Starting phenix.real_space_refine on Sun Mar 3 22:59:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fky_29261/03_2024/8fky_29261_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fky_29261/03_2024/8fky_29261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fky_29261/03_2024/8fky_29261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fky_29261/03_2024/8fky_29261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fky_29261/03_2024/8fky_29261_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fky_29261/03_2024/8fky_29261_neut_updated.pdb" } resolution = 2.67 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= 0.051 sd= 0.192 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 3 6.06 5 P 2815 5.49 5 Mg 70 5.21 5 S 423 5.16 5 C 88901 2.51 5 N 29265 2.21 5 O 36806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BA GLU 21": "OE1" <-> "OE2" Residue "BA ASP 107": "OD1" <-> "OD2" Residue "BA GLU 124": "OE1" <-> "OE2" Residue "BA GLU 131": "OE1" <-> "OE2" Residue "BA GLU 161": "OE1" <-> "OE2" Residue "L6 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L6 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L6 GLU 108": "OE1" <-> "OE2" Residue "L7 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ASP 106": "OD1" <-> "OD2" Residue "L7 GLU 144": "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 32": "OD1" <-> "OD2" Residue "L8 ASP 39": "OD1" <-> "OD2" Residue "L8 ASP 59": "OD1" <-> "OD2" Residue "L8 GLU 96": "OE1" <-> "OE2" Residue "L9 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 ASP 17": "OD1" <-> "OD2" Residue "L9 ASP 46": "OD1" <-> "OD2" Residue "L9 GLU 123": "OE1" <-> "OE2" Residue "L9 ASP 147": "OD1" <-> "OD2" Residue "LA ASP 7": "OD1" <-> "OD2" Residue "LA GLU 89": "OE1" <-> "OE2" Residue "LA GLU 99": "OE1" <-> "OE2" Residue "LB ASP 10": "OD1" <-> "OD2" Residue "LB ASP 89": "OD1" <-> "OD2" Residue "LB ASP 129": "OD1" <-> "OD2" Residue "LC GLU 130": "OE1" <-> "OE2" Residue "LC GLU 131": "OE1" <-> "OE2" Residue "LC ASP 147": "OD1" <-> "OD2" Residue "LD TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 38": "OD1" <-> "OD2" Residue "LE GLU 118": "OE1" <-> "OE2" Residue "LE PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG ASP 59": "OD1" <-> "OD2" Residue "LG GLU 71": "OE1" <-> "OE2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 99": "OE1" <-> "OE2" Residue "LH GLU 16": "OE1" <-> "OE2" Residue "LH ASP 72": "OD1" <-> "OD2" Residue "LH ASP 120": "OD1" <-> "OD2" Residue "LI GLU 37": "OE1" <-> "OE2" Residue "LI GLU 54": "OE1" <-> "OE2" Residue "LI TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ ASP 30": "OD1" <-> "OD2" Residue "LJ ASP 35": "OD1" <-> "OD2" Residue "LJ TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL GLU 28": "OE1" <-> "OE2" Residue "LN GLU 59": "OE1" <-> "OE2" Residue "LN GLU 71": "OE1" <-> "OE2" Residue "LN GLU 74": "OE1" <-> "OE2" Residue "LN TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 80": "OE1" <-> "OE2" Residue "LO TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO ASP 101": "OD1" <-> "OD2" Residue "LS GLU 16": "OE1" <-> "OE2" Residue "LS ASP 22": "OD1" <-> "OD2" Residue "LS GLU 27": "OE1" <-> "OE2" Residue "LS GLU 67": "OE1" <-> "OE2" Residue "LS GLU 100": "OE1" <-> "OE2" Residue "LS GLU 111": "OE1" <-> "OE2" Residue "LT TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU ASP 42": "OD1" <-> "OD2" Residue "LU GLU 46": "OE1" <-> "OE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NB GLU 63": "OE1" <-> "OE2" Residue "NF GLU 22": "OE1" <-> "OE2" Residue "NF GLU 112": "OE1" <-> "OE2" Residue "NF TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF GLU 249": "OE1" <-> "OE2" Residue "NH GLU 14": "OE1" <-> "OE2" Residue "NH GLU 22": "OE1" <-> "OE2" Residue "NH GLU 49": "OE1" <-> "OE2" Residue "NH ASP 87": "OD1" <-> "OD2" Residue "NI PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NK GLU 16": "OE1" <-> "OE2" Residue "NK GLU 25": "OE1" <-> "OE2" Residue "NK TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NK GLU 110": "OE1" <-> "OE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 146": "OE1" <-> "OE2" Residue "SA GLU 149": "OE1" <-> "OE2" Residue "SA ASP 179": "OD1" <-> "OD2" Residue "SC TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC ASP 214": "OD1" <-> "OD2" Residue "SC GLU 244": "OE1" <-> "OE2" Residue "SC ASP 254": "OD1" <-> "OD2" Residue "SD PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 60": "OE1" <-> "OE2" Residue "SD GLU 86": "OE1" <-> "OE2" Residue "SD GLU 137": "OE1" <-> "OE2" Residue "SD ASP 238": "OD1" <-> "OD2" Residue "SE TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE ASP 88": "OD1" <-> "OD2" Residue "SE GLU 220": "OE1" <-> "OE2" Residue "SE ASP 228": "OD1" <-> "OD2" Residue "SE ASP 231": "OD1" <-> "OD2" Residue "SG ASP 37": "OD1" <-> "OD2" Residue "SG GLU 44": "OE1" <-> "OE2" Residue "SG GLU 66": "OE1" <-> "OE2" Residue "SG GLU 107": "OE1" <-> "OE2" Residue "SG GLU 120": "OE1" <-> "OE2" Residue "SG ASP 150": "OD1" <-> "OD2" Residue "SH ASP 57": "OD1" <-> "OD2" Residue "SH ASP 97": "OD1" <-> "OD2" Residue "SH GLU 129": "OE1" <-> "OE2" Residue "SH ASP 133": "OD1" <-> "OD2" Residue "SI ASP 92": "OD1" <-> "OD2" Residue "SJ ASP 697": "OD1" <-> "OD2" Residue "SJ GLU 777": "OE1" <-> "OE2" Residue "SJ PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 32": "OE1" <-> "OE2" Residue "SK GLU 124": "OE1" <-> "OE2" Residue "SK PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 168": "OE1" <-> "OE2" Residue "SL PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM GLU 337": "OE1" <-> "OE2" Residue "SM GLU 341": "OE1" <-> "OE2" Residue "SM GLU 353": "OE1" <-> "OE2" Residue "SN GLU 139": "OE1" <-> "OE2" Residue "SN GLU 162": "OE1" <-> "OE2" Residue "SN PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SP PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SP PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 256": "OD1" <-> "OD2" Residue "SR PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS GLU 168": "OE1" <-> "OE2" Residue "SS PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST ASP 283": "OD1" <-> "OD2" Residue "SU PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU GLU 482": "OE1" <-> "OE2" Residue "SU PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 84": "OE1" <-> "OE2" Residue "SV GLU 98": "OE1" <-> "OE2" Residue "SW GLU 262": "OE1" <-> "OE2" Residue "SW ASP 333": "OD1" <-> "OD2" Residue "SW PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 493": "OE1" <-> "OE2" Residue "SW PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY GLU 481": "OE1" <-> "OE2" Residue "SY GLU 493": "OE1" <-> "OE2" Residue "SY PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ ASP 129": "OD1" <-> "OD2" Residue "SZ ASP 143": "OD1" <-> "OD2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 158284 Number of models: 1 Model: "" Number of chains: 72 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: "BC" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2580 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 326} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L1" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3294 Classifications: {'RNA': 155} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 15, 'rna3p_pur': 60, 'rna3p_pyr': 65} Link IDs: {'rna2p': 29, 'rna3p': 125} 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: 55445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2585, 55445 Classifications: {'RNA': 2585} Modifications used: {'rna2p_pur': 239, 'rna2p_pyr': 149, 'rna3p_pur': 1183, 'rna3p_pyr': 1014} Link IDs: {'rna2p': 388, 'rna3p': 2196} Chain breaks: 42 Chain: "L6" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 998 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 110} Chain: "L7" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1650 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 191} Chain: "L8" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "L9" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1546 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "LA" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1106 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 1 Chain: "LB" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1223 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "LC" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1461 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain: "LD" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1117 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain breaks: 2 Chain: "LE" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 926 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain breaks: 2 Chain: "LG" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "LH" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1084 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain breaks: 1 Chain: "LI" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LJ" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "LK" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 642 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "LL" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "LN" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2884 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 345} Chain breaks: 2 Chain: "LO" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 738 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "LP" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 526 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 197 Chain: "LQ" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "LR" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 485 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain breaks: 1 Chain: "LS" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "LT" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "LU" Number of atoms: 840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} bond proxies already assigned to first conformer: 834 Chain: "LW" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 612 Classifications: {'peptide': 74} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 70} Chain: "NA" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3389 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 22, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 529 Unresolved non-hydrogen angles: 673 Unresolved non-hydrogen dihedrals: 439 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 9, 'GLU:plan': 7, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 251 Chain: "NB" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 603 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain breaks: 1 Chain: "NF" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1696 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 3 Chain: "NH" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1441 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "NI" Number of atoms: 4832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4832 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 29, 'TRANS': 582} Chain breaks: 5 Chain: "NK" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 581 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "SA" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2853 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 339} Chain: "SC" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1721 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 200} Chain breaks: 2 Chain: "SD" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "SE" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1498 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 175} Chain: "SG" Number of atoms: 1526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Conformer: "B" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} bond proxies already assigned to first conformer: 1528 Chain: "SH" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1267 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "SI" Number of atoms: 1896 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1885 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 229, 1885 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain breaks: 1 bond proxies already assigned to first conformer: 1909 Chain: "SJ" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1939 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain breaks: 3 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 100 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: 4113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4113 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 478} Chain breaks: 3 Chain: "SN" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1350 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "SO" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2460 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 274} Chain breaks: 1 Chain: "SP" Number of atoms: 2983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2983 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 12, 'TRANS': 384} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 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: 3841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3841 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 19, 'TRANS': 446} Chain: "SS" Number of atoms: 5041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5041 Classifications: {'peptide': 628} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 572} Chain: "ST" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1091 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 139} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "SU" Number of atoms: 4360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4360 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 530} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "SV" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1171 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "SW" Number of atoms: 3580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3580 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} 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: "L3" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Unusual residues: {' MG': 56} Classifications: {'undetermined': 56} Link IDs: {None: 55} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "LR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "NI" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "SA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SR" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' K': 1, ' MG': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "SU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 87345 SG CYSLR 46 106.717 185.179 124.388 1.00 43.03 S ATOM 87362 SG CYSLR 49 104.953 188.209 125.940 1.00 51.93 S ATOM 87575 SG CYSLR 83 102.899 186.248 123.534 1.00 29.10 S ATOM 87595 SG CYSLR 86 105.999 187.745 122.148 1.00 30.70 S ATOM 90575 SG CYSLW 19 122.053 127.953 150.967 1.00 25.88 S ATOM 90603 SG CYSLW 22 122.761 125.172 153.390 1.00 25.37 S ATOM 90694 SG CYSLW 34 124.710 128.506 153.509 1.00 23.17 S ATOM 90713 SG CYSLW 37 125.355 126.066 150.697 1.00 25.43 S ATOM A11WS SG CYSSV 6 90.314 184.485 236.366 1.00 25.77 S ATOM A11XL SG CYSSV 9 86.760 183.314 235.937 1.00 25.48 S ATOM A122P SG CYSSV 32 89.536 180.754 236.637 1.00 22.84 S ATOM A123J SG CYSSV 36 89.338 182.451 233.289 1.00 25.89 S Time building chain proxies: 59.81, per 1000 atoms: 0.38 Number of scatterers: 158284 At special positions: 0 Unit cell: (271.216, 299.088, 335.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 K 1 19.00 S 423 16.00 P 2815 15.00 Mg 70 11.99 O 36806 8.00 N 29265 7.00 C 88901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 54.51 Conformation dependent library (CDL) restraints added in 15.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLR 500 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 86 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 46 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 83 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 49 " pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " Number of angles added : 18 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23430 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: 458 helices and 115 sheets defined 49.4% alpha, 14.1% beta 905 base pairs and 1414 stacking pairs defined. Time for finding SS restraints: 93.95 Creating SS restraints... Processing helix chain 'BA' and resid 24 through 33 Proline residue: BA 30 - end of helix Processing helix chain 'BA' and resid 38 through 51 Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.578A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 5.013A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.539A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 Processing helix chain 'BB' and resid 6 through 25 Processing helix chain 'BB' and resid 70 through 81 Processing helix chain 'BB' and resid 86 through 97 removed outlier: 4.428A pdb=" N LYSBB 95 " --> pdb=" O LYSBB 91 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASNBB 96 " --> pdb=" O LYSBB 92 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LYSBB 97 " --> pdb=" O LEUBB 93 " (cutoff:3.500A) Processing helix chain 'BB' and resid 98 through 108 removed outlier: 4.873A pdb=" N ASPBB 108 " --> pdb=" O ALABB 104 " (cutoff:3.500A) Processing helix chain 'BB' and resid 113 through 124 removed outlier: 4.404A pdb=" N LYSBB 118 " --> pdb=" O GLUBB 114 " (cutoff:3.500A) removed outlier: 5.090A 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: 3.598A 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: 5.269A pdb=" N LYSBB 195 " --> pdb=" O VALBB 191 " (cutoff:3.500A) Processing helix chain 'BB' and resid 197 through 202 removed outlier: 3.953A pdb=" N VALBB 201 " --> pdb=" O ASNBB 197 " (cutoff:3.500A) removed outlier: 5.405A 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 'BC' and resid 324 through 330 removed outlier: 3.928A pdb=" N ALABC 329 " --> pdb=" O ALABC 325 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VALBC 330 " --> pdb=" O GLNBC 326 " (cutoff:3.500A) Processing helix chain 'BC' and resid 354 through 364 removed outlier: 4.498A pdb=" N PHEBC 358 " --> pdb=" O SERBC 354 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHEBC 359 " --> pdb=" O THRBC 355 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALABC 360 " --> pdb=" O ASPBC 356 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLYBC 361 " --> pdb=" O ASPBC 357 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEUBC 362 " --> pdb=" O PHEBC 358 " (cutoff:3.500A) Processing helix chain 'L6' and resid 17 through 22 removed outlier: 4.486A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 4.214A 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: 4.078A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.504A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 Processing helix chain 'L7' and resid 46 through 60 removed outlier: 3.735A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 Proline residue: L7 70 - end of helix Processing helix chain 'L7' and resid 75 through 89 Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 3.672A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.935A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.417A 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 151 through 190 removed outlier: 5.271A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.531A pdb=" N VALL7 195 " --> pdb=" O LYSL7 191 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HISL7 199 " --> pdb=" O VALL7 195 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.841A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLNL8 56 " --> pdb=" O PHEL8 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'L8' and resid 51 through 56' Processing helix chain 'L8' and resid 69 through 81 removed outlier: 3.544A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.572A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.943A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.977A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 4.903A 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: 3.840A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.701A 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: 6.124A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.895A 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 Processing helix chain 'L9' and resid 165 through 173 removed outlier: 3.581A pdb=" N LYSL9 170 " --> pdb=" O SERL9 166 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLYL9 173 " --> pdb=" O ARGL9 169 " (cutoff:3.500A) Processing helix chain 'L9' and resid 187 through 197 Processing helix chain 'LA' and resid 10 through 15 removed outlier: 3.526A pdb=" N SERLA 14 " --> pdb=" O ASNLA 10 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N CYSLA 15 " --> pdb=" O PROLA 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 10 through 15' Processing helix chain 'LA' and resid 25 through 37 removed outlier: 3.624A pdb=" N ALALA 35 " --> pdb=" O GLULA 31 " (cutoff:3.500A) Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 70 through 77 removed outlier: 4.255A pdb=" N LYSLA 74 " --> pdb=" O CYSLA 70 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLNLA 75 " --> pdb=" O ALALA 71 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYLA 77 " --> pdb=" O ALALA 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 70 through 77' Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.155A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 Processing helix chain 'LB' and resid 106 through 117 Processing helix chain 'LB' and resid 122 through 130 Processing helix chain 'LB' and resid 147 through 152 removed outlier: 