Starting phenix.real_space_refine on Sat Dec 9 10:35:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml4_23908/12_2023/7ml4_23908_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml4_23908/12_2023/7ml4_23908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml4_23908/12_2023/7ml4_23908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml4_23908/12_2023/7ml4_23908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml4_23908/12_2023/7ml4_23908_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml4_23908/12_2023/7ml4_23908_updated.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.002 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 Fe 4 7.16 5 Zn 15 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 347 5.16 5 C 39269 2.51 5 N 11015 2.21 5 O 11992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 110": "OD1" <-> "OD2" Residue "Q PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 83": "OD1" <-> "OD2" Residue "R TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 40": "OE1" <-> "OE2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 320": "NH1" <-> "NH2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A ASP 716": "OD1" <-> "OD2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1417": "OE1" <-> "OE2" Residue "A PHE 1441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B ASP 391": "OD1" <-> "OD2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 550": "OD1" <-> "OD2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B GLU 699": "OE1" <-> "OE2" Residue "B ASP 724": "OD1" <-> "OD2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 997": "OE1" <-> "OE2" Residue "B PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1061": "OE1" <-> "OE2" Residue "B PHE 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1132": "OE1" <-> "OE2" Residue "B TYR 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "I PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 113": "OD1" <-> "OD2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "L TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 375": "NH1" <-> "NH2" Residue "0 GLU 421": "OE1" <-> "OE2" Residue "0 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 175": "NH1" <-> "NH2" Residue "4 ARG 273": "NH1" <-> "NH2" Residue "4 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 378": "NH1" <-> "NH2" Residue "6 PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 286": "NH1" <-> "NH2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "2 PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 413": "OE1" <-> "OE2" Residue "2 ARG 450": "NH1" <-> "NH2" Residue "2 TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 197": "NH1" <-> "NH2" Residue "U TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 79": "NH1" <-> "NH2" Residue "O ARG 98": "NH1" <-> "NH2" Residue "O PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 65": "NH1" <-> "NH2" Residue "W ARG 108": "NH1" <-> "NH2" Residue "W TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 144": "NH1" <-> "NH2" Residue "W ARG 174": "NH1" <-> "NH2" Residue "W ARG 193": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 62733 Number of models: 1 Model: "" Number of chains: 42 Chain: "Q" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1039 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 152 Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1253 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 1 Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "M" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1805 Classifications: {'peptide': 234} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 11039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1405, 11039 Classifications: {'peptide': 1405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 62, 'TRANS': 1339} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 8861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8861 Classifications: {'peptide': 1114} Link IDs: {'CIS': 3, 'PTRANS': 50, 'TRANS': 1060} Chain breaks: 8 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 688 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 77} Chain: "H" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1068 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 919 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "L" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "3" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 361 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 71} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 153 Chain: "0" Number of atoms: 6108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6108 Classifications: {'peptide': 754} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 721} Chain: "4" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2041 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'UNK:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "6" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2527 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 20, 'TRANS': 330} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 2, 'UNK:plan-1': 13, 'ASP:plan': 6, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 140 Chain: "1" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2411 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 12, 'TRANS': 354} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 633 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'UNK:plan-1': 106, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 241 Chain: "7" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4447 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 162} Link IDs: {'CIS': 3, 'PTRANS': 26, 'TRANS': 604} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 312 Chain: "5" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 498 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 62} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "2" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3011 Classifications: {'peptide': 460} Incomplete info: {'backbone_only': 154, 'truncation_to_alanine': 14} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 727 Unresolved non-hydrogen angles: 1042 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 210 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 8, 'GLU:plan': 16, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 352 Chain: "X" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 921 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "U" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 383 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "V" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Chain: "N" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 791 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "T" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 968 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "O" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "W" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1469 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 182} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "P" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "W" 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 4794 SG CYS M 24 58.028 100.395 129.695 1.00110.50 S ATOM 4816 SG CYS M 27 54.128 100.591 129.928 1.00115.03 S ATOM 4956 SG CYS M 45 55.889 102.109 127.205 1.00109.04 S ATOM 4975 SG CYS M 48 56.307 103.661 130.592 1.00 92.60 S ATOM 7391 SG CYS A 107 126.662 117.400 110.991 1.00 23.17 S ATOM 7415 SG CYS A 110 127.562 116.948 114.506 1.00 23.38 S ATOM 7720 SG CYS A 148 129.266 119.454 112.197 1.00 24.08 S ATOM 7810 SG CYS A 167 130.035 115.715 111.858 1.00 25.98 S ATOM 7086 SG CYS A 67 83.357 101.068 119.837 1.00 20.38 S ATOM 7108 SG CYS A 70 84.372 100.258 123.442 1.00 20.45 S ATOM 7161 SG CYS A 77 83.031 104.128 121.710 1.00 18.80 S ATOM 25985 SG CYS B1163 96.335 106.674 131.442 1.00 15.39 S ATOM 26003 SG CYS B1166 96.359 108.013 128.230 1.00 15.37 S ATOM 26128 SG CYS B1182 95.459 104.365 128.596 1.00 18.55 S ATOM 26147 SG CYS B1185 99.120 105.531 129.152 1.00 18.12 S ATOM 27134 SG CYS C 86 18.863 126.378 121.485 1.00 9.53 S ATOM 27151 SG CYS C 88 20.618 124.231 119.346 1.00 8.80 S ATOM 27184 SG CYS C 92 17.259 126.105 118.366 1.00 10.47 S ATOM 27207 SG CYS C 95 20.770 127.868 118.484 1.00 9.60 S ATOM 32134 SG CYS I 7 123.629 164.058 63.110 1.00 14.23 S ATOM 32159 SG CYS I 10 123.847 160.048 63.086 1.00 14.85 S ATOM 32325 SG CYS I 29 124.528 161.768 66.107 1.00 14.43 S ATOM 32349 SG CYS I 32 126.761 162.391 63.009 1.00 15.54 S ATOM 32676 SG CYS I 75 89.635 192.317 74.083 1.00 10.20 S ATOM 32698 SG CYS I 78 86.957 193.086 71.054 1.00 11.15 S ATOM 32914 SG CYS I 103 87.264 189.811 72.222 1.00 11.45 S ATOM 32934 SG CYS I 106 90.334 190.902 70.953 1.00 11.36 S ATOM 33106 SG CYS J 7 34.416 153.498 106.504 1.00 8.02 S ATOM 33129 SG CYS J 10 31.081 154.893 108.428 1.00 7.76 S ATOM 33409 SG CYS J 45 34.103 157.071 107.594 1.00 7.48 S ATOM 33415 SG CYS J 46 31.861 156.027 105.261 1.00 8.35 S ATOM 34558 SG CYS L 31 42.150 119.261 80.687 1.00 15.39 S ATOM 34682 SG CYS L 48 42.063 116.165 78.295 1.00 15.92 S ATOM 36165 SG CYS 0 115 135.778 33.058 79.355 1.00117.61 S ATOM 36307 SG CYS 0 133 132.160 30.768 81.628 1.00 46.59 S ATOM 36492 SG CYS 0 156 