519A pdb=" N LYSSC 70 " --> pdb=" O LYSSC 66 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYRSC 73 " --> pdb=" O TYRSC 69 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.962A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.526A 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: 4.003A 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: 5.196A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.499A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 15 through 79 removed outlier: 3.617A pdb=" N ILESD 30 " --> pdb=" O ALASD 26 " (cutoff:3.500A) removed outlier: 3.674A 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: 3.607A pdb=" N METSD 132 " --> pdb=" O ALASD 128 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.171A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.679A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 3.577A pdb=" N LEUSD 208 " --> pdb=" O ALASD 204 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 238 through 248 removed outlier: 4.824A pdb=" N ARGSD 242 " --> pdb=" O ASPSD 238 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.830A pdb=" N ALASE 68 " --> pdb=" O GLNSE 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.568A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.618A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARGSE 103 " --> pdb=" O ALASE 99 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 124 removed outlier: 3.932A pdb=" N GLYSE 124 " --> pdb=" O LYSSE 120 " (cutoff:3.500A) Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 169 through 178 Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.678A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 231 removed outlier: 4.867A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASNSE 227 " --> pdb=" O ARGSE 223 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASPSE 228 " --> pdb=" O THRSE 224 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARGSE 229 " --> pdb=" O ASNSE 225 " (cutoff:3.500A) Processing helix chain 'SE' and resid 232 through 237 removed outlier: 4.150A pdb=" N HISSE 236 " --> pdb=" O GLUSE 232 " (cutoff:3.500A) removed outlier: 5.377A 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: 3.529A pdb=" N ALASG 68 " --> pdb=" O ARGSG 64 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.890A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.875A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.664A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLYSH 69 " --> pdb=" O PHESH 65 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SH' and resid 122 through 127 removed outlier: 5.881A 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: 3.519A pdb=" N PHESI 64 " --> pdb=" O ARGSI 60 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.137A 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: 3.610A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 5.184A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.198A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 5.172A 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: 4.419A 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) removed outlier: 3.575A pdb=" N GLNSI 253 " --> pdb=" O GLNSI 249 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 664 through 677 Processing helix chain 'SJ' and resid 678 through 690 removed outlier: 3.828A pdb=" N PHESJ 689 " --> pdb=" O ILESJ 685 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASNSJ 690 " --> pdb=" O ASPSJ 686 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 702 through 713 removed outlier: 3.761A pdb=" N GLNSJ 711 " --> pdb=" O GLNSJ 707 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HISSJ 712 " --> pdb=" O GLUSJ 708 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 720 through 731 removed outlier: 4.420A pdb=" N ARGSJ 730 " --> pdb=" O HISSJ 726 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRPSJ 731 " --> pdb=" O TYRSJ 727 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 825 through 843 removed outlier: 4.228A pdb=" N LYSSJ 829 " --> pdb=" O ASPSJ 825 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYSSJ 830 " --> pdb=" O SERSJ 826 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASPSJ 831 " --> pdb=" O ARGSJ 827 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 4.029A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.606A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 4.740A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 88 Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.542A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.363A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 229 through 237 removed outlier: 4.741A pdb=" N ALASK 233 " --> pdb=" O PROSK 229 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THRSK 234 " --> pdb=" O SERSK 230 " (cutoff:3.500A) Processing helix chain 'SK' and resid 238 through 244 Processing helix chain 'SL' and resid 32 through 50 Processing helix chain 'SL' and resid 106 through 122 Processing helix chain 'SL' and resid 131 through 138 Processing helix chain 'SL' and resid 141 through 153 removed outlier: 3.706A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 166 removed outlier: 3.749A pdb=" N ARGSL 162 " --> pdb=" O ASPSL 158 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) Proline residue: SL 166 - end of helix Processing helix chain 'SL' and resid 170 through 177 removed outlier: 3.957A 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 'SM' and resid 13 through 18 removed outlier: 5.215A pdb=" N ILESM 18 " --> pdb=" O ALASM 14 " (cutoff:3.500A) Processing helix chain 'SM' and resid 19 through 28 Processing helix chain 'SM' and resid 30 through 42 Processing helix chain 'SM' and resid 50 through 56 removed outlier: 3.630A pdb=" N VALSM 54 " --> pdb=" O HISSM 50 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 77 removed outlier: 4.005A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 3.910A 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: 3.623A pdb=" N LYSSM 86 " --> pdb=" O PHESM 82 " (cutoff:3.500A) Processing helix chain 'SM' and resid 100 through 111 Processing helix chain 'SM' and resid 116 through 125 Proline residue: SM 125 - end of helix Processing helix chain 'SM' and resid 126 through 135 removed outlier: 3.580A pdb=" N ASPSM 133 " --> pdb=" O ASPSM 129 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) Processing helix chain 'SM' and resid 136 through 148 removed outlier: 4.028A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.511A pdb=" N METSM 220 " --> pdb=" O ASPSM 216 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEUSM 242 " --> pdb=" O LEUSM 238 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 3.951A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.690A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEUSM 326 " --> pdb=" O LYSSM 322 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.551A pdb=" N GLYSM 351 " --> pdb=" O ILESM 347 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.484A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.459A 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: 3.526A 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 removed outlier: 3.503A pdb=" N LEUSN 126 " --> pdb=" O ARGSN 122 " (cutoff:3.500A) Processing helix chain 'SN' and resid 143 through 177 removed outlier: 4.098A pdb=" N GLUSN 165 " --> pdb=" O METSN 161 " (cutoff:3.500A) Processing helix chain 'SN' and resid 178 through 205 removed outlier: 3.745A pdb=" N METSN 195 " --> pdb=" O GLUSN 191 " (cutoff:3.500A) Processing helix chain 'SO' and resid 71 through 86 Proline residue: SO 86 - end of helix Processing helix chain 'SO' and resid 99 through 111 removed outlier: 4.270A pdb=" N ILESO 103 " --> pdb=" O LYSSO 99 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASNSO 104 " --> pdb=" O LEUSO 100 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLUSO 105 " --> pdb=" O PHESO 101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N METSO 109 " --> pdb=" O GLUSO 105 " (cutoff:3.500A) Processing helix chain 'SO' and resid 169 through 175 removed outlier: 4.525A pdb=" N ASPSO 173 " --> pdb=" O ASPSO 169 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLUSO 174 " --> pdb=" O PROSO 170 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEUSO 175 " --> pdb=" O ALASO 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'SO' and resid 169 through 175' Processing helix chain 'SO' and resid 176 through 190 Processing helix chain 'SO' and resid 261 through 293 removed outlier: 3.569A pdb=" N HISSO 265 " --> pdb=" O SERSO 261 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYRSO 277 " --> pdb=" O THRSO 273 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEUSO 289 " --> pdb=" O ASPSO 285 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLUSO 293 " --> pdb=" O LEUSO 289 " (cutoff:3.500A) Processing helix chain 'SO' and resid 303 through 309 removed outlier: 4.779A pdb=" N PHESO 307 " --> pdb=" O THRSO 303 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VALSO 308 " --> pdb=" O ALASO 304 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N THRSO 309 " --> pdb=" O ASPSO 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'SO' and resid 303 through 309' Processing helix chain 'SO' and resid 337 through 353 Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.245A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 50 through 61 removed outlier: 4.776A pdb=" N LYSSQ 54 " --> pdb=" O ASNSQ 50 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASPSQ 55 " --> pdb=" O SERSQ 51 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 4.139A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.308A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 149 through 157 Processing helix chain 'SQ' and resid 183 through 194 Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 68 removed outlier: 3.508A pdb=" N LYSSR 50 " --> pdb=" O PHESR 46 " (cutoff:3.500A) Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 120 removed outlier: 3.632A pdb=" N ASPSR 107 " --> pdb=" O LYSSR 103 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 145 removed outlier: 3.648A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) Processing helix chain 'SR' and resid 146 through 162 removed outlier: 3.514A pdb=" N ARGSR 160 " --> pdb=" O GLNSR 156 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.544A pdb=" N ASNSR 186 " --> pdb=" O SERSR 182 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VALSR 188 " --> pdb=" O PHESR 184 " (cutoff:3.500A) Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.563A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 229 through 234' Processing helix chain 'SR' and resid 235 through 247 removed outlier: 4.106A 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: 4.397A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 290 through 295 removed outlier: 3.805A pdb=" N LYSSR 294 " --> pdb=" O LYSSR 290 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARGSR 295 " --> pdb=" O CYSSR 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 290 through 295' Processing helix chain 'SR' and resid 300 through 314 removed outlier: 3.559A pdb=" N ILESR 306 " --> pdb=" O ASPSR 302 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 4.662A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 3.926A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.089A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 417 removed outlier: 4.684A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 417' Processing helix chain 'SR' and resid 437 through 442 removed outlier: 3.995A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 442' Processing helix chain 'SR' and resid 445 through 463 Processing helix chain 'SR' and resid 422 through 427 removed outlier: 3.832A pdb=" N LYSSR 425 " --> pdb=" O LEUSR 422 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N HISSR 426 " --> pdb=" O SERSR 423 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASPSR 427 " --> pdb=" O GLUSR 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 422 through 427' Processing helix chain 'SS' and resid 140 through 146 removed outlier: 4.515A pdb=" N TYRSS 144 " --> pdb=" O PROSS 140 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASPSS 145 " --> pdb=" O LEUSS 141 " (cutoff:3.500A) removed outlier: 4.824A 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 180 through 185 removed outlier: 5.974A pdb=" N VALSS 185 " --> pdb=" O TYRSS 181 " (cutoff:3.500A) Processing helix chain 'SS' and resid 197 through 210 Processing helix chain 'SS' and resid 242 through 248 removed outlier: 3.795A pdb=" N PHESS 246 " --> pdb=" O ASPSS 242 " (cutoff:3.500A) Proline residue: SS 248 - end of helix Processing helix chain 'SS' and resid 249 through 266 removed outlier: 3.522A pdb=" N LYSSS 253 " --> pdb=" O SERSS 249 " (cutoff:3.500A) Processing helix chain 'SS' and resid 323 through 334 removed outlier: 5.637A pdb=" N GLUSS 334 " --> pdb=" O TRPSS 330 " (cutoff:3.500A) Processing helix chain 'SS' and resid 358 through 372 removed outlier: 3.876A pdb=" N TYRSS 371 " --> pdb=" O CYSSS 367 " (cutoff:3.500A) Processing helix chain 'SS' and resid 384 through 390 Proline residue: SS 390 - end of helix Processing helix chain 'ST' and resid 169 through 198 removed outlier: 4.784A pdb=" N LYSST 198 " --> pdb=" O ALAST 194 " (cutoff:3.500A) Processing