3.935A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.504A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLNLC 125 " --> pdb=" O ALALC 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 120 through 125' Processing helix chain 'LC' and resid 133 through 138 removed outlier: 6.061A pdb=" N ARGLC 138 " --> pdb=" O ALALC 134 " (cutoff:3.500A) Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.501A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.030A 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 'LD' and resid 4 through 16 Processing helix chain 'LD' and resid 18 through 23 removed outlier: 3.574A pdb=" N VALLD 22 " --> pdb=" O GLYLD 18 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TRPLD 23 " --> pdb=" O LYSLD 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 18 through 23' Processing helix chain 'LD' and resid 28 through 36 removed outlier: 3.637A pdb=" N ALALD 35 " --> pdb=" O GLULD 31 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASNLD 36 " --> pdb=" O ILELD 32 " (cutoff:3.500A) Processing helix chain 'LD' and resid 37 through 48 Processing helix chain 'LD' and resid 63 through 73 Processing helix chain 'LD' and resid 90 through 113 removed outlier: 3.696A pdb=" N THRLD 94 " --> pdb=" O PROLD 90 " (cutoff:3.500A) Processing helix chain 'LD' and resid 116 through 130 Processing helix chain 'LD' and resid 134 through 155 Processing helix chain 'LE' and resid 92 through 97 removed outlier: 3.806A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYSLE 97 " --> pdb=" O ILELE 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 92 through 97' Processing helix chain 'LE' and resid 100 through 121 removed outlier: 4.175A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYSLE 110 " --> pdb=" O LEULE 106 " (cutoff:3.500A) Processing helix chain 'LG' and resid 122 through 130 Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 137 removed outlier: 5.597A pdb=" N GLYLG 137 " --> pdb=" O ALALG 133 " (cutoff:3.500A) Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.576A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 93 removed outlier: 3.575A pdb=" N ILELH 90 " --> pdb=" O ALALH 86 " (cutoff:3.500A) Processing helix chain 'LH' and resid 105 through 118 Processing helix chain 'LH' and resid 145 through 154 Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 4.119A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.158A 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: 4.053A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.579A 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 'LJ' and resid 58 through 67 removed outlier: 4.231A pdb=" N LYSLJ 67 " --> pdb=" O ALALJ 63 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 81 removed outlier: 4.817A pdb=" N METLJ 81 " --> pdb=" O TYRLJ 77 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 92 through 97 removed outlier: 4.332A pdb=" N ASNLJ 97 " --> pdb=" O LYSLJ 93 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 98 through 104 Proline residue: LJ 104 - end of helix Processing helix chain 'LJ' and resid 105 through 125 removed outlier: 3.600A pdb=" N LYSLJ 109 " --> pdb=" O ALALJ 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLYLJ 125 " --> pdb=" O ARGLJ 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 127 through 133 removed outlier: 3.797A pdb=" N PHELJ 131 " --> pdb=" O ASNLJ 127 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYSLJ 133 " --> pdb=" O TRPLJ 129 " (cutoff:3.500A) Processing helix chain 'LK' and resid 6 through 12 removed outlier: 3.934A pdb=" N LYSLK 10 " --> pdb=" O ARGLK 6 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARGLK 12 " --> pdb=" O THRLK 8 " (cutoff:3.500A) Processing helix chain 'LK' and resid 60 through 67 removed outlier: 5.509A pdb=" N GLNLK 67 " --> pdb=" O LEULK 63 " (cutoff:3.500A) Processing helix chain 'LK' and resid 74 through 83 removed outlier: 3.523A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 94 removed outlier: 4.440A pdb=" N LYSLK 94 " --> pdb=" O ALALK 90 " (cutoff:3.500A) Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.676A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 Processing helix chain 'LL' and resid 2 through 13 removed outlier: 5.372A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 72 through 77 removed outlier: 4.486A pdb=" N TYRLL 77 " --> pdb=" O PROLL 73 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.548A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 4.019A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LN' and resid 111 through 120 removed outlier: 3.979A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 4.157A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 157 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 3.902A pdb=" N LEULN 171 " --> pdb=" O GLNLN 167 " (cutoff:3.500A) Proline residue: LN 172 - end of helix No H-bonds generated for 'chain 'LN' and resid 167 through 172' Processing helix chain 'LN' and resid 189 through 201 Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.788A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 3.859A 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 'LO' and resid 13 through 25 removed outlier: 4.183A pdb=" N LYSLO 23 " --> pdb=" O GLNLO 19 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SERLO 24 " --> pdb=" O LEULO 20 " (cutoff:3.500A) Processing helix chain 'LO' and resid 30 through 41 removed outlier: 3.607A pdb=" N THRLO 34 " --> pdb=" O GLYLO 30 " (cutoff:3.500A) Processing helix chain 'LO' and resid 53 through 68 Processing helix chain 'LO' and resid 77 through 86 Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.784A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) Processing helix chain 'LP' and resid 37 through 57 removed outlier: 4.669A pdb=" N ALALP 42 " --> pdb=" O PHELP 38 " (cutoff:3.500A) Proline residue: LP 43 - end of helix Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 4.935A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 43 through 48 Processing helix chain 'LQ' and resid 81 through 90 removed outlier: 3.534A pdb=" N LEULQ 85 " --> pdb=" O ASNLQ 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLULQ 86 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 81 through 90' Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.649A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LR' and resid 68 through 73 removed outlier: 3.512A pdb=" N LYSLR 72 " --> pdb=" O SERLR 68 " (cutoff:3.500A) Processing helix chain 'LR' and resid 83 through 110 Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.794A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 removed outlier: 3.592A pdb=" N LEULS 24 " --> pdb=" O GLNLS 20 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLYLS 38 " --> pdb=" O ALALS 34 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.536A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 3.988A 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: 5.520A 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: 3.652A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.390A 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: 4.190A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.219A 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: 3.571A pdb=" N GLULU 46 " --> pdb=" O ASPLU 42 " (cutoff:3.500A) removed outlier: 3.626A 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 Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.623A 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: 4.292A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) Processing helix chain 'NA' and resid 150 through 164 Processing helix chain 'NA' and resid 166 through 186 Processing helix chain 'NA' and resid 187 through 195 removed outlier: 3.507A pdb=" N ALANA 191 " --> pdb=" O ASPNA 187 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYSNA 195 " --> pdb=" O ALANA 191 " (cutoff:3.500A) Processing helix chain 'NA' and resid 200 through 214 removed outlier: 3.544A pdb=" N ARGNA 213 " --> pdb=" O THRNA 209 " (cutoff:3.500A) Processing helix chain 'NA' and resid 215 through 224 removed outlier: 3.782A pdb=" N LEUNA 222 " --> pdb=" O CYSNA 218 " (cutoff:3.500A) Processing helix chain 'NA' and resid 242 through 264 removed outlier: 4.349A pdb=" N VALNA 248 " --> pdb=" O GLYNA 244 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASPNA 249 " --> pdb=" O LYSNA 245 " (cutoff:3.500A) Processing helix chain 'NA' and resid 266 through 281 Processing helix chain 'NA' and resid 282 through 288 removed outlier: 3.612A pdb=" N PHENA 287 " --> pdb=" O CYSNA 283 " (cutoff:3.500A) Proline residue: NA 288 - end of helix Processing helix chain 'NA' and resid 289 through 305 removed outlier: 3.654A pdb=" N LYSNA 296 " --> pdb=" O ARGNA 292 " (cutoff:3.500A) Processing helix chain 'NA' and resid 306 through 325 Processing helix chain 'NA' and resid 328 through 345 removed outlier: 4.044A pdb=" N VALNA 332 " --> pdb=" O PHENA 328 " (cutoff:3.500A) Processing helix chain 'NA' and resid 349 through 370 Proline residue: NA 353 - end of helix removed outlier: 3.601A pdb=" N THRNA 363 " --> pdb=" O GLNNA 359 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLUNA 364 " --> pdb=" O TRPNA 360 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEUNA 365 " --> pdb=" O THRNA 361 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEUNA 368 " --> pdb=" O GLUNA 364 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLUNA 369 " --> pdb=" O LEUNA 365 " (cutoff:3.500A) Proline residue: NA 370 - end of helix Processing helix chain 'NA' and resid 371 through 395 Processing helix chain 'NA' and resid 396 through 405 removed outlier: 3.635A pdb=" N TYRNA 400 " --> pdb=" O LYSNA 396 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLNNA 401 " --> pdb=" O LYSNA 397 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SERNA 402 " --> pdb=" O GLUNA 398 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VALNA 403 " --> pdb=" O THRNA 399 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASNNA 405 " --> pdb=" O GLNNA 401 " (cutoff:3.500A) Processing helix chain 'NA' and resid 406 through 421 removed outlier: 3.627A pdb=" N CYSNA 411 " --> pdb=" O GLNNA 407 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEUNA 412 " --> pdb=" O TYRNA 408 " (cutoff:3.500A) Processing helix chain 'NA' and resid 422 through 429 removed outlier: 3.987A pdb=" N GLUNA 426 " --> pdb=" O ALANA 422 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALANA 427 " --> pdb=" O GLYNA 423 " (cutoff:3.500A) Processing helix chain 'NA' and resid 430 through 447 Proline residue: NA 434 - end of helix removed outlier: 4.908A pdb=" N ILENA 446 " --> pdb=" O CYSNA 442 " (cutoff:3.500A) Proline residue: NA 447 - end of helix Processing helix chain 'NA' and resid 448 through 469 removed outlier: 4.078A pdb=" N TYRNA 452 " --> pdb=" O THRNA 448 " (cutoff:3.500A) Proline residue: NA 453 - end of helix Processing helix chain 'NA' and resid 474 through 486 removed outlier: 4.710A pdb=" N PHENA 478 " --> pdb=" O PRONA 474 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N METNA 482 " --> pdb=" O PHENA 478 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHENA 483 " --> pdb=" O ILENA 479 " (cutoff:3.500A) Processing helix chain 'NA' and resid 509 through 516 removed outlier: 3.677A pdb=" N GLNNA 514 " --> pdb=" O ASNNA 510 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYSNA 516 " --> pdb=" O ASNNA 512 " (cutoff:3.500A) Processing helix chain 'NA' and resid 517 through 538 removed outlier: 3.539A pdb=" N VALNA 523 " --> pdb=" O ARGNA 519 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLNNA 537 " --> pdb=" O TYRNA 533 " (cutoff:3.500A) Processing helix chain 'NA' and resid 542 through 561 Proline residue: NA 549 - end of helix Processing helix chain 'NA' and resid 564 through 592 removed outlier: 3.518A pdb=" N GLNNA 589 " --> pdb=" O CYSNA 585 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARGNA 590 " --> pdb=" O SERNA 586 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SERNA 592 " --> pdb=" O ARGNA 588 " (cutoff:3.500A) Processing helix chain 'NA' and resid 597 through 612 removed outlier: 3.734A pdb=" N VALNA 601 " --> pdb=" O GLUNA 597 " (cutoff:3.500A) Processing helix chain 'NA' and resid 613 through 634 removed outlier: 3.550A pdb=" N LEUNA 632 " --> pdb=" O ARGNA 628 " (cutoff:3.500A) Processing helix chain 'NB' and resid 14 through 36 Processing helix chain 'NB' and resid 56 through 81 Processing helix chain 'NF' and resid 5 through 14 removed outlier: 3.519A pdb=" N LEUNF 9 " --> pdb=" O GLUNF 5 " (cutoff:3.500A) Processing helix chain 'NF' and resid 21 through 35 removed outlier: 4.211A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N HISNF 33 " --> pdb=" O SERNF 29 " (cutoff:3.500A) Processing helix chain 'NF' and resid 44 through 72 Processing helix chain 'NF' and resid 97 through 116 Processing helix chain 'NF' and resid 173 through 178 removed outlier: 3.553A pdb=" N ARGNF 177 " --> pdb=" O PRONF 173 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N PHENF 178 " --> pdb=" O METNF 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'NF' and resid 173 through 178' Processing helix chain 'NF' and resid 205 through 212 Processing helix chain 'NF' and resid 247 through 252 Processing helix chain 'NH' and resid 5 through 20 removed outlier: 4.279A pdb=" N TYRNH 19 " --> pdb=" O LYSNH 15 " (cutoff:3.500A) Processing helix chain 'NH' and resid 22 through 30 removed outlier: 4.664A pdb=" N LEUNH 26 " --> pdb=" O GLUNH 22 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARGNH 30 " --> pdb=" O LEUNH 26 " (cutoff:3.500A) Processing helix chain 'NH' and resid 48 through 59 removed outlier: 3.518A pdb=" N ALANH 56 " --> pdb=" O METNH 52 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASNNH 57 " --> pdb=" O LYSNH 53 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILENH 58 " --> pdb=" O LEUNH 54 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SERNH 59 " --> pdb=" O ALANH 55 " (cutoff:3.500A) Processing helix chain 'NH' and resid 82 through 93 removed outlier: 4.456A pdb=" N LEUNH 86 " --> pdb=" O HISNH 82 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASPNH 87 " --> pdb=" O VALNH 83 " (cutoff:3.500A) removed outlier: 5.516A 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: 4.626A pdb=" N GLNNH 105 " --> pdb=" O PRONH 101 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N SERNH 106 " --> pdb=" O GLYNH 102 " (cutoff:3.500A) Processing helix chain 'NH' and resid 114 through 119 removed outlier: 5.524A pdb=" N GLYNH 119 " --> pdb=" O LYSNH 115 " (cutoff:3.500A) Processing helix chain 'NH' and resid 149 through 157 removed outlier: 3.793A pdb=" N ARGNH 154 " --> pdb=" O THRNH 150 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYSNH 155 " --> pdb=" O GLNNH 151 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASPNH 157 " --> pdb=" O CYSNH 153 " (cutoff:3.500A) Processing helix chain 'NH' and resid 169 through 175 removed outlier: 4.693A pdb=" N VALNH 173 " --> pdb=" O ILENH 169 " (cutoff:3.500A) Processing helix chain 'NI' and resid 97 through 102 removed outlier: 3.542A pdb=" N GLYNI 102 " --> pdb=" O PHENI 98 " (cutoff:3.500A) Processing helix chain 'NI' and resid 104 through 115 removed outlier: 3.581A pdb=" N GLYNI 110 " --> pdb=" O PRONI 106 " (cutoff:3.500A) Processing helix chain 'NI' and resid 120 through 133 Proline residue: NI 128 - end of helix Processing helix chain 'NI' and resid 145 through 159 removed outlier: 3.804A pdb=" N CYSNI 149 " --> pdb=" O GLYNI 145 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHENI 150 " --> pdb=" O LYSNI 146 " (cutoff:3.500A) Proline residue: NI 153 - end of helix Processing helix chain 'NI' and resid 175 through 190 Processing helix chain 'NI' and resid 205 through 216 removed outlier: 3.997A 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 Processing helix chain 'NI' and resid 257 through 269 removed outlier: 3.605A pdb=" N ALANI 266 " --> pdb=" O GLNNI 262 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARGNI 267 " --> pdb=" O GLUNI 263 " (cutoff:3.500A) Proline residue: NI 269 - end of helix Processing helix chain 'NI' and resid 282 through 293 Processing helix chain 'NI' and resid 301 through 307 removed outlier: 3.608A pdb=" N THRNI 305 " --> pdb=" O LEUNI 301 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSNI 306 " --> pdb=" O ASPNI 302 " (cutoff:3.500A) removed outlier: 5.189A 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: 4.833A pdb=" N ALANI 324 " --> pdb=" O GLUNI 320 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ALANI 325 " --> pdb=" O ASPNI 321 " (cutoff:3.500A) Processing helix chain 'NI' and resid 347 through 362 Processing helix chain 'NI' and resid 373 through 387 Processing helix chain 'NI' and resid 395 through 403 removed outlier: 5.054A pdb=" N GLYNI 401 " --> pdb=" O LEUNI 397 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEUNI 402 " --> pdb=" O ALANI 398 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASPNI 403 " --> pdb=" O ALANI 399 " (cutoff:3.500A) Processing helix chain 'NI' and resid 418 through 427 Processing helix chain 'NI' and resid 443 through 458 Proline residue: NI 448 - end of helix Processing helix chain 'NI' and resid 472 through 479 removed outlier: 5.279A pdb=" N GLYNI 478 " --> pdb=" O ALANI 474 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N METNI 479 " --> pdb=" O GLYNI 475 " (cutoff:3.500A) Processing helix chain 'NI' and resid 486 through 503 removed outlier: 4.138A pdb=" N GLYNI 494 " --> pdb=" O GLUNI 490 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SERNI 502 " --> pdb=" O THRNI 498 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEUNI 503 " --> pdb=" O LEUNI 499 " (cutoff:3.500A) Processing helix chain 'NI' and resid 504 through 523 Processing helix chain 'NI' and resid 527 through 543 removed outlier: 3.536A pdb=" N LYSNI 532 " --> pdb=" O PRONI 528 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASPNI 538 " --> pdb=" O ALANI 534 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEUNI 539 " --> pdb=" O LYSNI 535 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VALNI 540 " --> pdb=" O GLUNI 536 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLYNI 541 " --> pdb=" O METNI 537 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLYNI 543 " --> pdb=" O LEUNI 539 " (cutoff:3.500A) Processing helix chain 'NI' and resid 545 through 553 removed outlier: 4.230A pdb=" N ARGNI 551 " --> pdb=" O LEUNI 547 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHENI 552 " --> pdb=" O PHENI 548 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLUNI 553 " --> pdb=" O SERNI 549 " (cutoff:3.500A) Processing helix chain 'NI' and resid 554 through 569 removed outlier: 3.560A pdb=" N ILENI 566 " --> pdb=" O LEUNI 562 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYSNI 567 " --> pdb=" O VALNI 563 " (cutoff:3.500A) Processing helix chain 'NI' and resid 574 through 579 removed outlier: 4.993A 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: 3.607A pdb=" N GLYNI 710 " --> pdb=" O GLNNI 706 " (cutoff:3.500A) Processing helix chain 'NI' and resid 719 through 739 removed outlier: 3.913A pdb=" N THRNI 724 " --> pdb=" O ALANI 720 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARGNI 725 " --> pdb=" O GLNNI 721 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLYNI 726 " --> pdb=" O ASNNI 722 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARGNI 727 " --> pdb=" O LEUNI 723 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEUNI 730 " --> pdb=" O GLYNI 726 " (cutoff:3.500A) Processing helix chain 'NI' and resid 766 through 775 Processing helix chain 'NK' and resid 12 through 33 Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 98 through 112 Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.384A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALASA 30 " --> pdb=" O ALASA 26 " (cutoff:3.500A) Proline residue: SA 31 - end of helix No H-bonds generated for 'chain 'SA' and resid 25 through 31' Processing helix chain 'SA' and resid 33 through 49 removed outlier: 3.927A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.775A 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: 3.639A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.193A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 3.952A 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 removed outlier: 3.522A pdb=" N ALASA 167 " --> pdb=" O LYSSA 163 " (cutoff:3.500A) Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.689A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.503A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.524A 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: 3.659A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 Processing helix chain 'SA' and resid 296 through 303 removed outlier: 3.867A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.526A 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: 4.445A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SC' and resid 58 through 67 Processing helix chain 'SC' and resid 132 through 137 removed outlier: 6.035A pdb=" N VALSC 137 " --> pdb=" O PHESC 133 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.711A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILESC 195 " --> pdb=" O GLNSC 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 190 through 195' Processing helix chain 'SC' and resid 213 through 218 Processing helix chain 'SC' and resid 243 through 262 removed outlier: 3.517A 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: 5.304A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.397A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.673A 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: 3.579A pdb=" N METSD 132 " --> pdb=" O ALASD 128 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VALSD 