130.333 29.235 79.373 1.00 90.79 S ATOM 36793 SG CYS 0 191 136.102 26.541 79.405 1.00115.32 S ATOM 43171 SG CYS 4 289 197.682 26.792 49.225 1.00 0.00 S ATOM 43190 SG CYS 4 292 200.151 25.706 51.708 1.00 0.00 S ATOM 43275 SG CYS 4 305 199.325 23.464 48.465 1.00 0.00 S ATOM 43291 SG CYS 4 308 197.092 23.645 51.468 1.00 0.00 S ATOM 45589 SG CYS 6 403 219.443 35.762 76.697 1.00 0.00 S ATOM 45611 SG CYS 6 406 219.624 39.150 75.134 1.00 0.00 S ATOM 45779 SG CYS 6 437 217.369 38.561 78.113 1.00 0.00 S ATOM 45795 SG CYS 6 440 216.506 37.105 74.574 1.00 0.00 S ATOM 45737 SG CYS 6 429 211.125 27.836 72.024 1.00 0.00 S ATOM 45753 SG CYS 6 432 214.811 27.307 72.555 1.00 0.00 S ATOM 45873 SG CYS 6 451 213.752 30.309 70.643 1.00 0.00 S ATOM 45888 SG CYS 6 454 213.298 26.896 69.028 1.00 0.00 S ATOM 45234 SG CYS 6 349 201.272 42.722 35.784 1.00 0.00 S ATOM 45255 SG CYS 6 352 200.091 45.701 33.955 1.00 0.00 S ATOM 45324 SG CYS 6 363 198.512 44.831 37.368 1.00 0.00 S ATOM 45342 SG CYS 6 366 197.790 42.661 34.328 1.00 0.00 S ATOM 45151 SG CYS 6 336 202.771 57.246 38.043 1.00 30.00 S ATOM 45162 SG CYS 6 338 200.753 54.413 39.663 1.00 30.00 S ATOM 45289 SG CYS 6 357 203.553 56.142 41.620 1.00 30.00 S ATOM 62031 SG CYS W 124 84.143 82.171 122.446 1.00 0.00 S ATOM 62052 SG CYS W 127 84.288 84.184 122.183 1.00 0.00 S ATOM 62257 SG CYS W 152 80.110 83.129 120.844 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P DG N 27 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 27 " occ=0.00 residue: pdb=" P DG N 33 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 33 " occ=0.00 residue: pdb=" P DC T 133 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC T 133 " occ=0.00 residue: pdb=" P DC T 139 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC T 139 " occ=0.00 Time building chain proxies: 24.72, per 1000 atoms: 0.39 Number of scatterers: 62733 At special positions: 0 Unit cell: (268.18, 208.82, 186.56, 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 15 29.99 Fe 4 26.01 S 347 16.00 P 90 15.00 Mg 1 11.99 O 11992 8.00 N 11015 7.00 C 39269 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: 21.86 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 440 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 454 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 363 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" NE2 GLN A 68 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " Number of angles added : 72 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14630 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 301 helices and 63 sheets defined 38.9% alpha, 9.1% beta 30 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 21.56 Creating SS restraints... Processing helix chain 'Q' and resid 26 through 34 removed outlier: 3.646A pdb=" N PHE Q 31 " --> pdb=" O ARG Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 113 removed outlier: 3.598A pdb=" N ASN Q 113 " --> pdb=" O GLU Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 133 No H-bonds generated for 'chain 'Q' and resid 130 through 133' Processing helix chain 'Q' and resid 338 through 344 Processing helix chain 'Q' and resid 408 through 414 removed outlier: 4.089A pdb=" N ASP Q 414 " --> pdb=" O GLU Q 410 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 81 removed outlier: 4.945A pdb=" N LYS R 80 " --> pdb=" O PHE R 76 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 241 Processing helix chain 'R' and resid 296 through 310 Processing helix chain 'R' and resid 315 through 322 removed outlier: 3.594A pdb=" N LYS R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 335 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 55 through 75 removed outlier: 4.141A pdb=" N GLU D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN D 74 " --> pdb=" O PHE D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 4.037A pdb=" N ILE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'M' and resid 122 through 140 removed outlier: 3.838A pdb=" N GLU M 125 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 170 through 182 Processing helix chain 'M' and resid 189 through 195 Processing helix chain 'M' and resid 201 through 217 Processing helix chain 'M' and resid 236 through 246 Proline residue: M 240 - end of helix Processing helix chain 'M' and resid 250 through 266 removed outlier: 3.677A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 288 Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 308 through 323 removed outlier: 3.967A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU M 318 " --> pdb=" O LYS M 314 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP M 321 " --> pdb=" O TYR M 