helix chain 'ST' and resid 214 through 229 removed outlier: 4.173A pdb=" N THRST 229 " --> pdb=" O ALAST 225 " (cutoff:3.500A) Processing helix chain 'ST' and resid 260 through 276 Processing helix chain 'SV' and resid 33 through 43 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.366A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 removed outlier: 3.644A pdb=" N ARGSV 56 " --> pdb=" O THRSV 52 " (cutoff:3.500A) Processing helix chain 'SV' and resid 66 through 72 removed outlier: 3.861A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLUSV 72 " --> pdb=" O SERSV 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 72' Processing helix chain 'SV' and resid 82 through 135 removed outlier: 3.591A pdb=" N ARGSV 111 " --> pdb=" O PHESV 107 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEUSV 118 " --> pdb=" O LYSSV 114 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILESV 134 " --> pdb=" O ASNSV 130 " (cutoff:3.500A) Processing helix chain 'SW' and resid 178 through 187 removed outlier: 4.227A pdb=" N LEUSW 182 " --> pdb=" O SERSW 178 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASNSW 184 " --> pdb=" O ALASW 180 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEUSW 185 " --> pdb=" O SERSW 181 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASNSW 187 " --> pdb=" O CYSSW 183 " (cutoff:3.500A) Processing helix chain 'SW' and resid 188 through 198 Processing helix chain 'SW' and resid 203 through 216 removed outlier: 4.346A 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 Processing helix chain 'SW' and resid 290 through 301 Processing helix chain 'SW' and resid 308 through 318 Processing helix chain 'SW' and resid 334 through 342 Processing helix chain 'SW' and resid 343 through 355 Proline residue: SW 355 - end of helix Processing helix chain 'SW' and resid 368 through 379 removed outlier: 3.544A pdb=" N ILESW 377 " --> pdb=" O ASPSW 373 " (cutoff:3.500A) Processing helix chain 'SW' and resid 408 through 424 removed outlier: 4.874A pdb=" N PHESW 413 " --> pdb=" O SERSW 409 " (cutoff:3.500A) removed outlier: 5.125A 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 531 through 545 removed outlier: 3.506A pdb=" N LEUSW 535 " --> pdb=" O ARGSW 531 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLYSW 536 " --> pdb=" O PROSW 532 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHESW 537 " --> pdb=" O GLUSW 533 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEUSW 538 " --> pdb=" O GLUSW 534 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARGSW 539 " --> pdb=" O LEUSW 535 " (cutoff:3.500A) Processing helix chain 'SW' and resid 561 through 573 removed outlier: 5.103A pdb=" N TYRSW 573 " --> pdb=" O ILESW 569 " (cutoff:3.500A) Processing helix chain 'SW' and resid 574 through 593 Processing helix chain 'SW' and resid 595 through 600 Processing helix chain 'SW' and resid 605 through 614 Processing helix chain 'SY' and resid 223 through 234 Proline residue: SY 234 - end of helix Processing helix chain 'SY' and resid 235 through 253 Processing helix chain 'SY' and resid 262 through 279 Processing helix chain 'SY' and resid 281 through 292 removed outlier: 3.510A pdb=" N ASPSY 290 " --> pdb=" O GLYSY 286 " (cutoff:3.500A) Processing helix chain 'SY' and resid 294 through 307 removed outlier: 4.236A pdb=" N VALSY 298 " --> pdb=" O LEUSY 294 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLUSY 299 " --> pdb=" O SERSY 295 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLUSY 305 " --> pdb=" O LEUSY 301 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VALSY 306 " --> pdb=" O GLUSY 302 " (cutoff:3.500A) Proline residue: SY 307 - end of helix Processing helix chain 'SY' and resid 320 through 332 Processing helix chain 'SY' and resid 358 through 364 Processing helix chain 'SY' and resid 370 through 381 removed outlier: 3.615A pdb=" N LEUSY 375 " --> pdb=" O ALASY 371 " (cutoff:3.500A) Proline residue: SY 376 - end of helix Processing helix chain 'SY' and resid 396 through 407 Processing helix chain 'SY' and resid 419 through 433 removed outlier: 4.043A pdb=" N LYSSY 423 " --> pdb=" O ALASY 419 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SERSY 424 " --> pdb=" O GLUSY 420 " (cutoff:3.500A) Processing helix chain 'SY' and resid 468 through 473 Proline residue: SY 473 - end of helix Processing helix chain 'SY' and resid 480 through 503 removed outlier: 3.766A pdb=" N GLUSY 493 " --> pdb=" O HISSY 489 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASNSY 503 " --> pdb=" O ILESY 499 " (cutoff:3.500A) Processing helix chain 'SY' and resid 520 through 535 removed outlier: 3.591A pdb=" N GLUSY 525 " --> pdb=" O VALSY 521 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TRPSY 526 " --> pdb=" O GLUSY 522 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VALSY 527 " --> pdb=" O GLUSY 523 " (cutoff:3.500A) Processing helix chain 'SY' and resid 560 through 566 Processing helix chain 'SY' and resid 570 through 575 removed outlier: 3.515A pdb=" N ASNSY 575 " --> pdb=" O TYRSY 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'SY' and resid 570 through 575' Processing helix chain 'SZ' and resid 6 through 12 removed outlier: 4.000A pdb=" N ARGSZ 10 " --> pdb=" O GLYSZ 6 " (cutoff:3.500A) removed outlier: 5.509A 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 removed outlier: 3.541A pdb=" N ALASZ 42 " --> pdb=" O HISSZ 38 " (cutoff:3.500A) 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: 4.724A pdb=" N LEUSZ 94 " --> pdb=" O LYSSZ 90 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASNSZ 95 " --> pdb=" O PROSZ 91 " (cutoff:3.500A) removed outlier: 3.735A 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 136 Processing helix chain 'SZ' and resid 144 through 159 Processing helix chain 'SZ' and resid 160 through 178 Processing sheet with id= 1, first strand: chain 'BA' and resid 11 through 17 removed outlier: 4.329A 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: 6.945A pdb=" N LEUBB 163 " --> pdb=" O LEUBB 38 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VALBB 32 " --> pdb=" O VALBB 169 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 6, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 7, first strand: chain 'L8' and resid 11 through 15 removed outlier: 4.425A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) removed outlier: 6.782A 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: 6.406A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.791A 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: 3.864A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LA' and resid 14 through 20 removed outlier: 6.803A pdb=" N ILELA 149 " --> pdb=" O GLULA 115 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LA' and resid 116 through 122 Processing sheet with id= 12, first strand: chain 'LB' and resid 78 through 82 Processing sheet with id= 13, first strand: chain 'LB' and resid 98 through 101 Processing sheet with id= 14, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.605A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.275A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.824A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LE' and resid 39 through 43 removed outlier: 4.136A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 19, first strand: chain 'LG' and resid 35 through 39 removed outlier: 5.598A pdb=" N LYSLG 35 " --> pdb=" O CYSLG 28 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASNLG 101 " --> pdb=" O VALLG 25 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILELG 105 " --> pdb=" O ALALG 29 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LG' and resid 87 through 90 removed outlier: 4.297A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LG' and resid 82 through 85 removed outlier: 4.918A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.549A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.556A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LI' and resid 71 through 75 removed outlier: 3.570A pdb=" N GLNLI 72 " --> pdb=" O TYRLI 81 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.680A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 27, first strand: chain 'LN' and resid 41 through 44 removed outlier: 6.597A pdb=" N GLNLN 184 " --> pdb=" O THRLN 44 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LN' and resid 53 through 58 removed outlier: 6.730A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HISLN 275 " --> pdb=" O THRLN 223 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.775A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (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: 3.770A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 33, first strand: chain 'LT' and resid 56 through 60 removed outlier: 5.880A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THRLT 59 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LT' and resid 8 through 12 removed outlier: 6.060A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LT' and resid 6 through 10 Processing sheet with id= 36, first strand: chain 'LW' and resid 15 through 18 removed outlier: 8.474A pdb=" N THRLW 15 " --> pdb=" O HISLW 28 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HISLW 28 " --> pdb=" O THRLW 15 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N THRLW 17 " --> pdb=" O ALALW 26 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'NB' and resid 200 through 204 removed outlier: 3.532A pdb=" N PHENB 204 " --> pdb=" O LEUNB 177 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYSNB 172 " --> pdb=" O ASPNB 142 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLYNB 261 " --> pdb=" O SERNB 306 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'NF' and resid 189 through 194 removed outlier: 3.629A pdb=" N ALANF 190 " --> pdb=" O HISNF 185 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASNNF 255 " --> pdb=" O THRNF 245 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYRNF 241 " --> pdb=" O LEUNF 259 " (cutoff:3.500A) removed outlier: 4.586A 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: 6.997A pdb=" N VALNH 44 " --> pdb=" O PHENH 70 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'NH' and resid 95 through 99 removed outlier: 4.872A pdb=" N TYRNH 95 " --> pdb=" O GLYNH 130 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'NI' and resid 196 through 200 removed outlier: 3.785A pdb=" N ALANI 169 " --> pdb=" O ASPNI 218 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALNI 136 " --> pdb=" O THRNI 274 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALANI 140 " --> pdb=" O SERNI 278 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'NI' and resid 364 through 368 removed outlier: 4.151A pdb=" N METNI 479 " --> pdb=" O THRNI 313 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'NM' and resid 51 through 56 removed outlier: 5.278A pdb=" N CYSNM 61 " --> pdb=" O LEUNM 83 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'NQ' and resid 28 through 34 removed outlier: 4.302A pdb=" N ILENQ 19 " --> pdb=" O THRNQ 15 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N HISNQ 10 " --> pdb=" O SERNQ 320 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYSNQ 316 " --> pdb=" O GLYNQ 14 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'NQ' and resid 46 through 51 removed outlier: 4.393A pdb=" N ALANQ 47 " --> pdb=" O GLYNQ 61 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLNNQ 57 " --> pdb=" O GLYNQ 51 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THRNQ 56 " --> pdb=" O THRNQ 72 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THRNQ 66 " --> pdb=" O CYSNQ 62 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARGNQ 65 " --> pdb=" O CYSNQ 83 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLYNQ 79 " --> pdb=" O HISNQ 69 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'NQ' and resid 92 through 95 removed outlier: 3.838A pdb=" N GLYNQ 92 " --> pdb=" O CYSNQ 103 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEUNQ 125 " --> pdb=" O VALNQ 111 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'NQ' and resid 135 through 139 removed outlier: 5.662A pdb=" N VALNQ 145 " --> pdb=" O ASPNQ 139 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N HISNQ 144 " --> pdb=" O LEUNQ 160 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'NQ' and resid 188 through 192 removed outlier: 3.928A pdb=" N ASPNQ 188 " --> pdb=" O CYSNQ 201 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYSNQ 197 " --> pdb=" O LEUNQ 192 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HISNQ 205 " --> pdb=" O TYRNQ 225 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYRNQ 225 " --> pdb=" O HISNQ 205 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'NQ' and resid 232 through 236 removed outlier: 5.820A pdb=" N SERNQ 241 " --> pdb=" O THRNQ 236 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEUNQ 251 " --> pdb=" O LEUNQ 265 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLYNQ 263 " --> pdb=" O GLUNQ 253 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'NQ' and resid 273 through 278 removed outlier: 5.677A pdb=" N LEUNQ 283 " --> pdb=" O HISNQ 278 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLYNQ 288 " --> pdb=" O VALNQ 292 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VALNQ 292 " --> pdb=" O GLYNQ 288 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'NS' and