136 " --> pdb=" O METSD 132 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.045A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.722A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.100A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 238 through 248 removed outlier: 4.836A pdb=" N ARGSD 242 " --> pdb=" O ASPSD 238 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.560A pdb=" N ALASE 68 " --> pdb=" O GLNSE 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYRSE 71 " --> pdb=" O ARGSE 67 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.422A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.553A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARGSE 103 " --> pdb=" O ALASE 99 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 124 Processing helix chain 'SE' and resid 139 through 150 removed outlier: 3.953A pdb=" N VALSE 143 " --> pdb=" O GLYSE 139 " (cutoff:3.500A) Processing helix chain 'SE' and resid 164 through 178 removed outlier: 5.022A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEUSE 170 " --> pdb=" O LEUSE 166 " (cutoff:3.500A) Proline residue: SE 171 - end of helix Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.643A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 231 removed outlier: 4.666A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASPSE 228 " --> pdb=" O THRSE 224 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARGSE 229 " --> pdb=" O ASNSE 225 " (cutoff:3.500A) Processing helix chain 'SE' and resid 232 through 237 removed outlier: 3.918A pdb=" N HISSE 236 " --> pdb=" O GLUSE 232 " (cutoff:3.500A) removed outlier: 5.315A 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: 3.564A pdb=" N ALASG 68 " --> pdb=" O ARGSG 64 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.965A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.761A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.648A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SH' and resid 122 through 127 removed outlier: 5.788A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) Processing helix chain 'SH' and resid 143 through 151 removed outlier: 3.525A pdb=" N LYSSH 147 " --> pdb=" O TYRSH 143 " (cutoff:3.500A) Processing helix chain 'SH' and resid 154 through 180 Processing helix chain 'SI' and resid 34 through 46 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.504A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.121A 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: 3.660A pdb=" N HISSI 185 " --> pdb=" O VALSI 181 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 5.121A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.155A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 5.084A 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 238 Processing helix chain 'SI' and resid 245 through 255 removed outlier: 4.411A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 422 through 427 removed outlier: 3.721A pdb=" N ILESJ 426 " --> pdb=" O SERSJ 422 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARGSJ 427 " --> pdb=" O LEUSJ 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'SJ' and resid 422 through 427' Processing helix chain 'SJ' and resid 428 through 438 removed outlier: 3.547A pdb=" N LEUSJ 432 " --> pdb=" O GLYSJ 428 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 440 through 445 Processing helix chain 'SJ' and resid 520 through 532 removed outlier: 4.597A pdb=" N ALASJ 526 " --> pdb=" O GLNSJ 522 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYSSJ 532 " --> pdb=" O LEUSJ 528 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 539 through 561 removed outlier: 4.326A pdb=" N ALASJ 545 " --> pdb=" O ASPSJ 541 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEUSJ 546 " --> pdb=" O ALASJ 542 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLUSJ 547 " --> pdb=" O ASPSJ 543 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SERSJ 549 " --> pdb=" O ALASJ 545 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 664 through 677 Processing helix chain 'SJ' and resid 678 through 690 removed outlier: 3.758A pdb=" N PHESJ 689 " --> pdb=" O ILESJ 685 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASNSJ 690 " --> pdb=" O ASPSJ 686 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 702 through 713 removed outlier: 3.725A pdb=" N GLNSJ 711 " --> pdb=" O GLNSJ 707 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 720 through 733 removed outlier: 3.514A pdb=" N LYSSJ 729 " --> pdb=" O GLUSJ 725 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARGSJ 730 " --> pdb=" O HISSJ 726 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRPSJ 731 " --> pdb=" O TYRSJ 727 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARGSJ 732 " --> pdb=" O ARGSJ 728 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLUSJ 733 " --> pdb=" O LYSSJ 729 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 738 through 767 Processing helix chain 'SJ' and resid 775 through 790 Processing helix chain 'SJ' and resid 825 through 843 removed outlier: 4.137A pdb=" N LYSSJ 829 " --> pdb=" O ASPSJ 825 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYSSJ 830 " --> pdb=" O SERSJ 826 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASPSJ 831 " --> pdb=" O ARGSJ 827 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 3.926A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.513A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLUSK 41 " --> pdb=" O VALSK 37 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 4.949A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 88 Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 removed outlier: 3.512A pdb=" N GLUSK 126 " --> pdb=" O ASPSK 122 " (cutoff:3.500A) Processing helix chain 'SK' and resid 147 through 152 removed outlier: 3.637A pdb=" N TYRSK 151 " --> pdb=" O LEUSK 147 " (cutoff:3.500A) Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.553A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.289A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 3.728A pdb=" N SERSK 235 " --> pdb=" O THRSK 231 " (cutoff:3.500A) Processing helix chain 'SK' and resid 238 through 244 Processing helix chain 'SL' and resid 32 through 50 Processing helix chain 'SL' and resid 106 through 122 Processing helix chain 'SL' and resid 131 through 138 Processing helix chain 'SL' and resid 141 through 153 removed outlier: 3.654A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 169 removed outlier: 4.883A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEUSL 165 " --> pdb=" O ILESL 161 " (cutoff:3.500A) Proline residue: SL 166 - end of helix Processing helix chain 'SL' and resid 170 through 177 removed outlier: 4.002A 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 removed outlier: 3.505A pdb=" N GLUSL 239 " --> pdb=" O LYSSL 235 " (cutoff:3.500A) Processing helix chain 'SL' and resid 244 through 249 removed outlier: 6.648A pdb=" N VALSL 248 " --> pdb=" O LYSSL 244 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYSSL 249 " --> pdb=" O TRPSL 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 244 through 249' Processing helix chain 'SM' and resid 12 through 17 removed outlier: 4.305A pdb=" N ASNSM 16 " --> pdb=" O GLYSM 12 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYRSM 17 " --> pdb=" O SERSM 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'SM' and resid 12 through 17' Processing helix chain 'SM' and resid 19 through 28 removed outlier: 3.506A pdb=" N LYSSM 25 " --> pdb=" O ASNSM 21 " (cutoff:3.500A) Processing helix chain 'SM' and resid 30 through 42 Processing helix chain 'SM' and resid 50 through 56 removed outlier: 4.731A pdb=" N LYSSM 56 " --> pdb=" O LYSSM 52 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 77 removed outlier: 3.877A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.642A pdb=" N LYSSM 86 " --> pdb=" O PHESM 82 " (cutoff:3.500A) Processing helix chain 'SM' and resid 100 through 111 Processing helix chain 'SM' and resid 116 through 125 Proline residue: SM 125 - end of helix Processing helix chain 'SM' and resid 126 through 135 removed outlier: 4.701A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) Processing helix chain 'SM' and resid 136 through 148 removed outlier: 3.921A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 3.771A 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: 3.585A pdb=" N METSM 220 " --> pdb=" O ASPSM 216 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 3.502A pdb=" N GLUSM 274 " --> pdb=" O GLUSM 270 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.905A pdb=" N ALASM 319 " --> pdb=" O LYSSM 315 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLUSM 321 " --> pdb=" O LEUSM 317 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.498A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.512A 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 520 through 541 removed outlier: 3.630A pdb=" N METSM 539 " --> pdb=" O LEUSM 535 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N METSM 540 " --> pdb=" O ALASM 536 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYSSM 541 " --> pdb=" O ILESM 537 " (cutoff:3.500A) Processing helix chain 'SM' and resid 542 through 586 Processing helix chain 'SN' and resid 19 through 30 Processing helix chain 'SN' and resid 49 through 61 Processing helix chain 'SN' and resid 65 through 70 Processing helix chain 'SN' and resid 100 through 127 Proline residue: SN 121 - end of helix Processing helix chain 'SN' and resid 143 through 177 Processing helix chain 'SN' and resid 178 through 205 Processing helix chain 'SO' and resid 71 through 86 Proline residue: SO 86 - end of helix Processing helix chain 'SO' and resid 99 through 111 removed outlier: 4.259A pdb=" N ILESO 103 " --> pdb=" O LYSSO 99 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASNSO 104 " --> pdb=" O LEUSO 100 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLUSO 105 " --> pdb=" O PHESO 101 " (cutoff:3.500A) Processing helix chain 'SO' and resid 169 through 176 removed outlier: 4.570A pdb=" N ASPSO 173 " --> pdb=" O ASPSO 169 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLUSO 174 " --> pdb=" O PROSO 170 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEUSO 175 " --> pdb=" O ALASO 171 " (cutoff:3.500A) Proline residue: SO 176 - end of helix No H-bonds generated for 'chain 'SO' and resid 169 through 176' Processing helix chain 'SO' and resid 177 through 190 Processing helix chain 'SO' and resid 261 through 293 removed outlier: 3.824A pdb=" N HISSO 265 " --> pdb=" O SERSO 261 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLUSO 293 " --> pdb=" O LEUSO 289 " (cutoff:3.500A) Processing helix chain 'SO' and resid 337 through 353 removed outlier: 3.526A pdb=" N LYSSO 351 " --> pdb=" O METSO 347 " (cutoff:3.500A) Processing helix chain 'SP' and resid 29 through 46 Processing helix chain 'SP' and resid 65 through 74 Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.272A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 61 removed outlier: 3.588A pdb=" N ILESQ 56 " --> pdb=" O LYSSQ 52 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 3.903A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.375A 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: 3.558A 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: 3.803A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 145 removed outlier: 3.806A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) Processing helix chain 'SR' and resid 146 through 162 removed outlier: 3.583A pdb=" N GLNSR 153 " --> pdb=" O GLUSR 149 " (cutoff:3.500A) removed outlier: 3.504A 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: 3.520A pdb=" N ASNSR 186 " --> pdb=" O SERSR 182 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.645A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.642A 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: 4.083A 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: 4.536A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 295 through 300 removed outlier: 5.356A pdb=" N SERSR 300 " --> pdb=" O ILESR 296 " (cutoff:3.500A) Processing helix chain 'SR' and resid 301 through 314 removed outlier: 3.571A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 4.647A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 4.158A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HISSR 361 " --> pdb=" O LEUSR 357 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) Processing helix chain 'SR' and resid 378 through 391 removed outlier: 4.420A pdb=" N VALSR 382 " --> pdb=" O PROSR 378 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALASR 383 " --> pdb=" O GLUSR 379 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYSSR 386 " --> pdb=" O VALSR 382 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLUSR 389 " --> pdb=" O ARGSR 385 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THRSR 390 " --> pdb=" O LYSSR 386 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.203A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 418 removed outlier: 4.768A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASPSR 418 " --> pdb=" O GLNSR 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 418' Processing helix chain 'SR' and resid 421 through 426 removed outlier: 4.091A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N HISSR 426 " --> pdb=" O LEUSR 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 421 through 426' Processing helix chain 'SR' and resid 437 through 442 removed outlier: 4.058A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 442' Processing helix chain 'SR' and resid 445 through 464 removed outlier: 3.690A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SS' and resid 140 through 146 removed outlier: 4.591A pdb=" N TYRSS 144 " --> pdb=" O PROSS 140 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASPSS 145 " --> pdb=" O LEUSS 141 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASPSS 146 " --> pdb=" O GLUSS 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 140 through 146' Processing helix chain 'SS' and resid 167 through 177 removed outlier: 3.550A pdb=" N PHESS 172 " --> pdb=" O GLUSS 168 " (cutoff:3.500A) Processing helix chain 'SS' and resid 197 through 210 Processing helix chain 'SS' and resid 242 through 248 removed outlier: 4.039A pdb=" N PHESS 246 " --> pdb=" O ASPSS 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILESS 247 " --> pdb=" O LYSSS 243 " (cutoff:3.500A) Proline residue: SS 248 - end of helix No H-bonds generated for 'chain 'SS' and resid 242 through 248' Processing helix chain 'SS' and resid 249 through 266 removed outlier: 3.685A pdb=" N LYSSS 253 " --> pdb=" O SERSS 249 " (cutoff:3.500A) Processing helix chain 'SS' and resid 317 through 322 removed outlier: 3.867A pdb=" N LEUSS 321 " --> pdb=" O PROSS 317 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEUSS 322 " --> pdb=" O PROSS 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 317 through 322' Processing helix chain 'SS' and resid 323 through 334 removed outlier: 5.542A pdb=" N GLUSS 334 " --> pdb=" O TRPSS 330 " (cutoff:3.500A) Processing helix chain 'SS' and resid 349 through 354 removed outlier: 3.526A pdb=" N VALSS 353 " --> pdb=" O SERSS 349 " (cutoff:3.500A) Proline residue: SS 354 - end of helix No H-bonds generated for 'chain 'SS' and resid 349 through 354' Processing helix chain 'SS' and resid 358 through 372 removed outlier: 3.841A pdb=" N TYRSS 371 " --> pdb=" O CYSSS 367 " (cutoff:3.500A) Processing helix chain 'SS' and resid 384 through 390 removed outlier: 3.722A pdb=" N LEUSS 388 " --> pdb=" O ASPSS 384 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILESS 389 " --> pdb=" O PROSS 385 " (cutoff:3.500A) Proline residue: SS 390 - end of helix No H-bonds generated for 'chain 'SS' and resid 384 through 390' Processing helix chain 'SS' and resid 394 through 399 removed outlier: 3.749A pdb=" N LEUSS 398 " --> pdb=" O ARGSS 394 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLNSS 399 " --> pdb=" O PROSS 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 394 through 399' Processing helix chain 'SS' and resid 488 through 502 removed outlier: 3.833A pdb=" N PHESS 502 " --> pdb=" O LEUSS 498 " (cutoff:3.500A) Processing helix chain 'SS' and resid 519 through 526 removed outlier: 3.979A pdb=" N VALSS 525 " --> pdb=" O GLUSS 521 " (cutoff:3.500A) Processing helix chain 'ST' and resid 169 through 198 removed outlier: 4.676A pdb=" N ALAST 196 " --> pdb=" O ASNST 192 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N HISST 197 " --> pdb=" O LEUST 193 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYSST 198 " --> pdb=" O ALAST 194 " (cutoff:3.500A) Processing helix chain 'ST' and resid 214 through 229 removed outlier: 3.603A pdb=" N GLNST 223 " --> pdb=" O GLYST 219 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THRST 229 " --> pdb=" O ALAST 225 " (cutoff:3.500A) Processing helix chain 'ST' and resid 260 through 277 removed outlier: 4.092A pdb=" N GLUST 264 " --> pdb=" O ASPST 260 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYSST 265 " --> pdb=" O PHEST 261 " (cutoff:3.500A) Processing helix chain 'ST' and resid 283 through 303 Processing helix chain 'SU' and resid 200 through 229 removed outlier: 3.517A pdb=" N ALASU 219 " --> pdb=" O LYSSU 215 " (cutoff:3.500A) Proline residue: SU 229 - end of helix Processing helix chain 'SU' and resid 230 through 245 removed outlier: 6.015A pdb=" N LYSSU 234 " --> pdb=" O GLUSU 230 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYSSU 235 " --> pdb=" O ASNSU 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N METSU 242 " --> pdb=" O GLUSU 238 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEUSU 243 " --> pdb=" O LEUSU 239 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N METSU 244 " --> pdb=" O ARGSU 240 " (cutoff:3.500A) Processing helix chain 'SU' and resid 250 through 270 Processing helix chain 'SU' and resid 289 through 322 Processing helix chain 'SU' and resid 332 through 353 removed outlier: 4.532A pdb=" N LYSSU 336 " --> pdb=" O LEUSU 332 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYSU 337 " --> pdb=" O LYSSU 333 " (cutoff:3.500A) Processing helix chain 'SU' and resid 358 through 372 removed outlier: 3.618A pdb=" N ILESU 362 " --> pdb=" O PHESU 358 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEUSU 365 " --> pdb=" O ASNSU 361 " (cutoff:3.500A) Proline residue: SU 368 - end of helix removed outlier: 4.081A pdb=" N ASNSU 371 " --> pdb=" O VALSU 367 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASPSU 372 " --> pdb=" O PROSU 368 " (cutoff:3.500A) Processing helix chain 'SU' and resid 374 through 392 Processing helix chain 'SU' and resid 395 through 413 removed outlier: 3.557A pdb=" N ASNSU 413 " --> pdb=" O VALSU 409 " (cutoff:3.500A) Processing helix chain 'SU' and resid 417 through 427 removed outlier: 4.718A pdb=" N LEUSU 421 " --> pdb=" O ARGSU 417 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYSSU 422 " --> pdb=" O PROSU 418 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THRSU 423 " --> pdb=" O GLUSU 419 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHESU 424 " --> pdb=" O METSU 420 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEUSU 425 " --> pdb=" O LEUSU 421 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYSSU 426 " --> pdb=" O LYSSU 422 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEUSU 427 " --> pdb=" O THRSU 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 417 through 427' Processing helix chain 'SU' and resid 430 through 444 Proline residue: SU 444 - end of helix Processing helix chain 'SU' and resid 470 through 508 Processing helix chain 'SU' and resid 514 through 526 Processing helix chain 'SU' and resid 530 through 548 removed outlier: 4.350A pdb=" N PHESU 534 " --> pdb=" O ASNSU 530 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASPSU 535 " --> pdb=" O VALSU 531 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASPSU 536 " --> pdb=" O GLUSU 532 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VALSU 539 " --> pdb=" O ASPSU 535 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLYSU 548 " --> pdb=" O LEUSU 544 " (cutoff:3.500A) Processing helix chain 'SU' and resid 551 through 568 removed outlier: 4.177A pdb=" N GLYSU 568 " --> pdb=" O HISSU 564 " (cutoff:3.500A) Processing helix chain 'SU' and resid 569 through 574 removed outlier: 4.863A pdb=" N LEUSU 573 " --> pdb=" O GLNSU 569 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASNSU 574 " --> pdb=" O GLYSU 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 569 through 574' Processing helix chain 'SU' and resid 577 through 588 Processing helix chain 'SU' and resid 596 through 611 removed outlier: 4.327A pdb=" N VALSU 600 " --> pdb=" O THRSU 596 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLUSU 601 " --> pdb=" O ASNSU 597 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILESU 602 " --> pdb=" O GLUSU 598 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VALSU 603 " --> pdb=" O GLYSU 599 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLNSU 605 " --> pdb=" O GLUSU 601 " (cutoff:3.500A) Processing helix chain 'SU' and resid 614 through 619 removed outlier: 5.734A pdb=" N SERSU 619 " --> pdb=" O ARGSU 615 " (cutoff:3.500A) Processing helix chain 'SU' and resid 620 through 637 removed outlier: 3.560A pdb=" N LEUSU 635 " --> pdb=" O CYSSU 631 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HISSU 636 " --> pdb=" O THRSU 632 " (cutoff:3.500A) Processing helix chain 'SU' and resid 638 through 656 removed outlier: 3.553A pdb=" N GLYSU 644 " --> pdb=" O ASNSU 640 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N HISSU 654 " --> pdb=" O ARGSU 650 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THRSU 655 " --> pdb=" O ILESU 651 