317 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS M 322 " --> pdb=" O GLU M 318 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU M 323 " --> pdb=" O HIS M 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 105 removed outlier: 4.859A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.604A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.690A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.743A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix No H-bonds generated for 'chain 'A' and resid 473 through 478' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.564A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 574 through 581 removed outlier: 4.009A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 660 Proline residue: A 639 - end of helix Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 810 through 844 removed outlier: 3.584A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 916 through 919 No H-bonds generated for 'chain 'A' and resid 916 through 919' Processing helix chain 'A' and resid 926 through 946 Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 Processing helix chain 'A' and resid 1005 through 1025 removed outlier: 4.619A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1078 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1097 through 1105 Processing helix chain 'A' and resid 1128 through 1138 Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1259 through 1269 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 3.883A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1359 removed outlier: 7.514A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1376 Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1396 through 1400 Processing helix chain 'A' and resid 1405 through 1414 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'B' and resid 27 through 36 Processing helix chain 'B' and resid 45 through 63 removed outlier: 5.418A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 180 through 183 removed outlier: 4.364A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 294 through 299 Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 371 through 389 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 436 removed outlier: 4.082A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 666 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.729A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 700' Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.819A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 751 through 755' Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 775 removed outlier: 4.304A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 810 Processing helix chain 'B' and resid 814 through 816 No H-bonds generated for 'chain 'B' and resid 814 through 816' Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 890 through 892 No H-bonds generated for 'chain 'B' and resid 890 through 892' Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1061 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1122 through 1124 No H-bonds generated for 'chain 'B' and resid 1122 through 1124' Processing helix chain 'B' and resid 1132 through 1140 Processing helix chain 'B' and resid 1144 through 1152 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.912A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 267 Processing helix chain 'E' and resid 4 through 26 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 removed outlier: 3.836A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 102 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 127 removed outlier: 3.604A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 17 through 28 Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 44 through 51 removed outlier: 4.016A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 removed outlier: 3.740A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.934A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 110 Processing helix chain '3' and resid 76 through 90 removed outlier: 3.504A pdb=" N LYS 3 80 " --> pdb=" O VAL 3 76 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU 3 81 " --> pdb=" O GLU 3 77 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL 3 82 " --> pdb=" O VAL 3 78 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP 3 83 " --> pdb=" O GLU 3 79 " (cutoff:3.500A) Processing helix chain '3' and resid 92 through 94 No H-bonds generated for 'chain '3' and resid 92 through 94' Processing helix chain '3' and resid 103 through 122 removed outlier: 3.882A pdb=" N LYS 3 119 " --> pdb=" O ASP 3 115 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS 3 122 " --> pdb=" O TYR 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 128 through 144 Processing helix chain '0' and resid 19 through 33 removed outlier: 3.815A pdb=" N LYS 0 30 " --> pdb=" O CYS 0 26 " (cutoff:3.500A) Processing helix chain '0' and resid 48 through 62 removed outlier: 3.644A pdb=" N THR 0 56 " --> pdb=" O LEU 0 52 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN 0 60 " --> pdb=" O THR 0 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET 0 61 " --> pdb=" O ILE 0 57 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS 0 62 " --> pdb=" O ALA 0 58 " (cutoff:3.500A) Processing helix chain '0' and resid 76 through 97 removed outlier: 3.906A pdb=" N ASN 0 88 " --> pdb=" O VAL 0 84 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU 0 89 " --> pdb=" O GLU 0 85 " (cutoff:3.500A) Processing helix chain '0' and resid 118 through 121 No H-bonds generated for 'chain '0' and resid 118 through 121' Processing helix chain '0' and resid 126 through 136 Processing helix chain '0' and resid 142 through 146 removed outlier: 3.551A pdb=" N GLU 0 146 " --> pdb=" O ARG 0 143 " (cutoff:3.500A) Processing helix chain '0' and resid 159 through 164 Processing helix chain '0' and resid 178 through 187 removed outlier: 3.738A pdb=" N GLU 0 187 " --> pdb=" O LYS 0 183 " (cutoff:3.500A) Processing helix chain '0' and resid 192 through 201 removed outlier: 3.544A pdb=" N ARG 0 198 " --> pdb=" O PHE 0 194 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N SER 0 201 " --> pdb=" O ARG 0 197 " (cutoff:3.500A) Processing helix chain '0' and resid 211 through 214 No H-bonds generated for 'chain '0' and resid 211 through 214' Processing helix chain '0' and resid 224 through 226 No H-bonds generated for 'chain '0' and resid 224 through 226' Processing helix chain '0' and resid 237 through 239 No H-bonds generated for 'chain '0' and resid 237 through 239' Processing helix chain '0' and resid 241 through 248 removed outlier: 3.561A pdb=" N GLU 0 246 " --> pdb=" O ASN 0 242 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 277 removed outlier: 3.585A pdb=" N ARG 0 258 " --> pdb=" O THR 0 254 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG 0 275 " --> pdb=" O ILE 0 271 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS 0 276 " --> pdb=" O SER 0 272 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL 0 277 " --> pdb=" O GLU 0 273 " (cutoff:3.500A) Processing helix chain '0' and resid 279 through 291 removed outlier: 3.577A pdb=" N GLU 0 285 " --> pdb=" O LYS 0 281 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR 0 286 " --> pdb=" O LEU 0 282 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL 0 290 " --> pdb=" O TYR 0 286 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN 0 291 " --> pdb=" O GLU 0 287 " (cutoff:3.500A) Processing helix chain '0' and resid 295 through 298 No H-bonds generated for 'chain '0' and resid 295 through 298' Processing helix chain '0' and resid 328 through 344 removed outlier: 3.680A pdb=" N PHE 0 334 " --> pdb=" O HIS 0 330 " (cutoff:3.500A) Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 388 removed outlier: 4.132A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS 0 377 " --> pdb=" O PRO 0 373 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER 0 382 " --> pdb=" O SER 0 378 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR 0 387 " --> pdb=" O LEU 0 383 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 0 388 " --> pdb=" O LEU 0 384 " (cutoff:3.500A) Processing helix chain '0' and resid 397 through 409 removed outlier: 3.606A pdb=" N ASP 0 401 " --> pdb=" O THR 0 397 " (cutoff:3.500A) Processing helix chain '0' and resid 425 through 427 No H-bonds generated for 'chain '0' and resid 425 through 427' Processing helix chain '0' and resid 442 through 452 removed outlier: 4.333A pdb=" N LYS 0 447 " --> pdb=" O ILE 0 444 " (cutoff:3.500A) Proline residue: 0 448 - end of helix removed outlier: 3.842A pdb=" N ARG 0 452 " --> pdb=" O VAL 0 449 " (cutoff:3.500A) Processing helix chain '0' and resid 468 through 473 Processing helix chain '0' and resid 516 through 532 removed outlier: 3.834A pdb=" N ARG 0 520 " --> pdb=" O PRO 0 516 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASN 0 521 " --> pdb=" O SER 0 517 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE 0 532 " --> pdb=" O GLU 0 528 " (cutoff:3.500A) Processing helix chain '0' and resid 544 through 556 removed outlier: 3.860A pdb=" N SER 0 549 " --> pdb=" O LEU 0 545 " (cutoff:3.500A) Processing helix chain '0' and resid 559 through 566 removed outlier: 4.078A pdb=" N VAL 0 563 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 591 