resid 169 through 173 removed outlier: 4.882A pdb=" N THRNS 148 " --> pdb=" O TYRNS 173 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLUNS 200 " --> pdb=" O SERNS 149 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'NS' and resid 244 through 249 removed outlier: 3.699A pdb=" N PHENS 312 " --> pdb=" O PHENS 290 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SA' and resid 7 through 10 removed outlier: 5.125A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.397A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SC' and resid 147 through 153 removed outlier: 4.344A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 57, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.458A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SD' and resid 158 through 162 removed outlier: 6.803A pdb=" N GLYSD 158 " --> pdb=" O LEUSD 169 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 60, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.765A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 62, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.469A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.494A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'SH' and resid 72 through 77 removed outlier: 3.633A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYRSH 88 " --> pdb=" O SERSH 77 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SI' and resid 147 through 151 removed outlier: 3.510A pdb=" N GLYSI 150 " --> pdb=" O PHESI 98 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARGSI 101 " --> pdb=" O SERSI 126 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'SK' and resid 1 through 5 removed outlier: 3.752A pdb=" N ALASK 204 " --> pdb=" O METSK 1 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 68, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 69, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 70, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.555A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEUSL 78 " --> pdb=" O ILESL 205 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SL' and resid 127 through 130 Processing sheet with id= 72, first strand: chain 'SL' and resid 210 through 216 removed outlier: 6.216A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYSSL 249 " --> pdb=" O SERSL 266 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHESL 264 " --> pdb=" O LEUSL 251 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'SM' and resid 179 through 184 Processing sheet with id= 74, first strand: chain 'SM' and resid 352 through 356 removed outlier: 3.511A pdb=" N ASNSM 335 " --> pdb=" O ILESM 377 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SO' and resid 87 through 91 removed outlier: 4.147A pdb=" N ASPSO 91 " --> pdb=" O ILESO 64 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N SERSO 66 " --> pdb=" O ASPSO 91 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALASO 120 " --> pdb=" O SERSO 67 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEUSO 126 " --> pdb=" O VALSO 143 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYSSO 140 " --> pdb=" O ILESO 241 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ALASO 228 " --> pdb=" O ILESO 223 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASNSO 219 " --> pdb=" O ILESO 232 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHESO 217 " --> pdb=" O PROSO 234 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHESO 236 " --> pdb=" O ILESO 215 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILESO 215 " --> pdb=" O PHESO 236 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASPSO 203 " --> pdb=" O ILESO 222 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SO' and resid 137 through 140 removed outlier: 3.564A pdb=" N LYSSO 242 " --> pdb=" O LYSSO 140 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 5.318A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.750A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 80, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.820A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.395A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'SR' and resid 204 through 211 removed outlier: 7.523A pdb=" N SERSR 204 " --> pdb=" O PROSR 223 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'SV' and resid 3 through 6 removed outlier: 6.556A pdb=" N GLUSV 4 " --> pdb=" O PROSV 12 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N CYSSV 6 " --> pdb=" O SERSV 10 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'SV' and resid 18 through 22 Processing sheet with id= 85, first strand: chain 'SW' and resid 281 through 285 Processing sheet with id= 86, first strand: chain 'SW' and resid 400 through 406 Processing sheet with id= 87, first strand: chain 'SW' and resid 452 through 455 Processing sheet with id= 88, first strand: chain 'SY' and resid 334 through 337 removed outlier: 6.859A pdb=" N ASNSY 334 " --> pdb=" O TYRSY 349 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THRSY 344 " --> pdb=" O THRSY 314 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VALSY 310 " --> pdb=" O VALSY 348 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N HISSY 365 " --> pdb=" O ASNSY 315 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'SY' and resid 436 through 442 removed outlier: 5.452A pdb=" N ASNSY 436 " --> pdb=" O GLYSY 410 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYRSY 442 " --> pdb=" O ASPSY 416 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASPSY 460 " --> pdb=" O METSY 391 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N CYSSY 517 " --> pdb=" O ALASY 461 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLYSY 510 " --> pdb=" O LYSSY 586 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYSSY 583 " --> pdb=" O VALSY 540 " (cutoff:3.500A) 4061 hydrogen bonds defined for protein. 12059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1982 hydrogen bonds 3440 hydrogen bond angles 0 basepair planarities 755 basepair parallelities 1185 stacking parallelities Total time for adding SS restraints: 121.97 Time building geometry restraints manager: 49.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 56371 1.41 - 1.63: 85415 1.63 - 1.86: 552 1.86 - 2.09: 0 2.09 - 2.31: 12 Bond restraints: 142350 Sorted by residual: bond pdb=" N7 GDPSR1001 " pdb=" C5 GDPSR1001 " ideal model delta sigma weight residual 1.350 1.517 -0.167 2.00e-02 2.50e+03 7.01e+01 bond pdb=" C6 GDPSR1001 " pdb=" O6 GDPSR1001 " ideal model delta sigma weight residual 1.250 1.395 -0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C2 GDPSR1001 " pdb=" N2 GDPSR1001 " ideal model delta sigma weight residual 1.355 1.450 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" N1 GDPSR1001 " pdb=" C2 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.403 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1' GDPSR1001 " pdb=" N9 GDPSR1001 " ideal model delta sigma weight residual 1.485 1.422 0.063 2.00e-02 2.50e+03 9.81e+00 ... (remaining 142345 not shown) Histogram of bond angle deviations from ideal: 71.66 - 85.20: 12 85.20 - 98.74: 0 98.74 - 112.28: 88573 112.28 - 125.82: 106205 125.82 - 139.36: 8725 Bond angle restraints: 203515 Sorted by residual: angle pdb=" C8 GDPSR1001 " pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 108.00 121.14 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" N ILESO 232 " pdb=" CA ILESO 232 " pdb=" C ILESO 232 " ideal model delta sigma weight residual 111.90 108.86 3.04 8.10e-01 1.52e+00 1.41e+01 angle pdb=" CA LYSSS 378 " pdb=" CB LYSSS 378 " pdb=" CG LYSSS 378 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 angle pdb=" C4' GL34520 " pdb=" C3' GL34520 " pdb=" O3' GL34520 " ideal model delta sigma weight residual 109.40 113.89 -4.49 1.50e+00 4.44e-01 8.97e+00 angle pdb=" C3' GL34520 " pdb=" O3' GL34520 " pdb=" P UL34521 " ideal model delta sigma weight residual 120.20 124.67 -4.47 1.50e+00 4.44e-01 8.88e+00 ... (remaining 203510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 83657 35.17 - 70.33: 5857 70.33 - 105.50: 798 105.50 - 140.66: 6 140.66 - 175.83: 8 Dihedral angle restraints: 90326 sinusoidal: 58913 harmonic: 31413 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 28.56 171.44 1 1.50e+01 4.44e-03 8.49e+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 52.23 147.77 1 1.50e+01 4.44e-03 7.88e+01 dihedral pdb=" O4' UL33964 " pdb=" C1' UL33964 " pdb=" N1 UL33964 " pdb=" C2 UL33964 " ideal model delta sinusoidal sigma weight residual -128.00 47.83 -175.83 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 90323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 21785 0.056 - 0.112: 2301 0.112 - 0.168: 416 0.168 - 0.224: 13 0.224 - 0.279: 2 Chirality restraints: 24517 Sorted by residual: chirality pdb="FE1 SF4NM 401 " pdb=" S2 SF4NM 401 " pdb=" S3 SF4NM 401 " pdb=" S4 SF4NM 401 " both_signs ideal model delta sigma weight residual False -10.55 -10.28 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C1' UL34493 " pdb=" O4' UL34493 " pdb=" C2' UL34493 " pdb=" N1 UL34493 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1' GL3 448 " pdb=" O4' GL3 448 " pdb=" C2' GL3 448 " pdb=" N9 GL3 448 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 24514 not shown) Planarity restraints: 17261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILENO 344 " 0.059 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRONO 345 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRONO 345 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRONO 345 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' GL1 39 " -0.046 2.00e-02 2.50e+03 1.86e-02 1.04e+01 pdb=" N9 GL1 39 " 0.039 2.00e-02 2.50e+03 pdb=" C8 GL1 39 " 0.009 2.00e-02 2.50e+03 pdb=" N7 GL1 39 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GL1 39 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GL1 39 " -0.005 2.00e-02 2.50e+03 pdb=" O6 GL1 39 " -0.015 2.00e-02 2.50e+03 pdb=" N1 GL1 39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GL1 39 " 0.003 2.00e-02 2.50e+03 pdb=" N2 GL1 39 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GL1 39 " 0.010 2.00e-02 2.50e+03 pdb=" C4 GL1 39 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AL34510 " 0.038 2.00e-02 2.50e+03 1.74e-02 8.28e+00 pdb=" N9 AL34510 " -0.040 2.00e-02 2.50e+03 pdb=" C8 AL34510 " -0.005 2.00e-02 2.50e+03 pdb=" N7 AL34510 " 0.002 2.00e-02 2.50e+03 pdb=" C5 AL34510 " 0.001 2.00e-02 2.50e+03 pdb=" C6 AL34510 " 0.004 2.00e-02 2.50e+03 pdb=" N6 AL34510 " 0.011 2.00e-02 2.50e+03 pdb=" N1 AL34510 " 0.002 2.00e-02 2.50e+03 pdb=" C2 AL34510 " -0.004 2.00e-02 2.50e+03 pdb=" N3 AL34510 " -0.004 2.00e-02 2.50e+03 pdb=" C4 AL34510 " -0.005 2.00e-02 2.50e+03 ... (remaining 17258 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.58: 879 2.58 - 3.22: 119873 3.22 - 3.86: 283290 3.86 - 4.50: 397300 4.50 - 5.14: 560321 Nonbonded interactions: 1361663 Sorted by model distance: nonbonded pdb=" O2' UL3 184 " pdb=" OP2 GL3 189 " model vdw 1.945 2.440 nonbonded pdb=" O1B ADPNI1001 " pdb="MG MGNI1002 " model vdw 1.961 2.170 nonbonded pdb=" OP2 GL3 356 " pdb="MG MGL36008 " model vdw 1.979 2.170 nonbonded pdb=" OG SERNB 324 " pdb=" OG SERNB 327 " model vdw 1.983 2.440 nonbonded pdb=" OP2 AL31917 " pdb="MG MGL36027 " model vdw 1.996 2.170 ... (remaining 1361658 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 25.150 Check model and map are aligned: 1.430 Set scattering table: 0.890 Process input model: 435.110 Find NCS groups from input model: 3.770 Set up NCS constraints: 0.360 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: 0.030 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 483.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.004 0.167 142350 Z= 0.279 Angle : 0.592 13.137 203515 Z= 0.310 Chirality : 0.038 0.279 24517 Planarity : 0.005 0.088 17261 Dihedral : 19.918 175.827 69944 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.02 % Allowed : 0.19 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.08), residues: 10627 helix: 1.84 (0.08), residues: 4451 sheet: 0.70 (0.13), residues: 1500 loop : 0.49 (0.09), residues: 4676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPSK 202 HIS 0.012 0.001 HISLA 25 PHE 0.026 0.002 PHESO 65 TYR 0.032 0.002 TYRSM 548 ARG 0.012 0.001 ARGLK 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1056 time to evaluate : 8.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 62 MET cc_start: 0.8099 (ttm) cc_final: 0.7808 (ttp) REVERT: L9 19 MET cc_start: 0.8641 (mmm) cc_final: 0.8400 (mmp) REVERT: LB 150 ARG cc_start: 0.6906 (mtm110) cc_final: 0.6499 (mtp85) REVERT: SJ 707 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7729 (mm110) REVERT: SJ 713 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7838 (ttp80) REVERT: SV 93 MET cc_start: 0.7645 (ttp) cc_final: 0.7393 (ttp) outliers start: 2 outliers final: 1 residues processed: 1057 average time/residue: 2.0329 time to fit residues: 3052.6094 Evaluate side-chains 834 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 833 time to evaluate : 8.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 65 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1090 optimal weight: 10.0000 chunk 978 optimal weight: 0.8980 chunk 542 optimal weight: 8.9990 chunk 334 optimal weight: 9.9990 chunk 660 optimal weight: 50.0000 chunk 522 optimal weight: 9.9990 chunk 1011 optimal weight: 6.9990 chunk 391 optimal weight: 9.9990 chunk 615 optimal weight: 30.0000 chunk 753 optimal weight: 1.9990 chunk 1172 optimal weight: 40.