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHESU 656 " --> pdb=" O LEUSU 652 " (cutoff:3.500A) Processing helix chain 'SU' and resid 659 through 665 removed outlier: 4.520A pdb=" N LEUSU 663 " --> pdb=" O THRSU 659 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASPSU 664 " --> pdb=" O ASPSU 660 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SERSU 665 " --> pdb=" O LEUSU 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 659 through 665' Processing helix chain 'SU' and resid 679 through 684 removed outlier: 4.053A pdb=" N CYSSU 683 " --> pdb=" O GLUSU 679 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASNSU 684 " --> pdb=" O PROSU 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 679 through 684' Processing helix chain 'SU' and resid 691 through 699 removed outlier: 4.302A pdb=" N ALASU 695 " --> pdb=" O TRPSU 691 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HISSU 699 " --> pdb=" O ALASU 695 " (cutoff:3.500A) Processing helix chain 'SU' and resid 701 through 714 removed outlier: 3.814A pdb=" N ALASU 713 " --> pdb=" O ALASU 709 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLYSU 714 " --> pdb=" O HISSU 710 " (cutoff:3.500A) Processing helix chain 'SU' and resid 724 through 731 removed outlier: 3.814A pdb=" N ARGSU 730 " --> pdb=" O GLUSU 726 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SERSU 731 " --> pdb=" O LEUSU 727 " (cutoff:3.500A) Processing helix chain 'SU' and resid 732 through 740 removed outlier: 4.492A pdb=" N SERSU 740 " --> pdb=" O PHESU 736 " (cutoff:3.500A) Processing helix chain 'SU' and resid 769 through 784 removed outlier: 4.378A pdb=" N VALSU 783 " --> pdb=" O TYRSU 779 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALASU 784 " --> pdb=" O SERSU 780 " (cutoff:3.500A) Processing helix chain 'SV' and resid 33 through 43 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.221A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.172A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 71' Processing helix chain 'SV' and resid 82 through 130 removed outlier: 4.041A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASNSV 87 " --> pdb=" O ARGSV 83 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASPSV 91 " --> pdb=" O ASNSV 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARGSV 111 " --> pdb=" O PHESV 107 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) Processing helix chain 'SV' and resid 131 through 136 removed outlier: 3.880A pdb=" N ALASV 136 " --> pdb=" O HISSV 132 " (cutoff:3.500A) Processing helix chain 'SW' and resid 178 through 184 removed outlier: 3.878A pdb=" N LEUSW 182 " --> pdb=" O SERSW 178 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYSSW 183 " --> pdb=" O PHESW 179 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASNSW 184 " --> pdb=" O ALASW 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'SW' and resid 178 through 184' Processing helix chain 'SW' and resid 187 through 198 Processing helix chain 'SW' and resid 203 through 216 removed outlier: 4.217A pdb=" N ARGSW 211 " --> pdb=" O HISSW 207 " (cutoff:3.500A) Proline residue: SW 212 - end of helix Processing helix chain 'SW' and resid 228 through 245 Proline residue: SW 236 - end of helix Processing helix chain 'SW' and resid 260 through 276 removed outlier: 3.768A pdb=" N THRSW 276 " --> pdb=" O LYSSW 272 " (cutoff:3.500A) Processing helix chain 'SW' and resid 290 through 301 Processing helix chain 'SW' and resid 308 through 318 removed outlier: 3.559A pdb=" N ASPSW 314 " --> pdb=" O GLYSW 310 " (cutoff:3.500A) Processing helix chain 'SW' and resid 334 through 342 removed outlier: 3.689A pdb=" N GLYSW 342 " --> pdb=" O ILESW 338 " (cutoff:3.500A) Processing helix chain 'SW' and resid 343 through 355 Proline residue: SW 355 - end of helix Processing helix chain 'SW' and resid 368 through 379 removed outlier: 3.537A pdb=" N ILESW 377 " --> pdb=" O ASPSW 373 " (cutoff:3.500A) Processing helix chain 'SW' and resid 408 through 424 removed outlier: 5.066A pdb=" N PHESW 413 " --> pdb=" O SERSW 409 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEUSW 414 " --> pdb=" O GLUSW 410 " (cutoff:3.500A) Processing helix chain 'SW' and resid 434 through 449 Processing helix chain 'SW' and resid 460 through 474 Processing helix chain 'SW' and resid 482 through 487 Processing helix chain 'SW' and resid 505 through 516 Processing helix chain 'SW' and resid 534 through 545 removed outlier: 4.718A pdb=" N LEUSW 538 " --> pdb=" O GLUSW 534 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARGSW 539 " --> pdb=" O LEUSW 535 " (cutoff:3.500A) Processing helix chain 'SW' and resid 561 through 572 Processing helix chain 'SW' and resid 573 through 593 Processing helix chain 'SW' and resid 595 through 600 Processing helix chain 'SW' and resid 605 through 614 removed outlier: 3.558A pdb=" N PHESW 613 " --> pdb=" O VALSW 609 " (cutoff:3.500A) Processing helix chain 'SY' and resid 223 through 234 removed outlier: 3.638A pdb=" N GLUSY 228 " --> pdb=" O ALASY 224 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLNSY 229 " --> pdb=" O GLYSY 225 " (cutoff:3.500A) Proline residue: SY 234 - end of helix Processing helix chain 'SY' and resid 235 through 253 Processing helix chain 'SY' and resid 262 through 279 Processing helix chain 'SY' and resid 281 through 293 Proline residue: SY 293 - end of helix Processing helix chain 'SY' and resid 294 through 307 removed outlier: 4.180A pdb=" N VALSY 298 " --> pdb=" O LEUSY 294 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLUSY 299 " --> pdb=" O SERSY 295 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLUSY 305 " --> pdb=" O LEUSY 301 " (cutoff:3.500A) removed outlier: 3.718A 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: 3.537A 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 418 through 433 removed outlier: 3.649A pdb=" N LEUSY 422 " --> pdb=" O ASNSY 418 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYSSY 423 " --> pdb=" O ALASY 419 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SERSY 424 " --> pdb=" O GLUSY 420 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLYSY 427 " --> pdb=" O LYSSY 423 " (cutoff:3.500A) Processing helix chain 'SY' and resid 468 through 473 Proline residue: SY 473 - end of helix Processing helix chain 'SY' and resid 480 through 503 removed outlier: 5.476A pdb=" N ASNSY 503 " --> pdb=" O ILESY 499 " (cutoff:3.500A) Processing helix chain 'SY' and resid 520 through 535 removed outlier: 4.345A pdb=" N TRPSY 526 " --> pdb=" O GLUSY 522 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VALSY 527 " --> pdb=" O GLUSY 523 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VALSY 528 " --> pdb=" O ASNSY 524 " (cutoff:3.500A) Processing helix chain 'SY' and resid 560 through 566 removed outlier: 3.569A pdb=" N ARGSY 564 " --> pdb=" O PROSY 561 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 6 through 12 removed outlier: 3.790A pdb=" N ARGSZ 10 " --> pdb=" O GLYSZ 6 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LYSSZ 12 " --> pdb=" O THRSZ 8 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 18 through 32 Proline residue: SZ 32 - end of helix Processing helix chain 'SZ' and resid 36 through 43 Processing helix chain 'SZ' and resid 48 through 57 Processing helix chain 'SZ' and resid 61 through 67 Proline residue: SZ 67 - end of helix Processing helix chain 'SZ' and resid 90 through 103 removed outlier: 4.517A pdb=" N LEUSZ 94 " --> pdb=" O LYSSZ 90 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEUSZ 103 " --> pdb=" O ALASZ 99 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 112 through 126 Processing helix chain 'SZ' and resid 129 through 137 removed outlier: 5.668A pdb=" N GLUSZ 137 " --> pdb=" O METSZ 133 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 144 through 159 removed outlier: 3.653A pdb=" N TYRSZ 155 " --> pdb=" O LYSSZ 151 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 160 through 178 Processing sheet with id= 1, first strand: chain 'BA' and resid 11 through 17 removed outlier: 4.130A 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: 6.607A pdb=" N LEUBB 163 " --> pdb=" O LEUBB 38 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VALBB 32 " --> pdb=" O VALBB 169 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEUBB 204 " --> pdb=" O LEUBB 216 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'BC' and resid 31 through 37 removed outlier: 8.172A pdb=" N THRBC 31 " --> pdb=" O ASPBC 323 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASPBC 323 " --> pdb=" O THRBC 31 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLUBC 33 " --> pdb=" O PHEBC 321 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHEBC 321 " --> pdb=" O GLUBC 33 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLNBC 317 " --> pdb=" O LEUBC 37 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARGBC 318 " --> pdb=" O GLYBC 314 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N PHEBC 309 " --> pdb=" O SERBC 304 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'BC' and resid 43 through 47 removed outlier: 5.555A pdb=" N LEUBC 52 " --> pdb=" O HISBC 47 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASPBC 61 " --> pdb=" O ASPBC 57 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VALBC 64 " --> pdb=" O LEUBC 77 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SERBC 68 " --> pdb=" O GLUBC 73 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLUBC 73 " --> pdb=" O SERBC 68 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'BC' and resid 89 through 93 removed outlier: 3.642A pdb=" N ALABC 89 " --> pdb=" O VALBC 102 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYSBC 98 " --> pdb=" O SERBC 93 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N GLNBC 97 " --> pdb=" O VALBC 113 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALABC 107 " --> pdb=" O SERBC 103 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VALBC 110 " --> pdb=" O GLUBC 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLNBC 117 " --> pdb=" O ASPBC 112 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'BC' and resid 132 through 136 removed outlier: 6.589A pdb=" N VALBC 140 " --> pdb=" O VALBC 136 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASNBC 139 " --> pdb=" O GLNBC 155 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLYBC 149 " --> pdb=" O ASPBC 145 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N METBC 162 " --> pdb=" O LEUBC 152 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'BC' and resid 173 through 177 removed outlier: 3.525A pdb=" N ASPBC 173 " --> pdb=" O ALABC 186 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEUBC 182 " --> pdb=" O ASPBC 177 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LYSBC 181 " --> pdb=" O ILEBC 197 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SERBC 187 " --> pdb=" O CYSBC 191 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N CYSBC 191 " --> pdb=" O SERBC 187 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEUBC 192 " --> pdb=" O SERBC 206 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'BC' and resid 215 through 219 removed outlier: 4.250A pdb=" N SERBC 215 " --> pdb=" O GLYBC 228 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLYBC 232 " --> pdb=" O LEUBC 251 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'BC' and resid 258 through 262 removed outlier: 6.496A pdb=" N LEUBC 266 " --> pdb=" O VALBC 262 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SERBC 265 " --> pdb=" O ILEBC 281 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILEBC 276 " --> pdb=" O VALBC 290 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLYBC 288 " --> pdb=" O ALABC 278 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'BC' and resid 61 through 64 removed outlier: 3.547A pdb=" N TRPBC 78 " --> pdb=" O VALBC 64 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'BC' and resid 107 through 110 Processing sheet with id= 14, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 15, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 16, first strand: chain 'L8' and resid 11 through 15 removed outlier: 4.514A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEUL8 37 " --> pdb=" O VALL8 28 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.106A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.669A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LA' and resid 16 through 20 removed outlier: 5.339A pdb=" N SERLA 111 " --> pdb=" O LYSLA 153 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LA' and resid 116 through 122 removed outlier: 3.643A pdb=" N ALALA 122 " --> pdb=" O PROLA 143 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LB' and resid 118 through 121 removed outlier: 4.762A pdb=" N LYSLB 99 " --> pdb=" O LYSLB 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.632A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.090A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.665A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 26, first strand: chain 'LG' and resid 36 through 39 removed outlier: 4.677A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASNLG 101 " --> pdb=" O VALLG 25 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILELG 105 " --> pdb=" O ALALG 29 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LG' and resid 87 through 90 removed outlier: 4.676A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LG' and resid 82 through 85 removed outlier: 4.451A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.660A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.755A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LI' and resid 71 through 75 Processing sheet with id= 32, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.518A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LJ' and resid 9 through 13 removed outlier: 4.471A pdb=" N LYSLJ 9 " --> pdb=" O ILELJ 25 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARGLJ 21 " --> pdb=" O VALLJ 13 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEULJ 42 " --> pdb=" O VALLJ 26 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 35, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.288A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LN' and resid 41 through 44 removed outlier: 6.625A pdb=" N GLNLN 184 " --> pdb=" O THRLN 44 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LN' and resid 53 through 58 removed outlier: 6.638A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HISLN 275 " --> pdb=" O THRLN 223 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.768A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LN' and resid 286 through 289 removed outlier: 3.589A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LN' and resid 77 through 80 Processing sheet with id= 41, first strand: chain 'LN' and resid 88 through 93 removed outlier: 3.724A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LN' and resid 215 through 218 removed outlier: 4.149A pdb=" N GLULN 215 " --> pdb=" O ILELN 284 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LO' and resid 26 through 29 removed outlier: 6.380A pdb=" N LYSLO 26 " --> pdb=" O ILELO 97 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEULO 45 " --> pdb=" O ILELO 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLYLO 70 " --> pdb=" O LYSLO 44 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.827A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 46, first strand: chain 'LT' and resid 56 through 59 removed outlier: 4.426A pdb=" N THRLT 59 " --> pdb=" O LYSLT 63 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYSLT 63 " --> pdb=" O THRLT 59 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VALLT 50 " --> pdb=" O ARGLT 100 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARGLT 100 " --> pdb=" O VALLT 50 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LT' and resid 72 through 75 removed outlier: 6.643A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LW' and resid 15 through 18 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'NF' and resid 189 through 194 removed outlier: 3.597A pdb=" N ALANF 190 " --> pdb=" O HISNF 185 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASNNF 255 " --> pdb=" O THRNF 245 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYRNF 241 " --> pdb=" O LEUNF 259 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THRNF 218 " --> pdb=" O VALNF 244 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'NH' and resid 36 through 39 removed outlier: 6.927A pdb=" N VALNH 44 " --> pdb=" O PHENH 70 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'NH' and resid 95 through 99 removed outlier: 4.965A pdb=" N TYRNH 95 " --> pdb=" O GLYNH 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLYNH 142 " --> pdb=" O VALNH 133 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'NI' and resid 196 through 200 removed outlier: 3.812A pdb=" N VALNI 136 " --> pdb=" O THRNI 274 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALANI 140 " --> pdb=" O SERNI 278 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'NI' and resid 311 through 317 Processing sheet with id= 54, first strand: chain 'SA' and resid 7 through 10 removed outlier: 4.920A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.373A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SC' and resid 90 through 95 removed outlier: 8.746A pdb=" N ALASC 90 " --> pdb=" O LEUSC 109 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VALSC 107 " --> pdb=" O VALSC 92 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SC' and resid 149 through 153 removed outlier: 4.142A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 59, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.380A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'SD' and resid 159 through 162 Processing sheet with id= 61, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 62, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.789A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SG' and resid 16 through 20 removed outlier: 3.541A pdb=" N GLYSG 32 " --> pdb=" O GLYSG 29 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.480A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.677A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'SH' and resid 72 through 76 removed outlier: 3.644A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'SI' and resid 147 through 151 removed outlier: 4.238A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SJ' and resid 798 through 802 Processing sheet with id= 69, first strand: chain 'SK' and resid 1 through 5 Processing sheet with id= 70, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 71, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 72, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 73, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 74, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.156A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEUSL 78 " --> pdb=" O ILESL 205 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SL' and resid 127 through 130 Processing sheet with id= 76, first strand: chain 'SL' and resid 210 through 217 removed outlier: 6.012A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEUSL 251 " --> pdb=" O ILESL 263 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'SM' and resid 179 through 184 Processing sheet with id= 78, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 79, first strand: chain 'SO' and resid 87 through 91 removed outlier: 4.068A pdb=" N ASPSO 91 " --> pdb=" O ILESO 64 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SERSO 66 " --> pdb=" O ASPSO 91 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALASO 120 " --> pdb=" O SERSO 67 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEUSO 126 " --> pdb=" O VALSO 143 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSSO 140 " --> pdb=" O ILESO 241 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALASO 228 " --> pdb=" O ILESO 223 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASNSO 219 " --> pdb=" O ILESO 232 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHESO 217 " --> pdb=" O PROSO 234 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHESO 236 " --> pdb=" O ILESO 215 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILESO 215 " --> pdb=" O PHESO 236 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASPSO 203 " --> pdb=" O ILESO 222 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'SO' and resid 137 through 140 removed outlier: 3.601A pdb=" N LYSSO 242 " --> pdb=" O LYSSO 140 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'SP' and resid 21 through 25 removed outlier: 6.804A pdb=" N GLUSP 52 " --> pdb=" O LYSSP 88 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'SP' and resid 96 through 100 removed outlier: 3.878A pdb=" N GLNSP 96 " --> pdb=" O SERSP 411 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASNSP 407 " --> pdb=" O HISSP 100 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLYSP 398 " --> pdb=" O TYRSP 414 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEUSP 399 " --> pdb=" O THRSP 395 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'SP' and resid 105 through 109 removed outlier: 4.205A pdb=" N SERSP 106 " --> pdb=" O GLYSP 117 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SERSP 118 " --> pdb=" O THRSP 122 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THRSP 122 " --> pdb=" O SERSP 118 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'SP' and resid 144 through 149 removed outlier: 6.396A pdb=" N LEUSP 157 " --> pdb=" O VALSP 149 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEUSP 169 " --> pdb=" O LEUSP 182 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'SP' and resid 193 through 198 removed outlier: 4.245A pdb=" N SERSP 194 " --> pdb=" O GLYSP 207 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LYSSP 