removed outlier: 3.745A pdb=" N LYS 0 588 " --> pdb=" O GLU 0 584 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA 0 589 " --> pdb=" O THR 0 585 " (cutoff:3.500A) Processing helix chain '0' and resid 606 through 609 No H-bonds generated for 'chain '0' and resid 606 through 609' Processing helix chain '0' and resid 633 through 645 removed outlier: 3.842A pdb=" N PHE 0 641 " --> pdb=" O ALA 0 637 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET 0 642 " --> pdb=" O ARG 0 638 " (cutoff:3.500A) Processing helix chain '0' and resid 650 through 669 removed outlier: 3.649A pdb=" N GLY 0 667 " --> pdb=" O ALA 0 663 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 690 removed outlier: 3.589A pdb=" N LYS 0 689 " --> pdb=" O PHE 0 686 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) Processing helix chain '0' and resid 695 through 700 removed outlier: 3.637A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 703 through 705 No H-bonds generated for 'chain '0' and resid 703 through 705' Processing helix chain '0' and resid 710 through 724 Processing helix chain '0' and resid 744 through 752 removed outlier: 4.131A pdb=" N SER 0 750 " --> pdb=" O LYS 0 746 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG 0 751 " --> pdb=" O HIS 0 747 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 42 removed outlier: 3.605A pdb=" N THR 4 38 " --> pdb=" O PRO 4 34 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR 4 39 " --> pdb=" O LYS 4 35 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE 4 40 " --> pdb=" O LEU 4 36 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP 4 41 " --> pdb=" O TRP 4 37 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU 4 42 " --> pdb=" O THR 4 38 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 34 through 42' Processing helix chain '4' and resid 51 through 67 removed outlier: 3.570A pdb=" N LEU 4 57 " --> pdb=" O VAL 4 53 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 134 Processing helix chain '4' and resid 138 through 142 Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 191 through 205 removed outlier: 4.389A pdb=" N ILE 4 194 " --> pdb=" O PHE 4 191 " (cutoff:3.500A) Proline residue: 4 195 - end of helix Processing helix chain '4' and resid 222 through 231 removed outlier: 3.583A pdb=" N THR 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP 4 229 " --> pdb=" O GLN 4 225 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 251 Processing helix chain '4' and resid 314 through 322 Processing helix chain '6' and resid 134 through 137 No H-bonds generated for 'chain '6' and resid 134 through 137' Processing helix chain '6' and resid 145 through 163 removed outlier: 3.673A pdb=" N GLN 6 151 " --> pdb=" O ALA 6 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS 6 158 " --> pdb=" O ILE 6 154 " (cutoff:3.500A) Processing helix chain '6' and resid 189 through 201 removed outlier: 3.568A pdb=" N SER 6 198 " --> pdb=" O ASP 6 194 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 220 removed outlier: 3.519A pdb=" N GLY 6 219 " --> pdb=" O GLU 6 215 " (cutoff:3.500A) Processing helix chain '6' and resid 247 through 256 Processing helix chain '6' and resid 271 through 280 Processing helix chain '6' and resid 294 through 305 removed outlier: 3.778A pdb=" N LYS 6 298 " --> pdb=" O GLU 6 294 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU 6 300 " --> pdb=" O HIS 6 296 " (cutoff:3.500A) Processing helix chain '6' and resid 374 through 383 removed outlier: 3.509A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 445 removed outlier: 3.526A pdb=" N PHE 6 443 " --> pdb=" O ASP 6 439 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS 6 445 " --> pdb=" O ASP 6 441 " (cutoff:3.500A) Processing helix chain '6' and resid 452 through 455 No H-bonds generated for 'chain '6' and resid 452 through 455' Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 206 through 225 removed outlier: 3.689A pdb=" N TRP 1 210 " --> pdb=" O PRO 1 206 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER 1 211 " --> pdb=" O SER 1 207 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE 1 214 " --> pdb=" O TRP 1 210 " (cutoff:3.500A) Proline residue: 1 215 - end of helix removed outlier: 3.555A pdb=" N ALA 1 221 " --> pdb=" O LEU 1 217 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N UNK 1 223 " --> pdb=" O UNK 1 219 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N UNK 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 252 through 262 removed outlier: 3.599A pdb=" N ILE 1 256 " --> pdb=" O SER 1 252 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN 1 258 " --> pdb=" O GLU 1 254 " (cutoff:3.500A) Processing