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN L6 15 HIS L7 90 HIS L8 78 GLN ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 145 ASN LB 21 GLN LC 36 ASN LC 37 HIS LE 112 ASN LH 33 HIS LI 14 ASN LK 62 HIS LN 3 HIS LN 42 HIS LN 208 ASN LU 26 HIS NB 16 HIS NB 52 ASN NB 360 ASN ** NB 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NH 151 GLN ** NH 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 333 ASN ** NI 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NI 412 ASN NI 454 HIS NM 60 GLN NM 97 ASN NM 172 GLN NO 66 GLN ** NQ 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NS 212 HIS ** NS 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NS 348 HIS SA 60 HIS ** SA 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 245 HIS SC 136 HIS SC 190 HIS SC 211 HIS SC 227 HIS SD 131 ASN SG 42 ASN SG 78 GLN SG 106 GLN SG 138 GLN SG 140 GLN SG 163 GLN SH 67 GLN SI 71 GLN SI 153 ASN SJ 687 ASN SJ 712 HIS SJ 726 HIS SK 83 HIS SL 46 HIS SM 16 ASN SM 154 HIS SM 323 HIS SN 48 ASN SN 146 GLN SO 258 HIS SQ 24 GLN SQ 25 ASN ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SR 27 GLN SR 35 HIS SR 37 HIS SR 98 GLN SR 157 HIS SR 186 ASN ** SR 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SR 239 GLN SR 246 HIS SS 310 HIS ST 208 HIS ST 255 GLN SV 45 ASN SW 278 HIS SW 499 GLN SW 593 HIS ** SY 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SY 268 ASN SY 574 HIS SZ 109 ASN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 142350 Z= 0.493 Angle : 0.688 12.766 203515 Z= 0.353 Chirality : 0.046 0.298 24517 Planarity : 0.006 0.076 17261 Dihedral : 21.439 177.439 49062 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.73 % Allowed : 6.61 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.30 (0.08), residues: 10627 helix: 1.78 (0.07), residues: 4560 sheet: 0.54 (0.13), residues: 1481 loop : 0.14 (0.09), residues: 4586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRPSS 182 HIS 0.018 0.002 HISLA 25 PHE 0.040 0.003 PHESY 579 TYR 0.037 0.003 TYRSA 122 ARG 0.025 0.001 ARGSS 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 869 time to evaluate : 8.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 62 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7002 (mm) REVERT: L7 106 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: L9 19 MET cc_start: 0.8761 (mmm) cc_final: 0.8475 (mmp) REVERT: LI 120 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: LN 174 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7121 (mmt90) REVERT: LN 383 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6871 (mm-30) REVERT: LQ 83 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8025 (tttm) REVERT: NB 454 PHE cc_start: 0.6689 (OUTLIER) cc_final: 0.5501 (t80) REVERT: NH 136 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.5313 (ttm) REVERT: NI 439 TYR cc_start: 0.6904 (m-80) cc_final: 0.6601 (m-80) REVERT: NK 82 ASN cc_start: 0.6247 (OUTLIER) cc_final: 0.5404 (t0) REVERT: NQ 1 MET cc_start: 0.4414 (tpp) cc_final: 0.3629 (ttp) REVERT: NQ 58 MET cc_start: 0.6914 (ttm) cc_final: 0.6710 (mtm) REVERT: SC 231 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6792 (mm-30) REVERT: SD 43 ARG cc_start: 0.7035 (ttm-80) cc_final: 0.6791 (ttm170) REVERT: SL 67 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6331 (mpt) REVERT: SR 405 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7117 (mtm) REVERT: SR 443 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7154 (t70) REVERT: SS 161 LYS cc_start: 0.7713 (mttt) cc_final: 0.7493 (mttt) REVERT: ST 213 GLN cc_start: 0.7834 (mt0) cc_final: 0.7597 (mt0) REVERT: ST 251 LYS cc_start: 0.5725 (tttm) cc_final: 0.5162 (tttp) REVERT: ST 266 LYS cc_start: 0.7852 (tmmt) cc_final: 0.7252 (tmmt) outliers start: 149 outliers final: 60 residues processed: 940 average time/residue: 2.0505 time to fit residues: 2730.3125 Evaluate side-chains 845 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 772 time to evaluate : 8.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 46 ILE Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 62 LEU Chi-restraints excluded: chain BA residue 65 GLN Chi-restraints excluded: chain BA residue 76 SER Chi-restraints excluded: chain BA residue 128 THR Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 106 ASP Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LA residue 156 ILE Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LB residue 107 SER Chi-restraints excluded: chain LE residue 146 LYS Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 120 GLU Chi-restraints excluded: chain LN residue 121 ASN Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 383 GLU Chi-restraints excluded: chain LQ residue 83 LYS Chi-restraints excluded: chain LQ residue 132 GLU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NB residue 454 PHE Chi-restraints excluded: chain NF residue 191 THR Chi-restraints excluded: chain NH residue 25 GLN Chi-restraints excluded: chain NH residue 136 MET Chi-restraints excluded: chain NH residue 139 ILE Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NO residue 39 ARG Chi-restraints excluded: chain NO residue 120 MET Chi-restraints excluded: chain NQ residue 97 ASP Chi-restraints excluded: chain NQ residue 105 ASP Chi-restraints excluded: chain NS residue 270 ASN Chi-restraints excluded: chain SA residue 353 LYS Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SC residue 231 GLU Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 154 THR Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SJ residue 663 LEU Chi-restraints excluded: chain SJ residue 824 VAL Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SL residue 67 MET Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SN residue 101 ASP Chi-restraints excluded: chain SN residue 199 ILE Chi-restraints excluded: chain SN residue 210 LEU Chi-restraints excluded: chain SQ residue 135 VAL Chi-restraints excluded: chain SR residue 210 MET Chi-restraints excluded: chain SR residue 269 LEU Chi-restraints excluded: chain SR residue 405 MET Chi-restraints excluded: chain SR residue 443 ASP Chi-restraints excluded: chain SS residue 184 THR Chi-restraints excluded: chain SS residue 233 ILE Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 104 GLN Chi-restraints excluded: chain SY residue 393 CYS Chi-restraints excluded: chain SZ residue 60 VAL Chi-restraints excluded: chain SZ residue 169 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 651 optimal weight: 4.9990 chunk 363 optimal weight: 0.9990 chunk 975 optimal weight: 0.7980 chunk 798 optimal weight: 7.9990 chunk 323 optimal weight: 0.8980 chunk 1174 optimal weight: 9.9990 chunk 1268 optimal weight: 1.9990 chunk 1045 optimal weight: 9.9990 chunk 1164 optimal weight: 4.9990 chunk 400 optimal weight: 0.9990 chunk 942 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN LA 10 ASN ** LA 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 21 GLN LC 50 GLN LE 112 ASN LI 14 ASN LT 21 GLN NB 16 HIS NB 52 ASN NB 343 GLN NB 360 ASN ** NH 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 412 ASN NQ 10 HIS NS 59 ASN NS 277 GLN SA 60 HIS SA 178 ASN SA 231 ASN SG 138 GLN SG 140 GLN SG 156 ASN SG 163 GLN SI 153 ASN SL 46 HIS SN 51 ASN SQ 24 GLN SQ 25 ASN ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SQ 91 GLN SR 209 HIS ** SR 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ST 255 GLN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 499 GLN SW 525 HIS SY 240 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.106 142350 Z= 0.149 Angle : 0.492 14.165 203515 Z= 0.256 Chirality : 0.035 0.258 24517 Planarity : 0.004 0.072 17261 Dihedral : 21.344 176.038 49062 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.42 % Allowed : 8.52 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.74 (0.08), residues: 10627 helix: 2.29 (0.08), residues: 4573 sheet: 0.54 (0.13), residues: 1484 loop : 0.27 (0.09), residues: 4570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLW 49 HIS 0.007 0.001 HISLA 25 PHE 0.026 0.001 PHESY 579 TYR 0.022 0.001 TYRLK 61 ARG 0.008 0.000 ARGSA 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 855 time to evaluate : 8.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 124 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: L9 19 MET cc_start: 0.8650 (mmm) cc_final: 0.8394 (mmp) REVERT: LK 65 ARG cc_start: 0.7063 (mtt180) cc_final: 0.6597 (mmt180) REVERT: LN 53 MET cc_start: 0.8903 (mtp) cc_final: 0.8426 (mtp) REVERT: LN 383 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6850 (mm-30) REVERT: LN 389 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8270 (mmm) REVERT: NB 76 GLN cc_start: 0.5973 (mm-40) cc_final: 0.5544 (tt0) REVERT: NB 454 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.5303 (t80) REVERT: NH 136 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5509 (ttm) REVERT: NI 321 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7066 (p0) REVERT: NK 82 ASN cc_start: 0.6061 (OUTLIER) cc_final: 0.5218 (t0) REVERT: NQ 1 MET cc_start: 0.4438 (tpp) cc_final: 0.3928 (ttp) REVERT: SC 231 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: SC 254 ASP cc_start: 0.7895 (m-30) cc_final: 0.7653 (m-30) REVERT: SD 46 ARG cc_start: 0.7732 (tpp80) cc_final: 0.7407 (ttt180) REVERT: SK 1 MET cc_start: 0.5728 (ttm) cc_final: 0.5302 (mtm) REVERT: SL 37 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7446 (ttp-110) REVERT: SL 67 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6347 (mpt) REVERT: SL 267 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: SN 72 VAL cc_start: 0.8134 (p) cc_final: 0.7914 (m) REVERT: SR 309 ASP cc_start: 0.6948 (m-30) cc_final: 0.6725 (m-30) REVERT: SS 184 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6608 (t) REVERT: ST 251 LYS cc_start: 0.5723 (tttm) cc_final: 0.5113 (tttp) outliers start: 122 outliers final: 55 residues processed: 913 average time/residue: 2.0468 time to fit residues: 2666.7036 Evaluate side-chains 851 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 785 time to evaluate : 8.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 37 LEU Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 65 GLN Chi-restraints excluded: chain BA residue 124 GLU Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 100 ASP Chi-restraints excluded: chain L7 residue 175 MET Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 57 SER Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LH residue 57 GLN Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 25 ILE Chi-restraints excluded: chain LI residue 120 GLU Chi-restraints excluded: chain LN residue 383 GLU Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 132 GLU Chi-restraints excluded: chain LS residue 16 GLU Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain NB residue 13 MET Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NB residue 454 PHE Chi-restraints excluded: chain NH residue 1 MET Chi-restraints excluded: chain NH residue 136 MET Chi-restraints excluded: chain NI residue 321 ASP Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 138 SER Chi-restraints excluded: chain NO residue 120 MET Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 52 PHE Chi-restraints excluded: chain NS residue 120 ASP Chi-restraints excluded: chain SC residue 231 GLU Chi-restraints excluded: chain SC residue 235 THR Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SH residue 54 ASN Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SJ residue 697 ASP Chi-restraints excluded: chain SJ residue 714 ILE Chi-restraints excluded: chain SJ residue 824 VAL Chi-restraints excluded: chain SL residue 67 MET Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SR residue 269 LEU Chi-restraints excluded: chain SR residue 354 ASN Chi-restraints excluded: chain SS residue 184 THR Chi-restraints excluded: chain SS residue 277 THR Chi-restraints excluded: chain ST residue 265 LYS Chi-restraints excluded: chain ST residue 269 LEU Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 104 GLN Chi-restraints excluded: chain SY residue 405 LEU Chi-restraints excluded: chain SZ residue 114 ASP Chi-restraints excluded: chain SZ residue 169 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1160 optimal weight: 0.2980 chunk 883 optimal weight: 4.9990 chunk 609 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 560 optimal weight: 0.0040 chunk 788 optimal weight: 3.9990 chunk 1178 optimal weight: 6.9990 chunk 1247 optimal weight: 9.9990 chunk 615 optimal weight: 40.0000 chunk 1117 optimal weight: 1.9990 chunk 336 optimal weight: 9.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 97 ASN LB 21 GLN LE 112 ASN LS 68 ASN LW 66 HIS NB 52 ASN NB 343 GLN NB 360 ASN ** NF 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NH 124 ASN ** NH 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 350 HIS NI 412 ASN NM 172 GLN NO 12 GLN NQ 306 HIS SA 60 HIS SG 78 GLN SG 138 GLN SG 140 GLN SI 153 ASN SM 375 HIS SN 51 ASN SN 103 GLN SQ 24 GLN SQ 25 ASN ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SQ 113 ASN ** SR 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ST 208 HIS ST 213 GLN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 499 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 142350 Z= 0.158 Angle : 0.472 13.467 203515 Z= 0.246 Chirality : 0.034 0.250 24517 Planarity : 0.004 0.070 17261 Dihedral : 21.254 176.826 49062 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.50 % Allowed : 9.37 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.08), residues: 10627 helix: 2.41 (0.08), residues: 4566 sheet: 0.54 (0.13), residues: 1497 loop : 0.29 (0.09), residues: 4564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPL9 120 HIS 0.009 0.001 HISNH 175 PHE 0.029 0.001 PHESY 579 TYR 0.045 0.001 TYRSM 548 ARG 0.008 0.000 ARGSA 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 825 time to evaluate : 8.