203 " --> pdb=" O ASPSP 198 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THRSP 202 " --> pdb=" O THRSP 218 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SERSP 208 " --> pdb=" O METSP 212 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N METSP 212 " --> pdb=" O SERSP 208 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VALSP 251 " --> pdb=" O ILESP 215 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'SP' and resid 261 through 266 removed outlier: 6.609A pdb=" N GLUSP 270 " --> pdb=" O SERSP 266 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLUSP 269 " --> pdb=" O VALSP 285 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VALSP 282 " --> pdb=" O LYSSP 291 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'SP' and resid 302 through 307 removed outlier: 3.722A pdb=" N ARGSP 311 " --> pdb=" O SERSP 306 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEUSP 336 " --> pdb=" O LEUSP 323 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'SP' and resid 347 through 351 removed outlier: 3.681A pdb=" N SERSP 347 " --> pdb=" O GLYSP 361 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLNSP 357 " --> pdb=" O SERSP 351 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLNSP 356 " --> pdb=" O THRSP 372 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYRSP 380 " --> pdb=" O LEUSP 369 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'SP' and resid 92 through 95 removed outlier: 7.072A pdb=" N SERSP 411 " --> pdb=" O GLUSP 95 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'SP' and resid 166 through 169 removed outlier: 3.585A pdb=" N HISSP 183 " --> pdb=" O LEUSP 169 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'SP' and resid 278 through 282 removed outlier: 5.505A pdb=" N HISSP 278 " --> pdb=" O GLYSP 296 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SERSP 292 " --> pdb=" O VALSP 282 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 5.185A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.822A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'SQ' and resid 160 through 163 Processing sheet with id= 95, first strand: chain 'SQ' and resid 213 through 217 Processing sheet with id= 96, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.238A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'SR' and resid 204 through 211 removed outlier: 7.565A pdb=" N SERSR 204 " --> pdb=" O PROSR 223 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEUSR 172 " --> pdb=" O ALASR 250 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'SS' and resid 183 through 188 removed outlier: 6.773A pdb=" N ARGSS 183 " --> pdb=" O LEUSS 196 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEUSS 196 " --> pdb=" O ARGSS 183 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARGSS 192 " --> pdb=" O ASPSS 187 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'SS' and resid 407 through 410 removed outlier: 3.610A pdb=" N LEUSS 407 " --> pdb=" O LEUSS 744 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THRSS 741 " --> pdb=" O GLYSS 737 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TRPSS 732 " --> pdb=" O HISSS 727 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASPSS 723 " --> pdb=" O SERSS 736 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'SS' and resid 418 through 422 removed outlier: 3.785A pdb=" N CYSSS 418 " --> pdb=" O GLYSS 431 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SERSS 422 " --> pdb=" O TRPSS 427 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TRPSS 427 " --> pdb=" O SERSS 422 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLNSS 426 " --> pdb=" O VALSS 442 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEUSS 439 " --> pdb=" O VALSS 448 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARGSS 446 " --> pdb=" O GLUSS 441 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'SS' and resid 459 through 463 removed outlier: 3.788A pdb=" N SERSS 459 " --> pdb=" O ALASS 474 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEUSS 470 " --> pdb=" O ASNSS 463 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEUSS 529 " --> pdb=" O LEUSS 481 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARGSS 528 " --> pdb=" O ALASS 518 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'SS' and resid 539 through 543 removed outlier: 3.569A pdb=" N GLNSS 539 " --> pdb=" O VALSS 552 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYRSS 548 " --> pdb=" O HISSS 543 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASPSS 547 " --> pdb=" O LEUSS 566 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLNSS 560 " --> pdb=" O LEUSS 553 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'SS' and resid 584 through 588 removed outlier: 5.402A pdb=" N PHESS 593 " --> pdb=" O HISSS 588 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SERSS 601 " --> pdb=" O SERSS 598 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYSSS 614 " --> pdb=" O LEUSS 604 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'SS' and resid 625 through 629 removed outlier: 5.630A pdb=" N ASNSS 634 " --> pdb=" O HISSS 629 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ASPSS 633 " --> pdb=" O LEUSS 649 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYSSS 643 " --> pdb=" O SERSS 639 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'SS' and resid 668 through 672 removed outlier: 3.537A pdb=" N ALASS 668 " --> pdb=" O GLYSS 681 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEUSS 677 " --> pdb=" O HISSS 672 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'SS' and resid 436 through 439 Processing sheet with id=107, first strand: chain 'SS' and resid 686 through 689 Processing sheet with id=108, first strand: chain 'SV' and resid 3 through 6 removed outlier: 6.493A pdb=" N GLUSV 4 " --> pdb=" O PROSV 12 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N CYSSV 6 " --> pdb=" O SERSV 10 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'SV' and resid 18 through 23 removed outlier: 3.886A pdb=" N LYSSV 27 " --> pdb=" O ARGSV 23 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'SW' and resid 281 through 285 removed outlier: 3.522A pdb=" N VALSW 386 " --> pdb=" O LEUSW 220 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALASW 222 " --> pdb=" O VALSW 386 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VALSW 388 " --> pdb=" O ALASW 222 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'SW' and resid 400 through 407 removed outlier: 3.543A pdb=" N TRPSW 496 " --> pdb=" O LYSSW 427 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'SW' and resid 452 through 455 Processing sheet with id=113, first strand: chain 'SY' and resid 334 through 337 removed outlier: 6.919A pdb=" N ASNSY 334 " --> pdb=" O TYRSY 349 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THRSY 344 " --> pdb=" O THRSY 314 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VALSY 310 " --> pdb=" O VALSY 348 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HISSY 365 " --> pdb=" O ASNSY 315 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'SY' and resid 436 through 442 removed outlier: 5.462A pdb=" N ASNSY 436 " --> pdb=" O GLYSY 410 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYRSY 442 " --> pdb=" O ASPSY 416 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASPSY 460 " --> pdb=" O METSY 391 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLYSY 510 " --> pdb=" O LYSSY 586 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LYSSY 583 " --> pdb=" O VALSY 540 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'SY' and resid 567 through 571 removed outlier: 6.681A pdb=" N ASPSY 577 " --> pdb=" O PROSY 571 " (cutoff:3.500A) 4696 hydrogen bonds defined for protein. 13922 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2371 hydrogen bonds 4098 hydrogen bond angles 0 basepair planarities 905 basepair parallelities 1414 stacking parallelities Total time for adding SS restraints: 180.31 Time building geometry restraints manager: 59.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 32819 1.33 - 1.45: 51639 1.45 - 1.58: 76393 1.58 - 1.70: 5585 1.70 - 1.82: 679 Bond restraints: 167115 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 1.398 -0.148 2.00e-02 2.50e+03 5.50e+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 2.24e+01 bond pdb=" N1 GDPSR1001 " pdb=" C2 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.404 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.278 0.059 2.00e-02 2.50e+03 8.59e+00 ... (remaining 167110 not shown) Histogram of bond angle deviations from ideal: 99.20 - 107.26: 19950 107.26 - 115.32: 106239 115.32 - 123.37: 96588 123.37 - 131.43: 15737 131.43 - 139.49: 669 Bond angle restraints: 239183 Sorted by residual: angle pdb=" N VALSE 140 " pdb=" CA VALSE 140 " pdb=" C VALSE 140 " ideal model delta sigma weight residual 111.90 108.37 3.53 8.10e-01 1.52e+00 1.90e+01 angle pdb=" C8 GDPSR1001 " pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 108.00 120.77 -12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" C ARGSY 555 " pdb=" CA ARGSY 555 " pdb=" CB ARGSY 555 " ideal model delta sigma weight residual 116.54 112.24 4.30 1.15e+00 7.56e-01 1.40e+01 angle pdb=" CB ARGLB 150 " pdb=" CG ARGLB 150 " pdb=" CD ARGLB 150 " ideal model delta sigma weight residual 111.30 119.05 -7.75 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA VALSK 179 " pdb=" C VALSK 179 " pdb=" N PROSK 180 " ideal model delta sigma weight residual 116.57 119.78 -3.21 9.80e-01 1.04e+00 1.07e+01 ... (remaining 239178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 98344 35.92 - 71.84: 6887 71.84 - 107.77: 932 107.77 - 143.69: 8 143.69 - 179.61: 15 Dihedral angle restraints: 106186 sinusoidal: 70077 harmonic: 36109 Sorted by residual: dihedral pdb=" O4' UL3 432 " pdb=" C1' UL3 432 " pdb=" N1 UL3 432 " pdb=" C2 UL3 432 " ideal model delta sinusoidal sigma weight residual 200.00 32.34 167.66 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' UL31381 " pdb=" C1' UL31381 " pdb=" N1 UL31381 " pdb=" C2 UL31381 " ideal model delta sinusoidal sigma weight residual 200.00 34.92 165.08 1 1.50e+01 4.44e-03 8.39e+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 40.04 159.96 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 106183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 24286 0.042 - 0.083: 3437 0.083 - 0.125: 1032 0.125 - 0.167: 162 0.167 - 0.208: 9 Chirality restraints: 28926 Sorted by residual: chirality pdb=" C1' AL32042 " pdb=" O4' AL32042 " pdb=" C2' AL32042 " pdb=" N9 AL32042 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB VALLA 2 " pdb=" CA VALLA 2 " pdb=" CG1 VALLA 2 " pdb=" CG2 VALLA 2 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' GL34520 " pdb=" C4' GL34520 " pdb=" O3' GL34520 " pdb=" C2' GL34520 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 28923 not shown) Planarity restraints: 19959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GL1 39 " 0.049 2.00e-02 2.50e+03 2.03e-02 1.23e+01 pdb=" N9 GL1 39 " -0.046 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 " 0.007 2.00e-02 2.50e+03 pdb=" O6 GL1 39 " 0.014 2.00e-02 2.50e+03 pdb=" N1 GL1 39 " 0.004 2.00e-02 2.50e+03 pdb=" C2 GL1 39 " -0.001 2.00e-02 2.50e+03 pdb=" N2 GL1 39 " -0.003 2.00e-02 2.50e+03 pdb=" N3 GL1 39 " -0.008 2.00e-02 2.50e+03 pdb=" C4 GL1 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THRSW 319 " 0.049 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PROSW 320 " -0.130 5.00e-02 4.00e+02 pdb=" CA PROSW 320 " 0.040 5.00e-02 4.00e+02 pdb=" CD PROSW 320 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' AL34510 " 0.039 2.00e-02 2.50e+03 1.76e-02 8.50e+00 pdb=" N9 AL34510 " -0.041 2.00e-02 2.50e+03 pdb=" C8 AL34510 " -0.003 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 " 0.002 2.00e-02 2.50e+03 pdb=" N6 AL34510 " 0.011 2.00e-02 2.50e+03 pdb=" N1 AL34510 " 0.003 2.00e-02 2.50e+03 pdb=" C2 AL34510 " -0.003 2.00e-02 2.50e+03 pdb=" N3 AL34510 " -0.006 2.00e-02 2.50e+03 pdb=" C4 AL34510 " -0.005 2.00e-02 2.50e+03 ... (remaining 19956 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.62: 2183 2.62 - 3.25: 148511 3.25 - 3.88: 339758 3.88 - 4.51: 466075 4.51 - 5.14: 650315 Nonbonded interactions: 1606842 Sorted by model distance: nonbonded pdb=" OG1 THRST 229 " pdb=" O SERST 231 " model vdw 1.992 2.440 nonbonded pdb=" O LEUSU 661 " pdb="MG MGSU1001 " model vdw 1.994 2.170 nonbonded pdb=" OP2 AL31917 " pdb="MG MGL36023 " model vdw 1.995 2.170 nonbonded pdb=" O2' UL3 184 " pdb=" OP2 GL3 189 " model vdw 1.998 2.440 nonbonded pdb=" OP2 AL31337 " pdb="MG MGL36009 " model vdw 2.002 2.170 ... (remaining 1606837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 26.370 Check model and map are aligned: 1.690 Set scattering table: 1.080 Process input model: 532.730 Find NCS groups from input model: 4.490 Set up NCS constraints: 0.470 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:10.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 583.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.167 167115 Z= 0.176 Angle : 0.535 12.772 239183 Z= 0.279 Chirality : 0.035 0.208 28926 Planarity : 0.004 0.101 19959 Dihedral : 20.106 179.609 82756 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.01 % Allowed : 0.06 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.07), residues: 12214 helix: 2.34 (0.07), residues: 5043 sheet: 0.92 (0.12), residues: 1835 loop : 0.42 (0.08), residues: 5336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRPSV 86 HIS 0.007 0.001 HISSR 228 PHE 0.016 0.001 PHESP 204 TYR 0.020 0.001 TYRSE 230 ARG 0.022 0.001 ARGLO 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1237 time to evaluate : 9.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 78 TRP cc_start: 0.6675 (p-90) cc_final: 0.6472 (p-90) REVERT: LA 31 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8274 (mm-30) REVERT: LC 131 GLU cc_start: 0.7633 (tt0) cc_final: 0.7385 (tm-30) REVERT: LH 33 HIS cc_start: 0.7979 (m170) cc_final: 0.6649 (t-170) REVERT: LK 65 ARG cc_start: 0.7285 (mmt180) cc_final: 0.6686 (mmt180) REVERT: LQ 55 MET cc_start: 0.8800 (mtm) cc_final: 0.8591 (mtp) REVERT: NI 590 MET cc_start: 0.8268 (tpt) cc_final: 0.8036 (tpp) REVERT: NK 97 MET cc_start: 0.8333 (ttm) cc_final: 0.7986 (ttm) REVERT: SA 269 LYS cc_start: 0.8423 (mtpp) cc_final: 0.8119 (mtpt) REVERT: SA 323 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7555 (mmm-85) REVERT: SC 245 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7118 (tp-100) REVERT: SD 41 MET cc_start: 0.7434 (mmm) cc_final: 0.7179 (tpp) REVERT: SE 165 GLU cc_start: 0.7896 (mp0) cc_final: 0.7656 (mp0) REVERT: SK 140 GLN cc_start: 0.7444 (tp40) cc_final: 0.7228 (tp40) REVERT: SO 347 MET cc_start: 0.7131 (tmm) cc_final: 0.6360 (tmm) REVERT: SS 138 ASN cc_start: 0.7414 (p0) cc_final: 0.7208 (p0) REVERT: SY 227 MET cc_start: 0.2696 (mpp) cc_final: 0.2061 (ptt) outliers start: 1 outliers final: 5 residues processed: 1238 average time/residue: 2.3746 time to fit residues: 4273.6520 Evaluate side-chains 982 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 977 time to evaluate : 10.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LO residue 77 ASN Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain NB residue 16 HIS Chi-restraints excluded: chain NB residue 66 LEU Chi-restraints excluded: chain SL residue 94 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1494 random chunks: chunk 1261 optimal weight: 2.9990 chunk 1132 optimal weight: 10.0000 chunk 628 optimal weight: 9.9990 chunk 386 optimal weight: 0.0070 chunk 763 optimal weight: 5.9990 chunk 604 optimal weight: 50.0000 chunk 1170 optimal weight: 20.0000 chunk 453 optimal weight: 8.9990 chunk 712 optimal weight: 0.6980 chunk 871 optimal weight: 5.9990 chunk 1356 optimal weight: 7.9990 overall best weight: 3.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN BA 147 HIS BC 209 GLN L6 13 HIS L6 67 HIS L6 115 GLN ** L7 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L7 90 HIS LA 93 HIS LA 116 HIS LC 92 ASN LC 122 HIS ** LD 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 141 HIS LE 58 HIS LG 36 ASN LH 69 ASN LH 105 ASN LH 108 GLN LH 151 ASN LI 40 GLN LI 43 ASN LI 65 GLN LI 86 GLN LL 6 GLN LL 100 ASN LN 42 HIS LN 184 GLN LS 65 GLN LU 26 HIS LW 30 GLN LW 66 HIS NA 376 HIS ** NA 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 457 HIS NA 484 GLN NA 621 HIS NF 10 HIS ** NI 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NI 332 HIS NI 333 ASN NK 101 GLN SC 136 HIS SC 190 HIS SD 24 ASN SD 131 ASN SD 151 ASN ** SE 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 94 GLN SG 42 ASN SG 140 GLN SI 219 HIS SI 225 HIS SJ 769 ASN ** SK 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 83 HIS SK 93 GLN ** SL 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN SL 218 HIS SM 154 HIS SM 211 HIS SM 243 ASN SM 375 HIS SN 194 HIS SP 165 GLN SP 173 ASN ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 217 GLN SR 35 HIS SR 157 HIS SR 209 HIS SR 228 HIS SR 239 GLN SR 274 ASN SR 342 HIS SS 296 HIS SS 310 HIS ST 276 ASN ST 291 GLN SU 203 HIS ** SU 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SU 491 HIS SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 636 HIS SU 699 HIS SV 17 HIS SV 24 ASN SV 67 ASN ** SV 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 115 ASN SV 119 GLN SW 402 GLN SW 499 GLN SW 511 HIS SW 593 HIS SY 304 ASN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 418 ASN Total number of N/Q/H flips: 88 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 167115 Z= 0.293 Angle : 0.568 14.957 239183 Z= 0.296 Chirality : 0.039 0.246 28926 Planarity : 0.005 0.071 19959 Dihedral : 21.670 179.541 58232 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.40 % Allowed : 6.00 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.07), residues: 12214 helix: 2.44 (0.07), residues: 5118 sheet: 0.76 (0.12), residues: 1805 loop : 0.26 (0.08), residues: 5291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPSP 216 HIS 0.012 0.002 HISNA 621 PHE 0.029 0.002 PHESW 233 TYR 0.029 0.002 TYRLK 61 ARG 0.010 0.001 ARGSG 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1043 time to evaluate : 10.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 78 TRP cc_start: 0.6620 (p-90) cc_final: 0.6416 (p-90) REVERT: L7 173 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7499 (tm-30) REVERT: L8 70 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: LB 17 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: LC 130 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7299 (tm-30) REVERT: LC 131 GLU cc_start: 0.7446 (tt0) cc_final: 0.6947 (tm-30) REVERT: LD 3 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7124 (mmt) REVERT: LD 22 VAL cc_start: 0.6526 (t) cc_final: 0.6261 (t) REVERT: LD 41 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8270 (mt) REVERT: LH 33 HIS cc_start: 0.8112 (m170) cc_final: 0.6562 (t-170) REVERT: LJ 99 ASP cc_start: 0.6744 (OUTLIER) cc_final: 0.6446 (p0) REVERT: LK 65 ARG cc_start: 0.7379 (mmt180) cc_final: 0.6663 (mmt180) REVERT: LO 40 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7309 (mt0) REVERT: LR 43 LYS cc_start: 0.7097 (pttm) cc_final: 0.6895 (pttm) REVERT: LR 105 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6843 (tttt) REVERT: LS 32 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7630 (mtp180) REVERT: NI 590 MET cc_start: 0.8360 (tpt) cc_final: 0.8100 (tpp) REVERT: NK 97 MET cc_start: 0.8377 (ttm) cc_final: 0.8041 (ttm) REVERT: SA 95 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7778 (pmm) REVERT: SA 201 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7463 (ttm170) REVERT: SC 68 MET cc_start: 0.5053 (OUTLIER) cc_final: 0.4841 (mmm) REVERT: SC 245 GLN cc_start: 0.7597 (tp-100) cc_final: 0.7395 (tp-100) REVERT: SO 347 MET cc_start: 0.6695 (tmm) cc_final: 0.6280 (tmm) REVERT: SU 744 MET cc_start: 0.8257 (tpp) cc_final: 0.7693 (tpp) REVERT: SU 775 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5615 (OUTLIER) outliers start: 143 outliers final: 51 residues processed: 1102 average time/residue: 2.3651 time to fit residues: 3722.2309 Evaluate side-chains 1011 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 950 time to evaluate : 9.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 101 SER Chi-restraints excluded: chain BA residue 141 CYS Chi-restraints excluded: chain BC residue 305 HIS Chi-restraints excluded: chain L7 residue 195 VAL Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LB residue 17 GLU Chi-restraints excluded: chain LC residue 17 LEU Chi-restraints excluded: chain LD residue 3 MET Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 30 ASN Chi-restraints excluded: chain LD residue 41 ILE Chi-restraints excluded: chain LD residue 67 THR Chi-restraints excluded: chain LD residue 119 MET Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 82 THR Chi-restraints excluded: chain LH residue 102 VAL Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LJ residue 54 THR Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 120 GLU Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LO residue 40 GLN Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 105 LYS Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 66 LEU Chi-restraints excluded: chain NF residue 103 SER Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NH residue 1 MET Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 201 ARG Chi-restraints excluded: chain SA residue 313 VAL Chi-restraints excluded: chain SC residue 68 MET Chi-restraints excluded: chain SD residue 187 MET Chi-restraints excluded: chain SD residue 224 THR Chi-restraints excluded: chain SE residue 131 LYS Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SH residue 82 THR Chi-restraints excluded: chain SJ residue 439 ASP Chi-restraints excluded: chain SJ residue 769 ASN Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SM residue 516 LEU Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 418 CYS Chi-restraints excluded: chain SS residue 575 PHE Chi-restraints excluded: chain ST residue 236 GLN Chi-restraints excluded: chain SU residue 775 LEU Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SZ residue 106 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1494 random chunks: chunk 754 optimal weight: 0.8980 chunk 421 optimal weight: 8.9990 chunk 1129 optimal weight: 9.9990 chunk 923 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 1359 optimal weight: 4.9990 chunk 1468 optimal weight: 4.9990 chunk 1210 optimal weight: 0.5980 chunk 1347 optimal weight: 4.9990 chunk 463 optimal weight: 6.9990 chunk 1090 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN ** BC 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 104 ASN L7 65 ASN L8 75 GLN L8 78 GLN LB 21 GLN LB 93 GLN LC 36 ASN LC 92 ASN LD 141 HIS LG 36 ASN LH 69 ASN LH 108 GLN LI 65 GLN LK 62 HIS LK 67 GLN LL 100 ASN LR 100 GLN LW 57 ASN NA 343 ASN ** NA 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS NH 23 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN SD 63 GLN SE 206 GLN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 10 ASN SK 93 GLN ** SL 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN SL 133 GLN ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 186 GLN SQ 217 GLN SR 342 HIS SR 351 ASN SS 138 ASN SS 483 ASN ** SS 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 200 GLN ST 223 GLN ST 276 ASN ** SU 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 701 HIS SV 119 GLN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 167115 Z= 0.259 Angle : 0.522 12.085 239183 Z= 0.272 Chirality : 0.037 0.266 28926 Planarity : 0.004 0.061 19959 Dihedral : 21.612 179.845 58223 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.75 % Allowed : 7.91 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 1.84 (0.07), residues: 12214 helix: 2.52 (0.07), residues: 5134 sheet: 0.66 (0.12), residues: 1796 loop : 0.18 (0.08), residues: 5284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPSP 216 HIS 0.012 0.001 HISNA 621 PHE 0.025 0.002 PHESU 297 TYR 0.026 0.002 TYRNA 618 ARG 0.007 0.000 ARGSA 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 995 time to evaluate : 10.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6843 (tm-30) REVERT: L7 34 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8397 (t) REVERT: L7 173 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7530 (tm-30) REVERT: L8 70 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: L8 81 ASP cc_start: 0.7226 (t70) cc_final: 0.6969 (t70) REVERT: LA 99 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6501 (tm-30) REVERT: LB 17 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: LC 130 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7328 (tm-30) REVERT: LC 131 GLU cc_start: 0.7489 (tt0) cc_final: 0.6351 (tm-30) REVERT: LD 3 MET cc_start: 0.7435 (tpp) cc_final: 0.7160 (mmt) REVERT: LD 22 VAL cc_start: 0.6572 (t) cc_final: 0.6324 (t) REVERT: LE 63 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6042 (ttt-90) REVERT: LG 15 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6772 (ttp-170) REVERT: LH 33 HIS cc_start: 0.8171 (m170) cc_final: 0.6521 (t-170) REVERT: LJ 99 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6354 (p0) REVERT: LK 65 ARG cc_start: 0.7363 (mmt180) cc_final: 0.6658 (mmt180) REVERT: LN 363 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7891 (pt) REVERT: LO 40 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7411 (mt0) REVERT: NB 63 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6690 (tm-30) REVERT: NB 67 ARG cc_start: 0.8246 (mmt90) cc_final: 0.7935 (mmm-85) REVERT: NK 97 MET cc_start: 0.8401 (ttm) cc_final: 0.8057 (ttm) REVERT: SA 95 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7744 (pmm) REVERT: SA 201 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7672 (ttm170) REVERT: SC 68 MET cc_start: 0.5208 (OUTLIER) cc_final: 0.4674 (mmm) REVERT: SJ 662 ILE cc_start: 0.7428 (mt) cc_final: 0.7055 (mm) REVERT: SM 388 ILE cc_start: 0.8271 (mm) cc_final: 0.8043 (mt) REVERT: SN 63 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6618 (p0) REVERT: SO 347 MET cc_start: 0.6619 (tmm) cc_final: 0.6353 (tmm) REVERT: SS 693 MET cc_start: 0.7374 (tpt) cc_final: 0.7125 (tpt) REVERT: SU 744 MET cc_start: 0.8300 (tpp) cc_final: 0.7773 (tpp) outliers start: 179 outliers final: 68 residues processed: 1073 average time/residue: 2.3688 time to fit residues: 3634.5127 Evaluate side-chains 1020 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 937 time to evaluate : 9.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 101 SER Chi-restraints excluded: chain BA residue 141 CYS Chi-restraints excluded: chain BC residue 305 HIS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 195 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 113 VAL Chi-restraints excluded: chain LB residue 17 GLU Chi-restraints excluded: chain LC residue 17 LEU Chi-restraints excluded: chain LC residue 159 LEU Chi-restraints excluded: chain LD residue 30 ASN Chi-restraints excluded: chain LD residue 67 THR Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 63 ARG Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LH residue 82 THR Chi-restraints excluded: chain LH residue 102 VAL Chi-restraints excluded: chain LH residue 118 ASP Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 54 THR Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 120 GLU Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 300 LYS Chi-restraints excluded: chain LN residue 363 ILE Chi-restraints excluded: chain LO residue 40 GLN Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 77 ASN Chi-restraints excluded: chain LS residue 107 GLN Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 63 GLU Chi-restraints excluded: chain NB residue 66 LEU Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NK residue 88 ASP Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 201 ARG Chi-restraints excluded: chain SA residue 289 LEU Chi-restraints excluded: chain SA residue 313 VAL Chi-restraints excluded: chain SC residue 68 MET Chi-restraints excluded: chain SD residue 187 MET Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SJ residue 784 SER Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SM residue 328 GLU Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SN residue 63 ASP Chi-restraints excluded: chain SN residue 195 MET Chi-restraints excluded: chain SO residue 83 MET Chi-restraints excluded: chain SP residue 297 ASN Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 33 VAL Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 291 CYS Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 525 VAL Chi-restraints excluded: chain SS residue 575 PHE Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 19 MET Chi-restraints excluded: chain SZ residue 106 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1494 random chunks: chunk 1342 optimal weight: 7.9990 chunk 1021 optimal weight: 5.9990 chunk 705 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 648 optimal weight: 1.9990 chunk 912 optimal weight: 3.9990 chunk 1364 optimal weight: 5.9990 chunk 1444 optimal weight: 5.9990 chunk 712 optimal weight: 0.0980 chunk 1292 optimal weight: 8.9990 chunk 389 optimal weight: 9.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN ** BC 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 75 GLN L8 78 GLN L9 196 ASN LA 93 HIS LB 93 GLN LD 141 HIS LH 69 ASN LI 65 GLN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 100 ASN LR 100 GLN LW 30 GLN LW 57 ASN ** NA 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 484 GLN NA 621 HIS NF 4 ASN NH 127 GLN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN SE 206 GLN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN SL 133 GLN SM 243 ASN SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 217 GLN SR 342 HIS SR 351 ASN SS 483 ASN ST 223 GLN ST 276 ASN ** SU 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 67 ASN SV 115 ASN SV 119 GLN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 167115 Z= 0.240 Angle : 0.509 10.985 239183 Z= 0.266 Chirality : 0.037 0.257 28926 Planarity : 0.004 0.056 19959 Dihedral : 21.561 179.201 58223 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.81 % Allowed : 9.22 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.07), residues: 12214 helix: 2.49 (0.07), residues: 5168 sheet: 0.54 (0.12), residues: 1784 loop : 0.12 (0.08), residues: 5262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPSU 319 HIS 0.011 0.001 HISNA 621 PHE 0.024 0.002 PHEBC 65 TYR 0.022 0.001 TYRSU 682 ARG 0.010 0.000 ARGSK 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 990 time to evaluate : 9.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 34 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8426 (t) REVERT: L7 173 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7486 (tm-30) REVERT: L8 70 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: LA 40 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7172 (t70) REVERT: LA 99 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6490 (tm-30) REVERT: LB 17 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7331 (pm20) REVERT: LC 130 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: LC 131 GLU cc_start: 0.7487 (tt0) cc_final: 0.6928 (tm-30) REVERT: LD 22 VAL cc_start: 0.6549 (t) cc_final: 0.6301 (t) REVERT: LE 63 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.6024 (ttt-90) REVERT: LE 102 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7248 (tpt-90) REVERT: LG 15 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6697 (mtp180) REVERT: LH 33 HIS cc_start: 0.8176 (m170) cc_final: 0.6268 (t-170) REVERT: LH 67 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6628 (ttm170) REVERT: LJ 99 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.6317 (p0) REVERT: LJ 101 PHE cc_start: 0.6101 (m-80) cc_final: 0.5889 (m-80) REVERT: LK 65 ARG cc_start: 0.7310 (mmt180) cc_final: 0.6625 (mmt180) REVERT: LN 363 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7858 (pt) REVERT: LO 40 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7483 (mt0) REVERT: NB 63 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: NB 67 ARG cc_start: 0.8248 (mmt90) cc_final: 0.7991 (mmm-85) REVERT: NK 97 MET cc_start: 0.8403 (ttm) cc_final: 0.8065 (ttm) REVERT: SA 95 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7676 (pmm) REVERT: SA 291 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6912 (ttp-170) REVERT: SC 68 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.4640 (mmm) REVERT: SD 63 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6528 (mt0) REVERT: SM 388 ILE cc_start: 0.8275 (mm) cc_final: 0.8063 (mt) REVERT: SN 63 ASP cc_start: 0.7057 (p0) cc_final: 0.6608 (p0) REVERT: SO 347 MET cc_start: 0.6583 (tmm) cc_final: 0.6326 (tmm) REVERT: SR 266 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6968 (tpt170) REVERT: SU 744 MET cc_start: 0.8335 (tpp) cc_final: 0.7797 (tpp) outliers start: 185 outliers final: 78 residues processed: 1087 average time/residue: 2.3191 time to fit residues: 3637.6212 Evaluate side-chains 1047 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 950 time to evaluate : 9.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 141 CYS Chi-restraints excluded: chain BC residue 305 HIS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 184 ASN Chi-restraints excluded: chain L7 residue 195 VAL Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L8 residue 58 THR Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 113 VAL Chi-restraints excluded: chain LB residue 17 GLU Chi-restraints excluded: chain LC residue 17 LEU Chi-restraints excluded: chain LC residue 130 GLU Chi-restraints excluded: chain LC residue 159 LEU Chi-restraints excluded: chain LD residue 30 ASN Chi-restraints excluded: chain LD residue 67 THR Chi-restraints excluded: chain LD residue 143 HIS Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 63 ARG Chi-restraints excluded: chain LE residue 102 ARG Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 67 ARG Chi-restraints excluded: chain LH residue 82 THR Chi-restraints excluded: chain LH residue 102 VAL Chi-restraints excluded: chain LH residue 118 ASP Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 33 THR Chi-restraints excluded: chain LJ residue 54 THR Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 120 GLU Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 363 ILE Chi-restraints excluded: chain LO residue 21 VAL Chi-restraints excluded: chain LO residue 40 GLN Chi-restraints excluded: chain LS residue 107 GLN Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain NA residue 329 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 63 GLU Chi-restraints excluded: chain NB residue 66 LEU Chi-restraints excluded: chain NF residue 103 SER Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 112 MET Chi-restraints excluded: chain NI residue 537 MET Chi-restraints excluded: chain NK residue 88 ASP Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 291 ARG Chi-restraints excluded: chain SA residue 313 VAL Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 68 MET Chi-restraints excluded: chain SD residue 63 GLN Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SP residue 297 ASN Chi-restraints excluded: chain SP residue 308 LEU Chi-restraints excluded: chain SQ residue 9 LYS Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 266 ARG Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 421 VAL Chi-restraints excluded: chain SS residue 525 VAL Chi-restraints excluded: chain SS residue 575 PHE Chi-restraints excluded: chain ST residue 283 ASP Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SY residue 496 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1494 random chunks: chunk 1202 optimal weight: 3.9990 chunk 819 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 1075 optimal weight: 2.9990 chunk 595 optimal weight: 4.9990 chunk 1232 optimal weight: 10.0000 chunk 998 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 737 optimal weight: 6.9990 chunk 1296 optimal weight: 10.0000 chunk 364 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN ** BC 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L8 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 75 GLN L8 78 GLN LB 93 GLN LD 7 GLN LD 141 HIS LI 65 GLN LI 91 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LK 67 GLN LL 100 ASN LO 33 GLN LW 57 ASN ** NA 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 484 GLN NA 621 HIS ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN ** SE 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 206 GLN SG 140 GLN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 93 GLN SK 178 GLN ** SL 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN SL 133 GLN ** SM 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SM 572 HIS SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SP 354 HIS SQ 217 GLN SR 342 HIS SR 351 ASN SS 138 ASN SS 581 GLN ** SU 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SU 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 119 GLN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 167115 Z= 0.394 Angle : 0.590 10.766 239183 Z= 0.304 Chirality : 0.041 0.285 28926 Planarity : 0.005 0.064 19959 Dihedral : 21.589 179.514 58223 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.22 % Allowed : 10.06 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 (0.07), residues: 12214 helix: 2.25 (0.07), residues: 5166 sheet: 0.41 (0.12), residues: 1783 loop : -0.05 (0.08), residues: 5265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPSU 319 HIS 0.012 0.002 HISNA 621 PHE 0.023 0.002 PHESW 233 TYR 0.025 0.002 TYRLK 61 ARG 0.008 0.001 ARGSK 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 996 time to evaluate : 10.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: L7 34 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8431 (t) REVERT: L7 173 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7508 (tm-30) REVERT: L8 70 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: LA 40 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7155 (t70) REVERT: LA 54 GLN cc_start: 0.7863 (mt0) cc_final: 0.7653 (mt0) REVERT: LA 99 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: LB 17 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: LC 70 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7569 (mmpt) REVERT: LC 130 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: LC 131 GLU cc_start: 0.7587 (tt0) cc_final: 0.6952 (tm-30) REVERT: LD 22 VAL cc_start: 0.6670 (t) cc_final: 0.6410 (t) REVERT: LG 15 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6660 (ttp-170) REVERT: LH 33 HIS cc_start: 0.8234 (m170) cc_final: 0.6132 (t-170) REVERT: LH 67 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6541 (ttm170) REVERT: LJ 99 ASP cc_start: 0.6615 (OUTLIER) cc_final: 0.6349 (p0) REVERT: LK 65 ARG cc_start: 0.7418 (mmt180) cc_final: 0.6637 (mmt180) REVERT: LL 64 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8254 (mt) REVERT: LN 363 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8043 (pt) REVERT: LO 40 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7531 (mt0) REVERT: NA 358 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6675 (ttm) REVERT: NB 22 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: NB 63 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: NB 67 ARG cc_start: 0.8288 (mmt90) cc_final: 0.7983 (mmm-85) REVERT: NK 97 MET cc_start: 0.8428 (ttm) cc_final: 0.8122 (ttm) REVERT: SA 95 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7717 (pmm) REVERT: SA 291 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6909 (ttp-170) REVERT: SA 323 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7607 (mmm-85) REVERT: SC 68 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4677 (mmm) REVERT: SC 245 GLN cc_start: 0.7823 (tp40) cc_final: 0.7614 (tp-100) REVERT: SD 63 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6545 (mt0) REVERT: SE 165 GLU cc_start: 0.7855 (mp0) cc_final: 0.7478 (mp0) REVERT: SM 388 ILE cc_start: 0.8331 (mm) cc_final: 0.8123 (mt) REVERT: SN 63 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6593 (p0) REVERT: SO 347 MET cc_start: 0.6630 (tmm) cc_final: 0.6346 (tmm) REVERT: SR 388 MET cc_start: 0.5344 (ttp) cc_final: 0.4231 (mtp) REVERT: SS 658 MET cc_start: 0.7491 (ttp) cc_final: 0.7228 (ttp) REVERT: SU 744 MET cc_start: 0.8353 (tpp) cc_final: 0.7730 (tpp) REVERT: SZ 143 ASP cc_start: 0.8096 (m-30) cc_final: 0.7888 (m-30) outliers start: 227 outliers final: 116 residues processed: 1117 average time/residue: 2.2220 time to fit residues: 3563.2282 Evaluate side-chains 1101 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 963 time to evaluate : 9.