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 62 MET cc_start: 0.8266 (ttm) cc_final: 0.8001 (ttp) REVERT: L8 50 MET cc_start: 0.8308 (mtp) cc_final: 0.7993 (ttm) REVERT: L9 19 MET cc_start: 0.8649 (mmm) cc_final: 0.8386 (mmp) REVERT: LI 52 ASP cc_start: 0.7066 (t0) cc_final: 0.6852 (t0) REVERT: LK 65 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6733 (mmt180) REVERT: LN 53 MET cc_start: 0.9018 (mtp) cc_final: 0.8516 (mtp) REVERT: LN 174 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7107 (mmt90) REVERT: LN 389 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8285 (mmm) REVERT: NB 76 GLN cc_start: 0.5920 (mm110) cc_final: 0.5593 (tt0) REVERT: NB 454 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.5298 (t80) REVERT: NH 136 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.5509 (ttm) REVERT: NI 439 TYR cc_start: 0.6728 (m-80) cc_final: 0.6444 (m-80) REVERT: NK 82 ASN cc_start: 0.6068 (OUTLIER) cc_final: 0.5169 (t0) REVERT: NM 24 LYS cc_start: 0.4586 (tttt) cc_final: 0.3813 (tttm) REVERT: NO 39 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7426 (ttt180) REVERT: NO 347 LYS cc_start: 0.4128 (mmtp) cc_final: 0.3131 (ttpt) REVERT: NQ 1 MET cc_start: 0.4472 (tpp) cc_final: 0.4178 (ttp) REVERT: SA 86 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6065 (tmt170) REVERT: SC 59 ARG cc_start: 0.6193 (OUTLIER) cc_final: 0.5721 (ttt180) REVERT: SC 231 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6735 (mm-30) REVERT: SC 254 ASP cc_start: 0.7895 (m-30) cc_final: 0.7637 (m-30) REVERT: SD 46 ARG cc_start: 0.7726 (tpp80) cc_final: 0.7436 (ttt180) REVERT: SK 1 MET cc_start: 0.5804 (ttm) cc_final: 0.5370 (mtm) REVERT: SS 184 THR cc_start: 0.6995 (OUTLIER) cc_final: 0.6577 (t) REVERT: ST 251 LYS cc_start: 0.5700 (tttm) cc_final: 0.5135 (tttp) outliers start: 129 outliers final: 69 residues processed: 887 average time/residue: 2.0210 time to fit residues: 2554.6715 Evaluate side-chains 866 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 787 time to evaluate : 8.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 65 GLN Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 175 MET Chi-restraints excluded: chain L8 residue 105 THR Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LA residue 156 ILE Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 57 GLN Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 120 GLU Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 61 TYR Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LQ residue 132 GLU Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain NB residue 13 MET Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 330 VAL Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NB residue 454 PHE Chi-restraints excluded: chain NF residue 105 MET Chi-restraints excluded: chain NH residue 1 MET Chi-restraints excluded: chain NH residue 136 MET Chi-restraints excluded: chain NH residue 139 ILE Chi-restraints excluded: chain NI residue 424 HIS Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 138 SER Chi-restraints excluded: chain NO residue 39 ARG Chi-restraints excluded: chain NO residue 120 MET Chi-restraints excluded: chain NO residue 192 LYS Chi-restraints excluded: chain NQ residue 20 LEU Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 120 ASP Chi-restraints excluded: chain NS residue 270 ASN Chi-restraints excluded: chain SA residue 86 ARG Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SC residue 59 ARG Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SC residue 231 GLU Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SE residue 223 ARG Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 54 ASN Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SJ residue 824 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SN residue 210 LEU Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SS residue 184 THR Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain ST residue 265 LYS Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 104 GLN Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 546 PHE Chi-restraints excluded: chain SZ residue 16 SER Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 114 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1039 optimal weight: 8.9990 chunk 708 optimal weight: 8.9990 chunk 18 optimal weight: 0.0980 chunk 929 optimal weight: 10.0000 chunk 514 optimal weight: 7.9990 chunk 1064 optimal weight: 9.9990 chunk 862 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 637 optimal weight: 3.9990 chunk 1120 optimal weight: 6.9990 chunk 314 optimal weight: 4.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 167 HIS ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 196 ASN LA 54 GLN LA 97 ASN LB 21 GLN LE 112 ASN LE 114 GLN LG 135 ASN LI 14 ASN NB 16 HIS NB 52 ASN NB 343 GLN NB 376 GLN NF 255 ASN ** NH 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 332 HIS NI 350 HIS NI 412 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN NM 160 ASN NO 12 GLN ** NQ 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 60 HIS SG 138 GLN SG 140 GLN SG 163 GLN SJ 687 ASN SN 48 ASN SN 51 ASN SN 148 GLN SQ 24 GLN SQ 25 ASN ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SR 228 HIS SR 273 GLN ** SR 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 208 HIS ST 223 GLN SW 328 GLN SW 499 GLN SZ 171 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 142350 Z= 0.407 Angle : 0.608 11.426 203515 Z= 0.312 Chirality : 0.042 0.269 24517 Planarity : 0.005 0.080 17261 Dihedral : 21.294 177.529 49062 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.22 % Allowed : 9.98 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.08), residues: 10627 helix: 2.05 (0.08), residues: 4570 sheet: 0.47 (0.13), residues: 1448 loop : 0.06 (0.09), residues: 4609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPL9 120 HIS 0.013 0.002 HISLA 25 PHE 0.031 0.002 PHESY 579 TYR 0.023 0.002 TYRLB 32 ARG 0.010 0.001 ARGL7 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 800 time to evaluate : 8.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 106 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: L8 81 ASP cc_start: 0.7054 (t0) cc_final: 0.6754 (t0) REVERT: L9 19 MET cc_start: 0.8770 (mmm) cc_final: 0.8499 (mmp) REVERT: LE 146 LYS cc_start: 0.7333 (pttm) cc_final: 0.7102 (pttt) REVERT: LH 55 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6807 (ttm110) REVERT: LI 120 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: LK 65 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6808 (mmt180) REVERT: LN 174 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7135 (mmt90) REVERT: LN 383 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6828 (mm-30) REVERT: LW 85 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.7034 (tttm) REVERT: NB 76 GLN cc_start: 0.6084 (mm110) cc_final: 0.5629 (tt0) REVERT: NB 454 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.5510 (t80) REVERT: NH 136 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5577 (ttm) REVERT: NI 439 TYR cc_start: 0.6806 (m-80) cc_final: 0.6534 (m-80) REVERT: NK 82 ASN cc_start: 0.6202 (OUTLIER) cc_final: 0.5331 (t0) REVERT: NO 347 LYS cc_start: 0.4386 (mmtp) cc_final: 0.3193 (ttpt) REVERT: NQ 1 MET cc_start: 0.4529 (tpp) cc_final: 0.4186 (ptm) REVERT: SA 86 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6362 (tmt170) REVERT: SC 59 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5861 (ttt180) REVERT: SD 46 ARG cc_start: 0.7789 (tpp80) cc_final: 0.7461 (ttt180) REVERT: SK 1 MET cc_start: 0.5993 (ttm) cc_final: 0.5647 (ttp) REVERT: SN 148 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7712 (tp-100) REVERT: SR 443 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7049 (t70) REVERT: ST 251 LYS cc_start: 0.5705 (tttm) cc_final: 0.5114 (tttp) outliers start: 191 outliers final: 96 residues processed: 912 average time/residue: 2.0487 time to fit residues: 2666.3054 Evaluate side-chains 884 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 775 time to evaluate : 7.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 46 ILE Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 63 THR Chi-restraints excluded: chain BA residue 65 GLN Chi-restraints excluded: chain BA residue 128 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 106 ASP Chi-restraints excluded: chain L7 residue 175 MET Chi-restraints excluded: chain L8 residue 2 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 105 THR Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LA residue 156 ILE Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 55 ARG Chi-restraints excluded: chain LH residue 57 GLN Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 25 ILE Chi-restraints excluded: chain LI residue 120 GLU Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 61 TYR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 383 GLU Chi-restraints excluded: chain LQ residue 132 GLU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LW residue 85 LYS Chi-restraints excluded: chain NB residue 13 MET Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 330 VAL Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 374 MET Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NB residue 454 PHE Chi-restraints excluded: chain NF residue 105 MET Chi-restraints excluded: chain NF residue 191 THR Chi-restraints excluded: chain NH residue 1 MET Chi-restraints excluded: chain NH residue 136 MET Chi-restraints excluded: chain NH residue 139 ILE Chi-restraints excluded: chain NI residue 681 TYR Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 65 MET Chi-restraints excluded: chain NM residue 138 SER Chi-restraints excluded: chain NO residue 120 MET Chi-restraints excluded: chain NO residue 192 LYS Chi-restraints excluded: chain NQ residue 20 LEU Chi-restraints excluded: chain NQ residue 97 ASP Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 270 ASN Chi-restraints excluded: chain SA residue 86 ARG Chi-restraints excluded: chain SC residue 59 ARG Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 42 LEU Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 54 ASN Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 154 THR Chi-restraints excluded: chain SH residue 161 MET Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SJ residue 824 VAL Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SK residue 45 THR Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SN residue 148 GLN Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SN residue 210 LEU Chi-restraints excluded: chain SQ residue 80 SER Chi-restraints excluded: chain SR residue 106 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 296 ILE Chi-restraints excluded: chain SR residue 354 ASN Chi-restraints excluded: chain SR residue 443 ASP Chi-restraints excluded: chain SS residue 184 THR Chi-restraints excluded: chain SS residue 233 ILE Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 277 THR Chi-restraints excluded: chain ST residue 203 SER Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 104 GLN Chi-restraints excluded: chain SV residue 108 ILE Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SZ residue 60 VAL Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 114 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 419 optimal weight: 1.9990 chunk 1123 optimal weight: 2.9990 chunk 246 optimal weight: 20.0000 chunk 732 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 1249 optimal weight: 10.0000 chunk 1036 optimal weight: 5.9990 chunk 578 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 413 optimal weight: 40.0000 chunk 655 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 65 GLN ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L7 63 ASN LA 10 ASN LA 54 GLN LB 21 GLN LE 112 ASN LI 14 ASN NB 52 ASN NB 376 GLN NF 255 ASN ** NH 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 332 HIS NI 350 HIS NI 412 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN NM 160 ASN NO 101 GLN ** NQ 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 60 HIS SG 138 GLN SG 140 GLN SI 153 ASN SJ 687 ASN SK 21 ASN SN 51 ASN ** SQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SR 218 GLN SR 228 HIS ** SR 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ST 208 HIS ST 223 GLN SW 328 GLN SW 499 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 142350 Z= 0.266 Angle : 0.528 11.749 203515 Z= 0.274 Chirality : 0.037 0.256 24517 Planarity : 0.004 0.066 17261 Dihedral : 21.283 177.348 49062 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.05 % Allowed : 10.82 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.08), residues: 10627 helix: 2.13 (0.08), residues: 4571 sheet: 0.43 (0.13), residues: 1448 loop : 0.05 (0.09), residues: 4608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPL9 120 HIS 0.008 0.001 HISLA 25 PHE 0.031 0.002 PHESY 579 TYR 0.046 0.002 TYRSM 548 ARG 0.012 0.000 ARGL7 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 795 time to evaluate : 8.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 37 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8625 (mtm180) REVERT: L8 81 ASP cc_start: 0.7051 (t0) cc_final: 0.6708 (t0) REVERT: L9 19 MET cc_start: 0.8732 (mmm) cc_final: 0.8483 (mmp) REVERT: L9 104 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: LA 54 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7403 (mt0) REVERT: LE 146 LYS cc_start: 0.7337 (pttm) cc_final: 0.7104 (pttt) REVERT: LI 51 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8688 (tttt) REVERT: LI 120 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: LK 65 ARG cc_start: 0.6986 (mtt180) cc_final: 0.6572 (mmt180) REVERT: LN 174 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7115 (mmt90) REVERT: LN 383 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6872 (mm-30) REVERT: LW 85 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7085 (tttm) REVERT: NB 76 GLN cc_start: 0.6179 (mm110) cc_final: 0.5675 (tt0) REVERT: NB 454 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.5430 (t80) REVERT: NH 136 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5629 (ttm) REVERT: NI 321 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7174 (p0) REVERT: NI 439 TYR cc_start: 0.6837 (m-80) cc_final: 0.6613 (m-80) REVERT: NK 82 ASN cc_start: 0.6150 (OUTLIER) cc_final: 0.5290 (t0) REVERT: NK 89 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6420 (pm20) REVERT: NQ 1 MET cc_start: 0.4507 (tpp) cc_final: 0.4179 (ptm) REVERT: NQ 113 HIS cc_start: 0.6781 (OUTLIER) cc_final: 0.6340 (m-70) REVERT: SA 86 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6420 (tmt170) REVERT: SC 59 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.5791 (ttt180) REVERT: SC 231 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: SD 46 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7398 (ttt180) REVERT: SK 1 MET cc_start: 0.6021 (ttm) cc_final: 0.5727 (ttp) REVERT: SL 67 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6471 (mpt) REVERT: SN 100 ASP cc_start: 0.5733 (t0) cc_final: 0.5407 (p0) REVERT: SR 443 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6997 (t70) REVERT: ST 215 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.6251 (ttmt) REVERT: ST 251 LYS cc_start: 0.5580 (tttm) cc_final: 0.4995 (tttp) REVERT: ST 266 LYS cc_start: 0.7637 (tmtt) cc_final: 0.7376 (ttpp) REVERT: SV 20 MET cc_start: 0.7954 (ttm) cc_final: 0.7632 (ttm) REVERT: SY 227 MET cc_start: 0.3009 (ttp) cc_final: 0.2426 (mtt) outliers start: 176 outliers final: 92 residues processed: 904 average time/residue: 2.0574 time to fit residues: 2661.4172 Evaluate side-chains 879 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 767 time to evaluate : 7.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 37 ARG Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 100 ASP Chi-restraints excluded: chain L7 residue 175 MET Chi-restraints excluded: chain L8 residue 2 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 105 THR Chi-restraints excluded: chain L9 residue 104 GLU Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 54 GLN Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LA residue 156 ILE Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 48 VAL Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 25 ILE Chi-restraints excluded: chain LI residue 51 LYS Chi-restraints excluded: chain LI residue 120 GLU Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 383 GLU Chi-restraints excluded: chain LQ residue 132 GLU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LW residue 85 LYS Chi-restraints excluded: chain NB residue 13 MET Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 330 VAL Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NB residue 454 PHE Chi-restraints excluded: chain NH residue 1 MET Chi-restraints excluded: chain NH residue 136 MET Chi-restraints excluded: chain NH residue 139 ILE Chi-restraints excluded: chain NI residue 321 ASP Chi-restraints excluded: chain NI residue 424 HIS Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 89 GLN Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 138 SER Chi-restraints excluded: chain NO residue 120 MET Chi-restraints excluded: chain NO residue 192 LYS Chi-restraints excluded: chain NQ residue 20 LEU Chi-restraints excluded: chain NQ residue 97 ASP Chi-restraints excluded: chain NQ residue 113 HIS Chi-restraints excluded: chain NQ residue 134 CYS Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 270 ASN Chi-restraints excluded: chain SA residue 86 ARG Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SC residue 59 ARG Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SC residue 231 GLU Chi-restraints excluded: chain SC residue 235 THR Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 54 ASN Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SI residue 110 LEU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SJ residue 823 VAL Chi-restraints excluded: chain SJ residue 824 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 67 MET Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 417 VAL Chi-restraints excluded: chain SN residue 101 ASP Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SN residue 210 LEU Chi-restraints excluded: chain SQ residue 80 SER Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 179 VAL Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 354 ASN Chi-restraints excluded: chain SR residue 443 ASP Chi-restraints excluded: chain SS residue 184 THR Chi-restraints excluded: chain SS residue 233 ILE Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 277 THR Chi-restraints excluded: chain ST residue 201 LEU Chi-restraints excluded: chain ST residue 203 SER Chi-restraints excluded: chain ST residue 215 LYS Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 104 GLN Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SZ residue 60 VAL Chi-restraints excluded: chain SZ residue 102 SER Chi-restraints excluded: chain SZ residue 114 ASP Chi-restraints excluded: chain SZ residue 169 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1204 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 711 optimal weight: 6.9990 chunk 912 optimal weight: 0.9980 chunk 706 optimal weight: 9.9990 chunk 1051 optimal weight: 0.8980 chunk 697 optimal weight: 2.9990 chunk 1244 optimal weight: 6.9990 chunk 778 optimal weight: 9.9990 chunk 758 optimal weight: 9.9990 chunk 574 optimal weight: 0.8980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LA 10 ASN ** LA 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 21 GLN LE 112 ASN LG 135 ASN LI 14 ASN NB 52 ASN NB 375 HIS NF 255 ASN ** NH 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NH 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 332 HIS NI 412 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN NM 160 ASN NO 101 GLN ** NQ 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 60 HIS SG 138 GLN SG 140 GLN SI 153 ASN SJ 687 ASN SJ 711 GLN SN 48 ASN SN 51 ASN SQ 24 GLN ** SQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SR 228 HIS ** SR 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ST 208 HIS ST 223 GLN SW 328 GLN SW 499 GLN SZ 171 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 142350 Z= 0.237 Angle : 0.514 11.858 203515 Z= 0.267 Chirality : 0.037 0.314 24517 Planarity : 0.004 0.065 17261 Dihedral : 21.253 177.249 49059 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.95 % Allowed : 11.48 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.08), residues: 10627 helix: 2.21 (0.08), residues: 4561 sheet: 0.41 (0.13), residues: 1467 loop : 0.07 (0.09), residues: 4599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPL9 120 HIS 0.007 0.001 HISLA 25 PHE 0.032 0.001 PHESY 579 TYR 0.019 0.001 TYRSQ 206 ARG 0.015 0.000 ARGSA 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 787 time to evaluate : 8.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 37 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8613 (mtm180) REVERT: L8 81 ASP cc_start: 0.7058 (t0) cc_final: 0.6817 (t0) REVERT: L9 19 MET cc_start: 0.8727 (mmm) cc_final: 0.8408 (mmm) REVERT: LH 55 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6769 (ttm110) REVERT: LI 51 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8673 (tttt) REVERT: LI 120 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: LK 65 ARG cc_start: 0.6964 (mtt180) cc_final: 0.6488 (mmt180) REVERT: LN 174 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7114 (mmt90) REVERT: LN 383 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6847 (mm-30) REVERT: LW 85 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7105 (tttm) REVERT: NB 76 GLN cc_start: 0.6156 (mm110) cc_final: 0.5695 (tt0) REVERT: NB 454 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.5267 (t80) REVERT: NH 136 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.5615 (ttm) REVERT: NI 321 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7305 (p0) REVERT: NK 82 ASN cc_start: 0.6118 (OUTLIER) cc_final: 0.5239 (t0) REVERT: NK 89 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6479 (pm20) REVERT: NO 347 LYS cc_start: 0.4413 (mmtp) cc_final: 0.3194 (ttpt) REVERT: NQ 1 MET cc_start: 0.4448 (tpp) cc_final: 0.4182 (ptm) REVERT: NQ 113 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6375 (m-70) REVERT: SA 86 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6440 (tmt170) REVERT: SC 59 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5816 (ttt180) REVERT: SD 46 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7404 (ttt180) REVERT: SJ 709 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7211 (mt-10) REVERT: SJ 713 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7496 (ttt-90) REVERT: SK 1 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5637 (ttp) REVERT: SR 443 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7021 (t70) REVERT: ST 251 LYS cc_start: 0.5618 (tttm) cc_final: 0.5018 (tttp) REVERT: ST 266 LYS cc_start: 0.7625 (tmtt) cc_final: 0.7394 (ttpp) REVERT: ST 271 LEU cc_start: 0.7150 (mp) cc_final: 0.6946 (mm) REVERT: SY 227 MET cc_start: 0.3177 (ttp) cc_final: 0.2578 (mtt) outliers start: 168 outliers final: 102 residues processed: 889 average time/residue: 2.0658 time to fit residues: 2629.0777 Evaluate side-chains 894 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 774 time to evaluate : 8.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 37 ARG Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 100 ASP Chi-restraints excluded: chain L7 residue 175 MET Chi-restraints excluded: chain L8 residue 2 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 105 THR Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LA residue 156 ILE Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 48 VAL Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 55 ARG Chi-restraints excluded: chain LH residue 57 GLN Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 51 LYS Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 120 GLU Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 383 GLU Chi-restraints excluded: chain LQ residue 132 GLU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LW residue 85 LYS Chi-restraints excluded: chain NB residue 13 MET Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 330 VAL Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 354 THR Chi-restraints excluded: chain NB residue 374 MET Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NB residue 454 PHE Chi-restraints excluded: chain NH residue 1 MET Chi-restraints excluded: chain NH residue 136 MET Chi-restraints excluded: chain NH residue 139 ILE Chi-restraints excluded: chain NI residue 321 ASP Chi-restraints excluded: chain NI residue 424 HIS Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 89 GLN Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 138 SER Chi-restraints excluded: chain NO residue 120 MET Chi-restraints excluded: chain NQ residue 20 LEU Chi-restraints excluded: chain NQ residue 97 ASP Chi-restraints excluded: chain NQ residue 113 HIS Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 52 PHE Chi-restraints excluded: chain NS residue 270 ASN Chi-restraints excluded: chain SA residue 86 ARG Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SC residue 54 ILE Chi-restraints excluded: chain SC residue 59 ARG Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SC residue 235 THR Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SE residue 56 LYS Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SE residue 223 ARG Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 54 ASN Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SI residue 110 LEU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SJ residue 713 ARG Chi-restraints excluded: chain SJ residue 823 VAL Chi-restraints excluded: chain SJ residue 824 VAL Chi-restraints excluded: chain SK residue 1 MET Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 417 VAL Chi-restraints excluded: chain SN residue 101 ASP Chi-restraints excluded: chain SN residue 119 VAL Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SN residue 210 LEU Chi-restraints excluded: chain SQ residue 7 ASP Chi-restraints excluded: chain SQ residue 80 SER Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 179 VAL Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 296 ILE Chi-restraints excluded: chain SR residue 354 ASN Chi-restraints excluded: chain SR residue 443 ASP Chi-restraints excluded: chain SS residue 184 THR Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 233 ILE Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 277 THR Chi-restraints excluded: chain ST residue 201 LEU Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 104 GLN Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SZ residue 60 VAL Chi-restraints excluded: chain SZ residue 114 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 769 optimal weight: 2.9990 chunk 496 optimal weight: 0.9980 chunk 743 optimal weight: 10.0000 chunk 374 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 791 optimal weight: 3.9990 chunk 847 optimal weight: 3.9990 chunk 615 optimal weight: 50.0000 chunk 115 optimal weight: 10.0000 chunk 978 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 21 GLN LE 112 ASN LI 14 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NB 52 ASN NF 255 ASN ** NH 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NH 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 332 HIS NI 412 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN NM 160 ASN NO 101 GLN ** NQ 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 60 HIS SG 138 GLN SG 140 GLN SI 153 ASN SJ 687 ASN SJ 711 GLN ** SK 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 48 ASN SN 51 ASN SN 148 GLN SQ 24 GLN ** SQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SR 228 HIS ** SR 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ST 208 HIS ST 223 GLN SW 328 GLN SW 499 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 142350 Z= 0.303 Angle : 0.548 11.265 203515 Z= 0.283 Chirality : 0.038 0.246 24517 Planarity : 0.005 0.072 17261 Dihedral : 21.249 177.452 49059 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.08 % Allowed : 11.73 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.41 (0.08), residues: 10627 helix: 2.10 (0.08), residues: 4562 sheet: 0.37 (0.13), residues: 1475 loop : -0.00 (0.09), residues: 4590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPL9 120 HIS 0.008 0.001 HISLA 25 PHE 0.021 0.002 PHESW 233 TYR 0.046 0.002 TYRSM 548 ARG 0.014 0.001 ARGL7 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 773 time to evaluate : 8.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 37 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8637 (mtm180) REVERT: L8 81 ASP cc_start: 0.7150 (t0) cc_final: 0.6846 (t0) REVERT: L8 84 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.7888 (p) REVERT: L9 19 MET cc_start: 0.8741 (mmm) cc_final: 0.8379 (mmp) REVERT: LE 146 LYS cc_start: 0.7276 (pttm) cc_final: 0.7047 (pttt) REVERT: LH 55 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6774 (ttm110) REVERT: LI 51 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8691 (tttt) REVERT: LI 120 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: LK 5 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8067 (mt) REVERT: LK 65 ARG cc_start: 0.6953 (mtt180) cc_final: 0.6502 (mmt180) REVERT: LN 174 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7117 (mmt90) REVERT: LN 383 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6866 (mm-30) REVERT: LW 85 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7122 (tttm) REVERT: NB 76 GLN cc_start: 0.6109 (mm110) cc_final: 0.5655 (tt0) REVERT: NB 328 ILE cc_start: 0.2864 (pp) cc_final: 0.2620 (mp) REVERT: NB 376 GLN cc_start: 0.2467 (pm20) cc_final: 0.1796 (pt0) REVERT: NB 380 ILE cc_start: 0.4703 (tp) cc_final: 0.4329 (mp) REVERT: NB 454 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.5149 (t80) REVERT: NH 136 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5624 (ttm) REVERT: NI 329 HIS cc_start: 0.8063 (t70) cc_final: 0.7774 (t70) REVERT: NI 439 TYR cc_start: 0.6772 (m-80) cc_final: 0.6561 (m-80) REVERT: NK 82 ASN cc_start: 0.6144 (OUTLIER) cc_final: 0.5267 (t0) REVERT: NK 89 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6491 (pm20) REVERT: NQ 113 HIS cc_start: 0.6790 (OUTLIER) cc_final: 0.6417 (m-70) REVERT: SA 86 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6468 (tmt170) REVERT: SC 59 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5858 (ttt180) REVERT: SD 46 ARG cc_start: 0.7754 (tpp80) cc_final: 0.7409 (ttt180) REVERT: SJ 709 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7523 (mt-10) REVERT: SJ 713 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7843 (ttt-90) REVERT: SK 1 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5688 (ttp) REVERT: SL 37 ARG cc_start: 0.7834 (ttp80) cc_final: 0.7479 (ttp-110) REVERT: SQ 48 MET cc_start: 0.8046 (ptp) cc_final: 0.7778 (mtm) REVERT: SR 443 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7084 (t70) REVERT: ST 251 LYS cc_start: 0.5582 (tttm) cc_final: 0.4999 (tttp) REVERT: SW 202 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7034 (tmm) REVERT: SW 286 MET cc_start: 0.7033 (mpp) cc_final: 0.6804 (mtm) REVERT: SY 227 MET cc_start: 0.3052 (ttp) cc_final: 0.2440 (mtt) outliers start: 179 outliers final: 108 residues processed: 882 average time/residue: 2.0586 time to fit residues: 2600.5526 Evaluate side-chains 884 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 756 time to evaluate : 8.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 37 ARG Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 100 ASP Chi-restraints excluded: chain L7 residue 152 VAL Chi-restraints excluded: chain L7 residue 175 MET Chi-restraints excluded: chain L8 residue 2 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 84 THR Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 105 THR Chi-restraints excluded: chain L9 residue 92 LEU Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LA residue 156 ILE Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 48 VAL Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 55 ARG Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 25 ILE Chi-restraints excluded: chain LI residue 51 LYS Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 120 GLU Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 383 GLU Chi-restraints excluded: chain LQ residue 132 GLU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LW residue 85 LYS Chi-restraints excluded: chain NB residue 13 MET Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NB residue 454 PHE Chi-restraints excluded: chain NH residue 1 MET Chi-restraints excluded: chain NH residue 136 MET Chi-restraints excluded: chain NH residue 139 ILE Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 89 GLN Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 65 MET Chi-restraints excluded: chain NM residue 138 SER Chi-restraints excluded: chain NO residue 120 MET Chi-restraints excluded: chain NO residue 192 LYS Chi-restraints excluded: chain NQ residue 20 LEU Chi-restraints excluded: chain NQ residue 113 HIS Chi-restraints excluded: chain NQ residue 134 CYS Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 52 PHE Chi-restraints excluded: chain NS residue 270 ASN Chi-restraints excluded: chain SA residue 86 ARG Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SC residue 54 ILE Chi-restraints excluded: chain SC residue 59 ARG Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SE residue 56 LYS Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SE residue 223 ARG Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 54 ASN Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 154 THR Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SJ residue 713 ARG Chi-restraints excluded: chain SJ residue 823 VAL Chi-restraints excluded: chain SJ residue 824 VAL Chi-restraints excluded: chain SK residue 1 MET Chi-restraints excluded: chain SK residue 45 THR Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 417 VAL Chi-restraints excluded: chain SN residue 101 ASP Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SN residue 210 LEU Chi-restraints excluded: chain SQ residue 7 ASP Chi-restraints excluded: chain SQ residue 80 SER Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 179 VAL Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 354 ASN Chi-restraints excluded: chain SR residue 443 ASP Chi-restraints excluded: chain SS residue 184 THR Chi-restraints excluded: chain SS residue 189 MET Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 233 ILE Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 277 THR Chi-restraints excluded: chain ST residue 201 LEU Chi-restraints excluded: chain ST residue 220 ARG Chi-restraints excluded: chain ST residue 265 LYS Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 104 GLN Chi-restraints excluded: chain SW residue 202 MET Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SZ residue 60 VAL Chi-restraints excluded: chain SZ residue 114 ASP Chi-restraints excluded: chain SZ residue 169 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1131 optimal weight: 9.9990 chunk 1192 optimal weight: 7.9990 chunk 1087 optimal weight: 10.0000 chunk 1159 optimal weight: 7.9990 chunk 1191 optimal weight: 10.0000 chunk 697 optimal weight: 1.9990 chunk 505 optimal weight: 4.9990 chunk 910 optimal weight: 0.0170 chunk 355 optimal weight: 6.9990 chunk 1047 optimal weight: 6.9990 chunk 1096 optimal weight: 2.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LA 10 ASN LA 25 HIS ** LA 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 21 GLN LC 50 GLN LE 112 ASN LI 14 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NB 52 ASN NF 255 ASN ** NH 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NH 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 332 HIS NI 412 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NM 160 ASN NO 101 GLN ** NQ 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 236 HIS SG 138 GLN SG 140 GLN SI 153 ASN SJ 687 ASN SJ 711 GLN ** SK 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 148 GLN SQ 24 GLN ** SQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 91 GLN SR 218 GLN SR 228 HIS ** SR 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SW 328 GLN SW 499 GLN SZ 171 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 142350 Z= 0.299 Angle : 0.547 11.222 203515 Z= 0.283 Chirality : 0.038 0.245 24517 Planarity : 0.004 0.067 17261 Dihedral : 21.254 177.314 49059 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.77 % Allowed : 12.35 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % 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: 1.40 (0.08), residues: 10627 helix: 2.10 (0.08), residues: 4556 sheet: 0.35 (0.13), residues: 1487 loop : -0.01 (0.09), residues: 4584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPNQ 112 HIS 0.008 0.001 HISLA 25 PHE 0.030 0.002 PHESY 579 TYR 0.020 0.002 TYRSQ 206 ARG 0.014 0.001 ARGSA 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 771 time to evaluate : 8.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 37 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8644 (mtm180) REVERT: L8 81 ASP cc_start: 0.7157 (t0) cc_final: 0.6837 (t0) REVERT: L8 84 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.7881 (p) REVERT: L9 19 MET cc_start: 0.8728 (mmm) cc_final: 0.8307 (mmm) REVERT: LE 146 LYS cc_start: 0.7520 (pttm) cc_final: 0.7262 (pttt) REVERT: LH 55 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6767 (ttm110) REVERT: LI 51 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8682 (tttt) REVERT: LI 120 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: LK 5 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8065 (mt) REVERT: LK 65 ARG cc_start: 0.6892 (mtt180) cc_final: 0.6463 (mmt180) REVERT: LN 174 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7122 (mmt90) REVERT: LN 383 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6861 (mm-30) REVERT: LW 85 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7117 (tttm) REVERT: NB 76 GLN cc_start: 0.6075 (mm110) cc_final: 0.5706 (tt0) REVERT: NB 376 GLN cc_start: 0.2436 (pm20) cc_final: 0.1663 (pt0) REVERT: NB 454 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.5184 (t80) REVERT: NH 136 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5631 (ttm) REVERT: NI 329 HIS cc_start: 0.8063 (t70) cc_final: 0.7770 (t70) REVERT: NI 439 TYR cc_start: 0.6805 (m-80) cc_final: 0.6549 (m-80) REVERT: NI 590 MET cc_start: 0.7811 (tpt) cc_final: 0.7108 (tpt) REVERT: NK 82 ASN cc_start: 0.6133 (OUTLIER) cc_final: 0.5263 (t0) REVERT: NK 89 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6490 (pm20) REVERT: NQ 113 HIS cc_start: 0.6749 (OUTLIER) cc_final: 0.6375 (m-70) REVERT: SA 86 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6498 (tmt170) REVERT: SC 59 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5871 (ttt180) REVERT: SD 46 ARG cc_start: 0.7740 (tpp80) cc_final: 0.7399 (ttt180) REVERT: SJ 709 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7410 (mt-10) REVERT: SK 1 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5695 (ttp) REVERT: SL 37 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7479 (ttp-110) REVERT: SQ 48 MET cc_start: 0.8044 (ptp) cc_final: 0.7788 (mtm) REVERT: SR 443 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7171 (t70) REVERT: ST 251 LYS cc_start: 0.5600 (tttm) cc_final: 0.4988 (tttp) REVERT: SW 202 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6856 (ptm) REVERT: SY 227 MET cc_start: 0.3064 (ttp) cc_final: 0.2443 (mtt) outliers start: 152 outliers final: 108 residues processed: 869 average time/residue: 2.0693 time to fit residues: 2579.5653 Evaluate side-chains 885 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 758 time to evaluate : 8.