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 101 SER Chi-restraints excluded: chain BA residue 141 CYS Chi-restraints excluded: chain BC residue 272 THR Chi-restraints excluded: chain BC residue 305 HIS Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 162 GLU Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 177 LEU Chi-restraints excluded: chain L7 residue 195 VAL Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 58 THR Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 113 VAL Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 17 GLU Chi-restraints excluded: chain LC residue 17 LEU Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LC residue 130 GLU Chi-restraints excluded: chain LC residue 159 LEU Chi-restraints excluded: chain LD residue 30 ASN Chi-restraints excluded: chain LD residue 67 THR Chi-restraints excluded: chain LD residue 91 GLU Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 67 ARG Chi-restraints excluded: chain LH residue 82 THR Chi-restraints excluded: chain LH residue 102 VAL Chi-restraints excluded: chain LH residue 118 ASP Chi-restraints excluded: chain LI residue 88 GLU Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 54 THR Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 120 GLU Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LL residue 64 ILE Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 338 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 363 ILE Chi-restraints excluded: chain LO residue 21 VAL Chi-restraints excluded: chain LO residue 40 GLN Chi-restraints excluded: chain LO residue 77 ASN Chi-restraints excluded: chain LQ residue 66 THR Chi-restraints excluded: chain LR residue 74 VAL Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 18 LEU Chi-restraints excluded: chain NA residue 329 LEU Chi-restraints excluded: chain NA residue 358 MET Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 22 GLN Chi-restraints excluded: chain NB residue 63 GLU Chi-restraints excluded: chain NB residue 66 LEU Chi-restraints excluded: chain NF residue 103 SER Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 112 MET Chi-restraints excluded: chain NI residue 537 MET Chi-restraints excluded: chain NK residue 31 SER Chi-restraints excluded: chain NK residue 85 THR Chi-restraints excluded: chain NK residue 88 ASP Chi-restraints excluded: chain NK residue 104 ARG Chi-restraints excluded: chain SA residue 95 MET Chi-restraints excluded: chain SA residue 291 ARG Chi-restraints excluded: chain SA residue 313 VAL Chi-restraints excluded: chain SA residue 349 LEU Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 68 MET Chi-restraints excluded: chain SC residue 92 VAL Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SD residue 63 GLN Chi-restraints excluded: chain SD residue 196 THR Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SH residue 82 THR Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SJ residue 760 THR Chi-restraints excluded: chain SJ residue 784 SER Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 76 LYS Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SM residue 320 GLN Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SN residue 63 ASP Chi-restraints excluded: chain SN residue 134 THR Chi-restraints excluded: chain SP residue 81 VAL Chi-restraints excluded: chain SP residue 216 TRP Chi-restraints excluded: chain SP residue 308 LEU Chi-restraints excluded: chain SQ residue 9 LYS Chi-restraints excluded: chain SR residue 33 VAL Chi-restraints excluded: chain SR residue 54 THR Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 291 CYS Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 418 CYS Chi-restraints excluded: chain SS residue 421 VAL Chi-restraints excluded: chain SS residue 525 VAL Chi-restraints excluded: chain SS residue 575 PHE Chi-restraints excluded: chain ST residue 285 THR Chi-restraints excluded: chain SU residue 242 MET Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SU residue 596 THR Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SY residue 486 ARG Chi-restraints excluded: chain SY residue 496 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1494 random chunks: chunk 485 optimal weight: 0.9980 chunk 1300 optimal weight: 2.9990 chunk 285 optimal weight: 20.0000 chunk 847 optimal weight: 1.9990 chunk 356 optimal weight: 0.9980 chunk 1445 optimal weight: 0.8980 chunk 1199 optimal weight: 10.0000 chunk 669 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 478 optimal weight: 5.9990 chunk 758 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 75 GLN LB 93 GLN LC 173 ASN LD 141 HIS LH 93 ASN LK 60 HIS LL 100 ASN LQ 102 ASN LW 30 GLN LW 57 ASN NA 343 ASN ** NA 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 484 GLN NA 621 HIS NH 124 ASN NH 127 GLN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN ** SE 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 206 GLN SL 133 GLN ** SM 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 217 GLN SR 342 HIS SR 351 ASN SR 426 HIS SS 149 HIS ST 223 GLN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SU 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS SU 597 ASN SV 119 GLN SV 129 GLN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 418 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 167115 Z= 0.143 Angle : 0.475 10.081 239183 Z= 0.248 Chirality : 0.034 0.239 28926 Planarity : 0.004 0.050 19959 Dihedral : 21.543 179.125 58223 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.55 % Allowed : 11.32 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.07), residues: 12214 helix: 2.56 (0.07), residues: 5152 sheet: 0.45 (0.12), residues: 1769 loop : 0.06 (0.08), residues: 5293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPSU 319 HIS 0.012 0.001 HISNA 621 PHE 0.021 0.001 PHESW 233 TYR 0.021 0.001 TYRSN 109 ARG 0.008 0.000 ARGSK 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1002 time to evaluate : 10.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: L7 34 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8418 (t) REVERT: L7 169 ARG cc_start: 0.7537 (mmt90) cc_final: 0.6985 (mtt180) REVERT: L7 173 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7483 (tm-30) REVERT: LA 40 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7103 (t70) REVERT: LA 99 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6505 (tm-30) REVERT: LB 17 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: LC 130 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: LC 131 GLU cc_start: 0.7472 (tt0) cc_final: 0.6892 (tm-30) REVERT: LD 22 VAL cc_start: 0.6562 (t) cc_final: 0.6315 (t) REVERT: LG 15 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6791 (mtp180) REVERT: LH 33 HIS cc_start: 0.8193 (m170) cc_final: 0.6148 (t-170) REVERT: LI 30 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8741 (mtp) REVERT: LJ 99 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6320 (p0) REVERT: LK 65 ARG cc_start: 0.7291 (mmt180) cc_final: 0.6588 (mmt180) REVERT: LO 40 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: NB 63 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6717 (tm-30) REVERT: NB 67 ARG cc_start: 0.8285 (mmt90) cc_final: 0.8027 (mmm-85) REVERT: NK 97 MET cc_start: 0.8376 (ttm) cc_final: 0.8043 (ttm) REVERT: SC 68 MET cc_start: 0.5190 (OUTLIER) cc_final: 0.4610 (mmm) REVERT: SC 245 GLN cc_start: 0.7782 (tp40) cc_final: 0.7567 (tp40) REVERT: SH 172 LEU cc_start: 0.8290 (tt) cc_final: 0.8054 (tp) REVERT: SN 63 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6555 (p0) REVERT: SO 345 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: SO 347 MET cc_start: 0.6559 (tmm) cc_final: 0.6300 (tmm) REVERT: SR 266 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6927 (tpt170) REVERT: SU 744 MET cc_start: 0.8341 (tpp) cc_final: 0.7735 (tpp) outliers start: 158 outliers final: 72 residues processed: 1087 average time/residue: 2.2011 time to fit residues: 3434.2021 Evaluate side-chains 1037 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 950 time to evaluate : 8.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 58 VAL Chi-restraints excluded: chain BC residue 305 HIS Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 184 ASN Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LB residue 17 GLU Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 17 LEU Chi-restraints excluded: chain LC residue 130 GLU Chi-restraints excluded: chain LD residue 30 ASN Chi-restraints excluded: chain LD residue 91 GLU Chi-restraints excluded: chain LD residue 143 HIS Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LE residue 159 MET Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LH residue 82 THR Chi-restraints excluded: chain LH residue 102 VAL Chi-restraints excluded: chain LH residue 118 ASP Chi-restraints excluded: chain LI residue 30 MET Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LJ residue 33 THR Chi-restraints excluded: chain LJ residue 54 THR Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 120 GLU Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LO residue 40 GLN Chi-restraints excluded: chain LO residue 77 ASN Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 60 LEU Chi-restraints excluded: chain NB residue 63 GLU Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 112 MET Chi-restraints excluded: chain NI residue 537 MET Chi-restraints excluded: chain NK residue 104 ARG Chi-restraints excluded: chain SA residue 313 VAL Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 68 MET Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SJ residue 664 ASP Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SL residue 76 LYS Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SM residue 320 GLN Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SN residue 63 ASP Chi-restraints excluded: chain SO residue 345 GLN Chi-restraints excluded: chain SP residue 216 TRP Chi-restraints excluded: chain SP residue 308 LEU Chi-restraints excluded: chain SQ residue 9 LYS Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 266 ARG Chi-restraints excluded: chain SS residue 139 VAL Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 421 VAL Chi-restraints excluded: chain SS residue 525 VAL Chi-restraints excluded: chain SS residue 575 PHE Chi-restraints excluded: chain ST residue 285 THR Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 19 MET Chi-restraints excluded: chain SY residue 486 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1494 random chunks: chunk 1393 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 823 optimal weight: 9.9990 chunk 1055 optimal weight: 4.9990 chunk 817 optimal weight: 7.9990 chunk 1216 optimal weight: 7.9990 chunk 807 optimal weight: 10.0000 chunk 1439 optimal weight: 8.9990 chunk 901 optimal weight: 7.9990 chunk 877 optimal weight: 9.9990 chunk 664 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN ** BC 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L7 167 HIS L8 70 GLN L8 75 GLN LB 93 GLN LC 173 ASN LD 40 GLN LD 141 HIS LH 93 ASN LI 14 ASN LI 65 GLN LI 91 ASN LL 6 GLN LL 100 ASN LN 322 HIS NA 343 ASN ** NA 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 539 HIS NA 621 HIS NH 127 GLN NI 361 GLN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN ** SE 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 206 GLN SG 140 GLN SG 156 ASN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 93 GLN ** SL 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SP 96 GLN SP 100 HIS SQ 25 ASN SQ 217 GLN SR 246 HIS SR 351 ASN SS 543 HIS SS 696 ASN ** SU 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS SV 129 GLN SY 330 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 167115 Z= 0.588 Angle : 0.707 11.782 239183 Z= 0.358 Chirality : 0.047 0.307 28926 Planarity : 0.006 0.086 19959 Dihedral : 21.612 179.201 58221 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.30 % Allowed : 11.21 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 1.16 (0.07), residues: 12214 helix: 2.02 (0.07), residues: 5137 sheet: 0.24 (0.12), residues: 1771 loop : -0.24 (0.08), residues: 5306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRPLT 6 HIS 0.013 0.002 HISSD 58 PHE 0.026 0.003 PHESO 65 TYR 0.028 0.003 TYRSN 202 ARG 0.011 0.001 ARGSS 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 982 time to evaluate : 9.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 245 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7942 (m) REVERT: L6 115 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: L7 33 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8677 (t) REVERT: L8 126 GLU cc_start: 0.7740 (tp30) cc_final: 0.7525 (tm-30) REVERT: LA 40 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7100 (t70) REVERT: LA 99 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: LB 17 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7357 (pt0) REVERT: LC 70 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7591 (mmpt) REVERT: LC 130 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7278 (tm-30) REVERT: LC 131 GLU cc_start: 0.7597 (tt0) cc_final: 0.6987 (tm-30) REVERT: LG 15 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.6770 (ttp-170) REVERT: LH 33 HIS cc_start: 0.8283 (m170) cc_final: 0.6119 (t-170) REVERT: LH 67 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6582 (ttm170) REVERT: LH 94 ASN cc_start: 0.8250 (t0) cc_final: 0.7937 (t0) REVERT: LJ 99 ASP cc_start: 0.6618 (OUTLIER) cc_final: 0.6338 (p0) REVERT: LK 65 ARG cc_start: 0.7440 (mmt180) cc_final: 0.6620 (mmt180) REVERT: LL 64 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8290 (mt) REVERT: LO 40 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: LS 20 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7242 (tp-100) REVERT: NA 358 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6683 (ttm) REVERT: NA 362 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7820 (tt) REVERT: NB 22 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: NB 63 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: NB 67 ARG cc_start: 0.8350 (mmt90) cc_final: 0.7755 (mtt-85) REVERT: NF 98 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5133 (pmm150) REVERT: NH 12 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7834 (ttm) REVERT: NI 255 MET cc_start: 0.7508 (mtp) cc_final: 0.7294 (mtt) REVERT: NK 97 MET cc_start: 0.8430 (ttm) cc_final: 0.8126 (ttm) REVERT: SA 201 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7576 (ttm170) REVERT: SA 291 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6974 (ttp-170) REVERT: SC 68 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4660 (mmm) REVERT: SN 63 ASP cc_start: 0.7064 (p0) cc_final: 0.6628 (p0) REVERT: SO 344 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.6799 (mmmt) REVERT: SO 345 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: SO 347 MET cc_start: 0.6665 (tmm) cc_final: 0.6350 (tmm) REVERT: SR 388 MET cc_start: 0.5286 (ttp) cc_final: 0.4339 (mtp) REVERT: ST 286 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8044 (mtp85) REVERT: SU 711 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7948 (mp) REVERT: SU 744 MET cc_start: 0.8405 (tpp) cc_final: 0.7725 (tpp) REVERT: SW 347 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8143 (tp) outliers start: 235 outliers final: 121 residues processed: 1113 average time/residue: 2.1480 time to fit residues: 3436.9321 Evaluate side-chains 1105 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 958 time to evaluate : 8.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 101 SER Chi-restraints excluded: chain BC residue 245 THR Chi-restraints excluded: chain BC residue 305 HIS Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 79 GLU Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 33 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 177 LEU Chi-restraints excluded: chain L7 residue 195 VAL Chi-restraints excluded: chain L7 residue 198 THR Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 113 VAL Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 17 GLU Chi-restraints excluded: chain LC residue 17 LEU Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 30 ASN Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LE residue 159 MET Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 43 SER Chi-restraints excluded: chain LH residue 67 ARG Chi-restraints excluded: chain LH residue 82 THR Chi-restraints excluded: chain LH residue 102 VAL Chi-restraints excluded: chain LH residue 118 ASP Chi-restraints excluded: chain LI residue 88 GLU Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 33 THR Chi-restraints excluded: chain LJ residue 54 THR Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 120 GLU Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LL residue 64 ILE Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 218 ASP Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 338 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LO residue 40 GLN Chi-restraints excluded: chain LO residue 75 SER Chi-restraints excluded: chain LO residue 77 ASN Chi-restraints excluded: chain LQ residue 66 THR Chi-restraints excluded: chain LR residue 74 VAL Chi-restraints excluded: chain LS residue 20 GLN Chi-restraints excluded: chain LS residue 107 GLN Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NA residue 358 MET Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 22 GLN Chi-restraints excluded: chain NB residue 32 LEU Chi-restraints excluded: chain NB residue 60 LEU Chi-restraints excluded: chain NB residue 63 GLU Chi-restraints excluded: chain NB residue 66 LEU Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NF residue 103 SER Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NH residue 12 MET Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NI residue 219 ILE Chi-restraints excluded: chain NI residue 234 MET Chi-restraints excluded: chain NI residue 537 MET Chi-restraints excluded: chain NK residue 88 ASP Chi-restraints excluded: chain NK residue 104 ARG Chi-restraints excluded: chain SA residue 201 ARG Chi-restraints excluded: chain SA residue 291 ARG Chi-restraints excluded: chain SA residue 313 VAL Chi-restraints excluded: chain SA residue 349 LEU Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 68 MET Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SD residue 187 MET Chi-restraints excluded: chain SE residue 96 LEU Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 201 THR Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SH residue 82 THR Chi-restraints excluded: chain SI residue 63 SER Chi-restraints excluded: chain SJ residue 440 MET Chi-restraints excluded: chain SJ residue 664 ASP Chi-restraints excluded: chain SJ residue 768 VAL Chi-restraints excluded: chain SJ residue 784 SER Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SL residue 76 LYS Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SM residue 320 GLN Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SO residue 83 MET Chi-restraints excluded: chain SO residue 94 MET Chi-restraints excluded: chain SO residue 344 LYS Chi-restraints excluded: chain SO residue 345 GLN Chi-restraints excluded: chain SP residue 216 TRP Chi-restraints excluded: chain SP residue 308 LEU Chi-restraints excluded: chain SR residue 33 VAL Chi-restraints excluded: chain SR residue 54 THR Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 291 CYS Chi-restraints excluded: chain SS residue 139 VAL Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 418 CYS Chi-restraints excluded: chain SS residue 421 VAL Chi-restraints excluded: chain SS residue 525 VAL Chi-restraints excluded: chain SS residue 575 PHE Chi-restraints excluded: chain SU residue 242 MET Chi-restraints excluded: chain SU residue 329 VAL Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SU residue 596 THR Chi-restraints excluded: chain SU residue 711 LEU Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 19 MET Chi-restraints excluded: chain SW residue 347 LEU Chi-restraints excluded: chain SY residue 486 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1494 random chunks: chunk 890 optimal weight: 5.9990 chunk 575 optimal weight: 0.9980 chunk 860 optimal weight: 6.9990 chunk 433 optimal weight: 0.9990 chunk 282 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 915 optimal weight: 0.7980 chunk 981 optimal weight: 10.0000 chunk 711 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 1131 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 70 GLN L8 75 GLN LD 141 HIS LH 93 ASN LI 14 ASN LI 65 GLN LI 91 ASN LL 100 ASN LQ 107 ASN LR 73 HIS LW 30 GLN LW 57 ASN NA 343 ASN ** NA 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 484 GLN NA 621 HIS NH 127 GLN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN ** SE 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 206 GLN SG 140 GLN SG 156 ASN SI 166 GLN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN ** SM 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 25 ASN SQ 217 GLN SR 342 HIS SR 351 ASN ** SS 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 696 ASN ** SU 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS SV 129 GLN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 418 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 167115 Z= 0.196 Angle : 0.512 13.406 239183 Z= 0.266 Chirality : 0.035 0.258 28926 Planarity : 0.004 0.050 19959 Dihedral : 21.564 179.009 58221 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.49 % Allowed : 12.28 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 1.48 (0.07), residues: 12214 helix: 2.36 (0.07), residues: 5156 sheet: 0.30 (0.12), residues: 1765 loop : -0.11 (0.08), residues: 5293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPSU 319 HIS 0.012 0.001 HISNA 621 PHE 0.022 0.001 PHESW 233 TYR 0.024 0.001 TYRSN 202 ARG 0.011 0.000 ARGSK 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 971 time to evaluate : 9.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 245 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7800 (m) REVERT: L6 115 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: L7 34 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8409 (t) REVERT: L7 169 ARG cc_start: 0.7574 (mmt90) cc_final: 0.7132 (mtt180) REVERT: LA 40 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7047 (t70) REVERT: LA 99 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6658 (tm-30) REVERT: LB 17 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7304 (pm20) REVERT: LC 130 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7295 (tm-30) REVERT: LC 131 GLU cc_start: 0.7545 (tt0) cc_final: 0.6959 (tm-30) REVERT: LD 22 VAL cc_start: 0.6574 (t) cc_final: 0.6272 (t) REVERT: LG 15 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6892 (mtp180) REVERT: LH 33 HIS cc_start: 0.8226 (m170) cc_final: 0.6140 (t-170) REVERT: LH 67 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6628 (ttm170) REVERT: LI 30 MET cc_start: 0.9097 (mtp) cc_final: 0.8694 (mtp) REVERT: LJ 91 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5059 (mp) REVERT: LJ 99 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6382 (p0) REVERT: LK 65 ARG cc_start: 0.7336 (mmt180) cc_final: 0.6561 (mmt180) REVERT: LO 40 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: NA 362 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7687 (tt) REVERT: NB 63 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: NB 67 ARG cc_start: 0.8305 (mmt90) cc_final: 0.8010 (mmm-85) REVERT: NK 97 MET cc_start: 0.8390 (ttm) cc_final: 0.8081 (ttm) REVERT: SA 323 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7757 (mmm-85) REVERT: SC 68 MET cc_start: 0.5175 (OUTLIER) cc_final: 0.4576 (mmm) REVERT: SN 63 ASP cc_start: 0.7039 (p0) cc_final: 0.6611 (p0) REVERT: SO 345 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: SO 347 MET cc_start: 0.6603 (tmm) cc_final: 0.6318 (tmm) REVERT: SR 388 MET cc_start: 0.5212 (ttp) cc_final: 0.4184 (mtp) REVERT: SU 744 MET cc_start: 0.8366 (tpp) cc_final: 0.7709 (tpp) outliers start: 152 outliers final: 90 residues processed: 1058 average time/residue: 2.1537 time to fit residues: 3276.3218 Evaluate side-chains 1054 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 949 time to evaluate : 8.