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L7 residue 37 ARG Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 100 ASP Chi-restraints excluded: chain L7 residue 152 VAL Chi-restraints excluded: chain L7 residue 175 MET Chi-restraints excluded: chain L8 residue 2 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 84 THR Chi-restraints excluded: chain L8 residue 99 GLU Chi-restraints excluded: chain L8 residue 105 THR Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LA residue 156 ILE Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 48 VAL Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 55 ARG Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 25 ILE Chi-restraints excluded: chain LI residue 51 LYS Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 120 GLU Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LN residue 383 GLU Chi-restraints excluded: chain LQ residue 132 GLU Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LW residue 85 LYS Chi-restraints excluded: chain NB residue 13 MET Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NB residue 383 VAL Chi-restraints excluded: chain NB residue 454 PHE Chi-restraints excluded: chain NH residue 1 MET Chi-restraints excluded: chain NH residue 136 MET Chi-restraints excluded: chain NH residue 139 ILE Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 89 GLN Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 42 SER Chi-restraints excluded: chain NM residue 138 SER Chi-restraints excluded: chain NO residue 192 LYS Chi-restraints excluded: chain NQ residue 20 LEU Chi-restraints excluded: chain NQ residue 113 HIS Chi-restraints excluded: chain NQ residue 134 CYS Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 52 PHE Chi-restraints excluded: chain NS residue 270 ASN Chi-restraints excluded: chain SA residue 86 ARG Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SC residue 54 ILE Chi-restraints excluded: chain SC residue 59 ARG Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SD residue 178 SER Chi-restraints excluded: chain SE residue 56 LYS Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SE residue 223 ARG Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 43 THR Chi-restraints excluded: chain SH residue 54 ASN Chi-restraints excluded: chain SH residue 59 THR Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 154 THR Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SJ residue 823 VAL Chi-restraints excluded: chain SJ residue 824 VAL Chi-restraints excluded: chain SK residue 1 MET Chi-restraints excluded: chain SK residue 45 THR Chi-restraints excluded: chain SK residue 106 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SL residue 101 ASP Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SL residue 271 TRP Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 362 ILE Chi-restraints excluded: chain SM residue 417 VAL Chi-restraints excluded: chain SN residue 101 ASP Chi-restraints excluded: chain SN residue 119 VAL Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SN residue 210 LEU Chi-restraints excluded: chain SQ residue 7 ASP Chi-restraints excluded: chain SR residue 32 THR Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 179 VAL Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 354 ASN Chi-restraints excluded: chain SR residue 443 ASP Chi-restraints excluded: chain SS residue 184 THR Chi-restraints excluded: chain SS residue 233 ILE Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 277 THR Chi-restraints excluded: chain ST residue 201 LEU Chi-restraints excluded: chain ST residue 207 LEU Chi-restraints excluded: chain ST residue 220 ARG Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 104 GLN Chi-restraints excluded: chain SW residue 202 MET Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 435 THR Chi-restraints excluded: chain SZ residue 60 VAL Chi-restraints excluded: chain SZ residue 114 ASP Chi-restraints excluded: chain SZ residue 169 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 1155 optimal weight: 2.9990 chunk 761 optimal weight: 5.9990 chunk 1226 optimal weight: 1.9990 chunk 748 optimal weight: 7.9990 chunk 581 optimal weight: 0.8980 chunk 852 optimal weight: 0.2980 chunk 1286 optimal weight: 8.9990 chunk 1183 optimal weight: 0.0470 chunk 1024 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 791 optimal weight: 3.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 97 ASN LB 21 GLN LC 50 GLN LE 112 ASN LI 14 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NB 52 ASN ** NH 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 332 HIS NI 412 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NM 2 GLN NM 160 ASN NO 101 GLN ** NQ 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 78 GLN SG 138 GLN SG 140 GLN SI 153 ASN SJ 687 ASN SJ 711 GLN ** SK 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 58 ASN SQ 91 GLN SR 218 GLN SR 228 HIS SR 354 ASN SS 234 HIS ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 208 HIS SV 17 HIS SW 328 GLN SW 499 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 142350 Z= 0.143 Angle : 0.480 12.341 203515 Z= 0.250 Chirality : 0.034 0.231 24517 Planarity : 0.004 0.074 17261 Dihedral : 21.217 177.310 49059 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.36 % Allowed : 12.90 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.08), residues: 10627 helix: 2.34 (0.08), residues: 4572 sheet: 0.46 (0.13), residues: 1477 loop : 0.11 (0.09), residues: 4578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPL9 120 HIS 0.005 0.001 HISLA 25 PHE 0.029 0.001 PHESY 579 TYR 0.030 0.001 TYRSM 548 ARG 0.025 0.000 ARGL7 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21254 Ramachandran restraints generated. 10627 Oldfield, 0 Emsley, 10627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 793 time to evaluate : 8.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 37 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8595 (mtm180) REVERT: L7 62 MET cc_start: 0.8319 (ttm) cc_final: 0.8058 (ttp) REVERT: L8 50 MET cc_start: 0.8319 (mtp) cc_final: 0.8107 (ttm) REVERT: L8 81 ASP cc_start: 0.7060 (t0) cc_final: 0.6772 (t0) REVERT: L9 19 MET cc_start: 0.8669 (mmm) cc_final: 0.8374 (mmm) REVERT: LH 55 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6781 (ttm110) REVERT: LI 51 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8628 (tttt) REVERT: LI 120 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: LK 65 ARG cc_start: 0.6874 (mtt180) cc_final: 0.6431 (mmt180) REVERT: LN 174 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7079 (mmt90) REVERT: NB 76 GLN cc_start: 0.6041 (mm110) cc_final: 0.5735 (tt0) REVERT: NB 376 GLN cc_start: 0.2099 (pm20) cc_final: 0.1395 (pt0) REVERT: NH 136 MET cc_start: 0.5915 (OUTLIER) cc_final: 0.5628 (ttm) REVERT: NI 329 HIS cc_start: 0.8026 (t70) cc_final: 0.7761 (t70) REVERT: NK 82 ASN cc_start: 0.6111 (OUTLIER) cc_final: 0.5251 (t0) REVERT: NK 89 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6480 (pm20) REVERT: NQ 113 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.6324 (m-70) REVERT: SC 59 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5643 (ttt180) REVERT: SD 46 ARG cc_start: 0.7656 (tpp80) cc_final: 0.7404 (mtt180) REVERT: SK 1 MET cc_start: 0.5992 (ttm) cc_final: 0.5686 (ttp) REVERT: SL 37 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7424 (ttp-110) REVERT: SQ 48 MET cc_start: 0.8025 (ptp) cc_final: 0.7760 (mtm) REVERT: ST 251 LYS cc_start: 0.5561 (tttm) cc_final: 0.5004 (tttp) REVERT: ST 271 LEU cc_start: 0.7372 (mp) cc_final: 0.7122 (mm) REVERT: SW 202 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6818 (ptm) REVERT: SW 265 MET cc_start: 0.7631 (mtm) cc_final: 0.7379 (mpp) REVERT: SY 227 MET cc_start: 0.3079 (ttp) cc_final: 0.2452 (mtt) outliers start: 117 outliers final: 68 residues processed: 869 average time/residue: 2.0994 time to fit residues: 2609.5912 Evaluate side-chains 840 residues out of total 9465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 761 time to evaluate : 8.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 59 THR Chi-restraints excluded: chain BA residue 63 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 37 ARG Chi-restraints excluded: chain L7 residue 67 SER Chi-restraints excluded: chain L7 residue 100 ASP Chi-restraints excluded: chain L7 residue 152 VAL Chi-restraints excluded: chain L7 residue 175 MET Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 105 THR Chi-restraints excluded: chain L9 residue 155 VAL Chi-restraints excluded: chain L9 residue 171 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 48 VAL Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 55 ARG Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 51 LYS Chi-restraints excluded: chain LI residue 120 GLU Chi-restraints excluded: chain LK residue 3 SER Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 174 ARG Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain NB residue 13 MET Chi-restraints excluded: chain NB residue 69 GLN Chi-restraints excluded: chain NB residue 350 VAL Chi-restraints excluded: chain NH residue 1 MET Chi-restraints excluded: chain NH residue 136 MET Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain NK residue 89 GLN Chi-restraints excluded: chain NM residue 13 ASN Chi-restraints excluded: chain NM residue 40 ASN Chi-restraints excluded: chain NM residue 138 SER Chi-restraints excluded: chain NO residue 192 LYS Chi-restraints excluded: chain NQ residue 20 LEU Chi-restraints excluded: chain NQ residue 113 HIS Chi-restraints excluded: chain NQ residue 134 CYS Chi-restraints excluded: chain NQ residue 242 VAL Chi-restraints excluded: chain NS residue 52 PHE Chi-restraints excluded: chain SC residue 54 ILE Chi-restraints excluded: chain SC residue 59 ARG Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 214 ASP Chi-restraints excluded: chain SE residue 56 LYS Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 54 ASN Chi-restraints excluded: chain SH residue 187 SER Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SJ residue 823 VAL Chi-restraints excluded: chain SJ residue 824 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 267 PHE Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 417 VAL Chi-restraints excluded: chain SN residue 119 VAL Chi-restraints excluded: chain SN residue 180 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 179 VAL Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SS residue 184 THR Chi-restraints excluded: chain SS residue 277 THR Chi-restraints excluded: chain ST residue 220 ARG Chi-restraints excluded: chain SV residue 25 ASP Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 104 GLN Chi-restraints excluded: chain SW residue 202 MET Chi-restraints excluded: chain SW residue 601 VAL Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SZ residue 60 VAL Chi-restraints excluded: chain SZ residue 114 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1291 random chunks: chunk 627 optimal weight: 6.9990 chunk 813 optimal weight: 9.9990 chunk 1090 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 chunk 944 optimal weight: 0.0870 chunk 151 optimal weight: 6.9990 chunk 284 optimal weight: 5.9990 chunk 1025 optimal weight: 0.9980 chunk 429 optimal weight: 7.9990 chunk 1053 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L6 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LA 10 ASN ** LA 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 97 ASN LE 112 ASN LI 14 ASN LS 68 ASN NB 52 ASN ** NH 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 332 HIS NI 412 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NM 160 ASN NO 101 GLN ** NQ 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 138 GLN SG 140 GLN SI 153 ASN SJ 687 ASN SJ 711 GLN ** SK 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SO 260 GLN SQ 91 GLN SR 228 HIS SR 354 ASN ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ST 208 HIS SV 115 ASN SW 328 GLN SW 499 GLN SZ 171 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.098215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.070230 restraints weight = 370607.193| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.70 r_work: 0.3018 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 142350 Z= 0.173 Angle : 0.481 11.907 203515 Z= 0.249 Chirality : 0.034 0.218 24517 Planarity : 0.004 0.062 17261 Dihedral : 21.178 177.076 49059 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.21 % Allowed : 13.32 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.08), residues: 10627 helix: 2.37 (0.08), residues: 4571 sheet: 0.44 (0.13), residues: 1504 loop : 0.14 (0.09), residues: 4552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPNQ 112 HIS 0.016 0.001 HISSW 207 PHE 0.031 0.001 PHEBA 106 TYR 0.026 0.001 TYRLG 38 ARG 0.018 0.000 ARGSA 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41988.25 seconds wall clock time: 729 minutes 11.61 seconds (43751.61 seconds total)