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 216 VAL Chi-restraints excluded: chain BC residue 245 THR Chi-restraints excluded: chain BC residue 260 VAL Chi-restraints excluded: chain BC residue 305 HIS Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 195 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 113 VAL Chi-restraints excluded: chain LB residue 17 GLU Chi-restraints excluded: chain LC residue 17 LEU Chi-restraints excluded: chain LD residue 30 ASN Chi-restraints excluded: chain LD residue 143 HIS Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 67 ARG Chi-restraints excluded: chain LH residue 82 THR Chi-restraints excluded: chain LH residue 102 VAL Chi-restraints excluded: chain LH residue 118 ASP Chi-restraints excluded: chain LI residue 88 GLU Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 33 THR Chi-restraints excluded: chain LJ residue 54 THR Chi-restraints excluded: chain LJ residue 91 LEU Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 120 GLU Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LO residue 40 GLN Chi-restraints excluded: chain LR residue 73 HIS Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 67 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 32 LEU Chi-restraints excluded: chain NB residue 60 LEU Chi-restraints excluded: chain NB residue 63 GLU Chi-restraints excluded: chain NB residue 66 LEU Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NF residue 231 THR Chi-restraints excluded: chain NH residue 29 ASP Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NI residue 537 MET Chi-restraints excluded: chain NK residue 104 ARG Chi-restraints excluded: chain SA residue 313 VAL Chi-restraints excluded: chain SA residue 349 LEU Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 68 MET Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SD residue 196 THR Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 201 THR Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SJ residue 440 MET Chi-restraints excluded: chain SJ residue 664 ASP Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SK residue 78 ASP Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 76 LYS Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SM residue 286 VAL Chi-restraints excluded: chain SM residue 320 GLN Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SO residue 94 MET Chi-restraints excluded: chain SO residue 345 GLN Chi-restraints excluded: chain SP residue 216 TRP Chi-restraints excluded: chain SP residue 308 LEU Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 291 CYS Chi-restraints excluded: chain SS residue 139 VAL Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 421 VAL Chi-restraints excluded: chain SS residue 575 PHE Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SY residue 486 ARG Chi-restraints excluded: chain SY residue 496 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1494 random chunks: chunk 1309 optimal weight: 9.9990 chunk 1379 optimal weight: 6.9990 chunk 1258 optimal weight: 0.9990 chunk 1341 optimal weight: 3.9990 chunk 807 optimal weight: 9.9990 chunk 584 optimal weight: 1.9990 chunk 1053 optimal weight: 7.9990 chunk 411 optimal weight: 3.9990 chunk 1212 optimal weight: 6.9990 chunk 1269 optimal weight: 7.9990 chunk 1337 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN ** BC 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 70 GLN LB 93 GLN LC 173 ASN ** LD 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 141 HIS LH 93 ASN LI 91 ASN LI 127 GLN LL 100 ASN LR 73 HIS ** NA 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS NH 124 ASN ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN ** SE 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 206 GLN SG 140 GLN SG 156 ASN SI 166 GLN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 133 GLN ** SM 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 25 ASN SR 342 HIS SR 351 ASN SR 361 HIS SS 696 ASN SU 592 HIS SU 597 ASN SY 330 ASN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 418 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 167115 Z= 0.318 Angle : 0.555 13.759 239183 Z= 0.286 Chirality : 0.038 0.269 28926 Planarity : 0.005 0.060 19959 Dihedral : 21.531 178.933 58221 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.57 % Allowed : 12.59 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 (0.07), residues: 12214 helix: 2.29 (0.07), residues: 5146 sheet: 0.28 (0.12), residues: 1771 loop : -0.15 (0.08), residues: 5297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPSU 319 HIS 0.012 0.001 HISNA 621 PHE 0.022 0.002 PHESW 233 TYR 0.027 0.002 TYRSN 202 ARG 0.015 0.001 ARGBA 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 965 time to evaluate : 9.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 245 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7811 (m) REVERT: L6 115 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: L7 34 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8421 (t) REVERT: LA 40 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.7063 (t70) REVERT: LA 99 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: LB 17 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: LC 130 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7253 (tm-30) REVERT: LC 131 GLU cc_start: 0.7561 (tt0) cc_final: 0.6880 (tt0) REVERT: LD 22 VAL cc_start: 0.6536 (t) cc_final: 0.6249 (t) REVERT: LG 15 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6899 (ttp-170) REVERT: LH 33 HIS cc_start: 0.8251 (m170) cc_final: 0.6132 (t-170) REVERT: LH 67 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6555 (ttm170) REVERT: LH 94 ASN cc_start: 0.8217 (t0) cc_final: 0.7931 (t0) REVERT: LJ 91 LEU cc_start: 0.5260 (OUTLIER) cc_final: 0.4938 (mp) REVERT: LJ 99 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6388 (p0) REVERT: LK 65 ARG cc_start: 0.7330 (mmt180) cc_final: 0.6575 (mmt180) REVERT: LO 40 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: NA 358 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6622 (ttm) REVERT: NA 362 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7846 (tt) REVERT: NB 63 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: NB 67 ARG cc_start: 0.8347 (mmt90) cc_final: 0.8042 (mmm-85) REVERT: NK 97 MET cc_start: 0.8411 (ttm) cc_final: 0.8100 (ttm) REVERT: SA 201 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7555 (ttm170) REVERT: SA 323 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7794 (mmm-85) REVERT: SC 68 MET cc_start: 0.5228 (OUTLIER) cc_final: 0.4566 (mmm) REVERT: SH 172 LEU cc_start: 0.8313 (tt) cc_final: 0.8094 (tp) REVERT: SN 63 ASP cc_start: 0.7054 (p0) cc_final: 0.6619 (p0) REVERT: SO 345 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: SO 347 MET cc_start: 0.6629 (tmm) cc_final: 0.6336 (tmm) REVERT: SR 248 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6480 (tpp-160) REVERT: SR 388 MET cc_start: 0.5150 (ttp) cc_final: 0.4173 (mtp) REVERT: SU 711 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7799 (mp) REVERT: SU 744 MET cc_start: 0.8394 (tpp) cc_final: 0.7891 (tpp) outliers start: 161 outliers final: 107 residues processed: 1063 average time/residue: 2.1173 time to fit residues: 3249.4276 Evaluate side-chains 1077 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 951 time to evaluate : 8.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 101 SER Chi-restraints excluded: chain BC residue 245 THR Chi-restraints excluded: chain BC residue 260 VAL Chi-restraints excluded: chain BC residue 305 HIS Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 4 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 195 VAL Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 113 VAL Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 17 GLU Chi-restraints excluded: chain LC residue 17 LEU Chi-restraints excluded: chain LD residue 30 ASN Chi-restraints excluded: chain LD residue 44 LEU Chi-restraints excluded: chain LD residue 67 THR Chi-restraints excluded: chain LD residue 91 GLU Chi-restraints excluded: chain LD residue 143 HIS Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 43 SER Chi-restraints excluded: chain LH residue 67 ARG Chi-restraints excluded: chain LH residue 82 THR Chi-restraints excluded: chain LH residue 102 VAL Chi-restraints excluded: chain LH residue 118 ASP Chi-restraints excluded: chain LI residue 88 GLU Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 33 THR Chi-restraints excluded: chain LJ residue 54 THR Chi-restraints excluded: chain LJ residue 91 LEU Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 120 GLU Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LO residue 16 SER Chi-restraints excluded: chain LO residue 40 GLN Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 67 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NA residue 329 LEU Chi-restraints excluded: chain NA residue 358 MET Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 32 LEU Chi-restraints excluded: chain NB residue 60 LEU Chi-restraints excluded: chain NB residue 63 GLU Chi-restraints excluded: chain NB residue 66 LEU Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NF residue 231 THR Chi-restraints excluded: chain NH residue 29 ASP Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NI residue 537 MET Chi-restraints excluded: chain NK residue 88 ASP Chi-restraints excluded: chain NK residue 104 ARG Chi-restraints excluded: chain SA residue 201 ARG Chi-restraints excluded: chain SA residue 313 VAL Chi-restraints excluded: chain SA residue 349 LEU Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 68 MET Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SD residue 196 THR Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 201 THR Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SJ residue 440 MET Chi-restraints excluded: chain SJ residue 664 ASP Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SL residue 76 LYS Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 286 VAL Chi-restraints excluded: chain SM residue 320 GLN Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SO residue 94 MET Chi-restraints excluded: chain SO residue 345 GLN Chi-restraints excluded: chain SP residue 216 TRP Chi-restraints excluded: chain SP residue 308 LEU Chi-restraints excluded: chain SR residue 33 VAL Chi-restraints excluded: chain SR residue 54 THR Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 248 ARG Chi-restraints excluded: chain SR residue 291 CYS Chi-restraints excluded: chain SS residue 139 VAL Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 421 VAL Chi-restraints excluded: chain SS residue 575 PHE Chi-restraints excluded: chain SU residue 515 LEU Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SU residue 711 LEU Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 486 ARG Chi-restraints excluded: chain SY residue 496 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1494 random chunks: chunk 881 optimal weight: 1.9990 chunk 1418 optimal weight: 4.9990 chunk 866 optimal weight: 4.9990 chunk 673 optimal weight: 10.0000 chunk 986 optimal weight: 5.9990 chunk 1488 optimal weight: 6.9990 chunk 1369 optimal weight: 0.7980 chunk 1185 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 915 optimal weight: 1.9990 chunk 726 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 70 GLN L8 75 GLN LA 101 ASN LB 93 GLN LD 40 GLN ** LD 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 141 HIS LH 93 ASN LI 127 GLN LL 100 ASN LR 73 HIS LW 30 GLN ** NA 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 92 GLN NK 101 GLN ** SE 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 206 GLN SG 140 GLN SG 156 ASN SH 135 ASN SI 166 GLN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 133 GLN ** SM 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 25 ASN SR 342 HIS SR 351 ASN SS 696 ASN ** SU 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 418 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 167115 Z= 0.253 Angle : 0.529 12.782 239183 Z= 0.274 Chirality : 0.037 0.261 28926 Planarity : 0.004 0.056 19959 Dihedral : 21.523 178.936 58221 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.40 % Allowed : 12.75 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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 (0.07), residues: 12214 helix: 2.34 (0.07), residues: 5159 sheet: 0.31 (0.12), residues: 1762 loop : -0.12 (0.08), residues: 5293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPL6 18 HIS 0.012 0.001 HISNA 621 PHE 0.023 0.001 PHESW 233 TYR 0.026 0.001 TYRSN 202 ARG 0.015 0.000 ARGBA 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24428 Ramachandran restraints generated. 12214 Oldfield, 0 Emsley, 12214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 956 time to evaluate : 9.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 146 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7643 (ttp-110) REVERT: BC 245 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7780 (m) REVERT: L6 115 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: L7 34 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8417 (t) REVERT: L7 169 ARG cc_start: 0.7600 (mmt90) cc_final: 0.7172 (mtt180) REVERT: LA 40 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7059 (t70) REVERT: LA 99 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: LB 17 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: LC 130 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7256 (tm-30) REVERT: LD 22 VAL cc_start: 0.6521 (t) cc_final: 0.6245 (t) REVERT: LD 30 ASN cc_start: 0.6641 (OUTLIER) cc_final: 0.6378 (p0) REVERT: LG 15 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6879 (ttp-170) REVERT: LH 33 HIS cc_start: 0.8242 (m170) cc_final: 0.6124 (t-170) REVERT: LH 67 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6574 (ttm170) REVERT: LI 30 MET cc_start: 0.9106 (mtp) cc_final: 0.8708 (mtp) REVERT: LJ 91 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4939 (mp) REVERT: LJ 99 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6386 (p0) REVERT: LK 65 ARG cc_start: 0.7284 (mmt180) cc_final: 0.6531 (mmt180) REVERT: LO 40 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: NA 362 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7803 (tt) REVERT: NB 63 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6779 (tm-30) REVERT: NB 67 ARG cc_start: 0.8368 (mmt90) cc_final: 0.8088 (mmm-85) REVERT: NK 97 MET cc_start: 0.8404 (ttm) cc_final: 0.8094 (ttm) REVERT: SA 201 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7564 (ttm170) REVERT: SA 323 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7782 (mmm-85) REVERT: SC 68 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4551 (mmm) REVERT: SD 74 MET cc_start: 0.7371 (mtm) cc_final: 0.7156 (mtp) REVERT: SH 172 LEU cc_start: 0.8308 (tt) cc_final: 0.8087 (tp) REVERT: SL 33 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6306 (mtmp) REVERT: SN 63 ASP cc_start: 0.7054 (p0) cc_final: 0.6621 (p0) REVERT: SO 345 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7337 (mt0) REVERT: SO 347 MET cc_start: 0.6615 (tmm) cc_final: 0.6324 (tmm) REVERT: SP 74 ASN cc_start: 0.5682 (m110) cc_final: 0.4757 (m-40) REVERT: SR 248 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6456 (tpp-160) REVERT: SR 388 MET cc_start: 0.4944 (ttp) cc_final: 0.4171 (mtp) REVERT: SU 744 MET cc_start: 0.8410 (tpp) cc_final: 0.7918 (tpp) outliers start: 143 outliers final: 105 residues processed: 1043 average time/residue: 2.0983 time to fit residues: 3158.2846 Evaluate side-chains 1069 residues out of total 10867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 945 time to evaluate : 9.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 101 SER Chi-restraints excluded: chain BC residue 245 THR Chi-restraints excluded: chain BC residue 260 VAL Chi-restraints excluded: chain BC residue 305 HIS Chi-restraints excluded: chain L6 residue 19 GLN Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 4 VAL Chi-restraints excluded: chain L7 residue 34 VAL Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 177 LEU Chi-restraints excluded: chain L7 residue 195 VAL Chi-restraints excluded: chain L7 residue 203 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 40 HIS Chi-restraints excluded: chain LA residue 99 GLU Chi-restraints excluded: chain LA residue 113 VAL Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 17 GLU Chi-restraints excluded: chain LC residue 17 LEU Chi-restraints excluded: chain LD residue 30 ASN Chi-restraints excluded: chain LD residue 67 THR Chi-restraints excluded: chain LD residue 91 GLU Chi-restraints excluded: chain LD residue 143 HIS Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 104 SER Chi-restraints excluded: chain LG residue 15 ARG Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LH residue 67 ARG Chi-restraints excluded: chain LH residue 82 THR Chi-restraints excluded: chain LH residue 102 VAL Chi-restraints excluded: chain LH residue 118 ASP Chi-restraints excluded: chain LI residue 88 GLU Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 111 LEU Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 33 THR Chi-restraints excluded: chain LJ residue 54 THR Chi-restraints excluded: chain LJ residue 91 LEU Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 120 GLU Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LK residue 11 LEU Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 95 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LO residue 40 GLN Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 58 VAL Chi-restraints excluded: chain LT residue 67 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 105 LEU Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 400 TYR Chi-restraints excluded: chain NA residue 510 ASN Chi-restraints excluded: chain NB residue 32 LEU Chi-restraints excluded: chain NB residue 60 LEU Chi-restraints excluded: chain NB residue 63 GLU Chi-restraints excluded: chain NB residue 66 LEU Chi-restraints excluded: chain NF residue 205 SER Chi-restraints excluded: chain NF residue 231 THR Chi-restraints excluded: chain NH residue 54 LEU Chi-restraints excluded: chain NH residue 149 SER Chi-restraints excluded: chain NI residue 537 MET Chi-restraints excluded: chain NK residue 104 ARG Chi-restraints excluded: chain SA residue 201 ARG Chi-restraints excluded: chain SA residue 313 VAL Chi-restraints excluded: chain SA residue 349 LEU Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 68 MET Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SD residue 196 THR Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 201 THR Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 110 SER Chi-restraints excluded: chain SJ residue 440 MET Chi-restraints excluded: chain SJ residue 664 ASP Chi-restraints excluded: chain SJ residue 826 SER Chi-restraints excluded: chain SK residue 107 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SK residue 186 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 33 LYS Chi-restraints excluded: chain SL residue 76 LYS Chi-restraints excluded: chain SL residue 153 ASP Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 286 VAL Chi-restraints excluded: chain SM residue 320 GLN Chi-restraints excluded: chain SM residue 552 MET Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SO residue 94 MET Chi-restraints excluded: chain SO residue 345 GLN Chi-restraints excluded: chain SP residue 216 TRP Chi-restraints excluded: chain SP residue 308 LEU Chi-restraints excluded: chain SR residue 21 LEU Chi-restraints excluded: chain SR residue 33 VAL Chi-restraints excluded: chain SR residue 54 THR Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 248 ARG Chi-restraints excluded: chain SR residue 291 CYS Chi-restraints excluded: chain SS residue 139 VAL Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 421 VAL Chi-restraints excluded: chain SS residue 575 PHE Chi-restraints excluded: chain SU residue 515 LEU Chi-restraints excluded: chain SU residue 518 VAL Chi-restraints excluded: chain SU residue 678 ASP Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 486 ARG Chi-restraints excluded: chain SY residue 496 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1494 random chunks: chunk 941 optimal weight: 0.9980 chunk 1262 optimal weight: 8.9990 chunk 363 optimal weight: 0.9980 chunk 1092 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 1187 optimal weight: 8.9990 chunk 496 optimal weight: 0.0070 chunk 1218 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 111 ASN ** BC 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 70 GLN LB 45 GLN LB 93 GLN ** LD 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 141 HIS LH 93 ASN LI 127 GLN LL 100 ASN LR 73 HIS ** NA 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 621 HIS ** NK 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 206 GLN SG 140 GLN SG 156 ASN SI 166 GLN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 133 GLN ** SM 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 124 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 25 ASN SR 342 HIS SR 351 ASN SS 696 ASN ST 200 GLN ** SU 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 592 HIS ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 418 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.093353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067340 restraints weight = 418205.227| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.96 r_work: 0.2969 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 167115 Z= 0.201 Angle : 0.505 12.345 239183 Z= 0.262 Chirality : 0.035 0.249 28926 Planarity : 0.004 0.053 19959 Dihedral : 21.496 178.757 58221 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.30 % Allowed : 12.93 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 1.56 (0.08), residues: 12214 helix: 2.44 (0.07), residues: 5156 sheet: 0.34 (0.12), residues: 1772 loop : -0.10 (0.08), residues: 5286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRPL6 18 HIS 0.014 0.001 HISSP 69 PHE 0.023 0.001 PHESW 233 TYR 0.025 0.001 TYRSN 109 ARG 0.015 0.000 ARGBA 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54502.31 seconds wall clock time: 942 minutes 48.37 seconds (56568.37 seconds total)