helix chain '1' and resid 264 through 274 removed outlier: 4.439A pdb=" N VAL 1 274 " --> pdb=" O TYR 1 270 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 294 removed outlier: 5.233A pdb=" N ALA 1 285 " --> pdb=" O PRO 1 281 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER 1 290 " --> pdb=" O ARG 1 286 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU 1 292 " --> pdb=" O PHE 1 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE 1 293 " --> pdb=" O SER 1 289 " (cutoff:3.500A) Processing helix chain '1' and resid 315 through 318 No H-bonds generated for 'chain '1' and resid 315 through 318' Processing helix chain '1' and resid 372 through 388 removed outlier: 3.507A pdb=" N LYS 1 376 " --> pdb=" O VAL 1 372 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY 1 377 " --> pdb=" O ASP 1 373 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET 1 385 " --> pdb=" O LEU 1 381 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET 1 387 " --> pdb=" O GLU 1 383 " (cutoff:3.500A) Processing helix chain '1' and resid 468 through 482 Processing helix chain '1' and resid 497 through 515 removed outlier: 3.785A pdb=" N UNK 1 501 " --> pdb=" O UNK 1 497 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG 1 502 " --> pdb=" O UNK 1 498 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN 1 510 " --> pdb=" O UNK 1 506 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 566 removed outlier: 3.798A pdb=" N CYS 1 557 " --> pdb=" O LEU 1 553 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE 1 560 " --> pdb=" O THR 1 556 " (cutoff:3.500A) Processing helix chain '1' and resid 576 through 604 Processing helix chain '1' and resid 607 through 638 removed outlier: 3.980A pdb=" N THR 1 611 " --> pdb=" O SER 1 607 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 1 614 " --> pdb=" O ASN 1 610 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR 1 615 " --> pdb=" O THR 1 611 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU 1 616 " --> pdb=" O CYS 1 612 " (cutoff:3.500A) Proline residue: 1 618 - end of helix Processing helix chain '7' and resid 105 through 108 Processing helix chain '7' and resid 125 through 127 No H-bonds generated for 'chain '7' and resid 125 through 127' Processing helix chain '7' and resid 150 through 160 Processing helix chain '7' and resid 178 through 186 removed outlier: 3.524A pdb=" N VAL 7 184 " --> pdb=" O TYR 7 181 " (cutoff:3.500A) Processing helix chain '7' and resid 190 through 200 removed outlier: 3.913A pdb=" N ILE 7 194 " --> pdb=" O THR 7 190 " (cutoff:3.500A) Processing helix chain '7' and resid 207 through 217 Processing helix chain '7' and resid 239 through 247 Processing helix chain '7' and resid 262 through 267 Processing helix chain '7' and resid 323 through 332 removed outlier: 3.747A pdb=" N GLN 7 331 " --> pdb=" O LYS 7 327 " (cutoff:3.500A) Processing helix chain '7' and resid 364 through 374 removed outlier: 4.398A pdb=" N LYS 7 368 " --> pdb=" O PRO 7 364 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER 7 369 " --> pdb=" O TYR 7 365 " (cutoff:3.500A) Processing helix chain '7' and resid 392 through 403 removed outlier: 4.538A pdb=" N GLY 7 396 " --> pdb=" O LYS 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 414 through 423 removed outlier: 3.787A pdb=" N MET 7 418 " --> pdb=" O SER 7 414 " (cutoff:3.500A) Processing helix chain '7' and resid 457 through 460 No H-bonds generated for 'chain '7' and resid 457 through 460' Processing helix chain '7' and resid 468 through 479 removed outlier: 3.526A pdb=" N THR 7 478 " --> pdb=" O MET 7 474 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 492 No H-bonds generated for 'chain '7' and resid 490 through 492' Processing helix chain '7' and resid 495 through 505 removed outlier: 3.631A pdb=" N ARG 7 499 " --> pdb=" O ALA 7 496 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL 7 501 " --> pdb=" O PHE 7 498 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER 7 503 " --> pdb=" O ARG 7 500 " (cutoff:3.500A) Processing helix chain '7' and resid 527 through 531 Processing helix chain '7' and resid 540 through 543 No H-bonds generated for 'chain '7' and resid 540 through 543' Processing helix chain '7' and resid 563 through 571 Processing helix chain '7' and resid 575 through 579 removed outlier: 4.038A pdb=" N LEU 7 579 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 600 removed outlier: 3.518A pdb=" N LEU 7 594 " --> pdb=" O ALA 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 613 through 620 removed outlier: 3.972A pdb=" N ALA 7 619 " --> pdb=" O LEU 7 615 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU 7 620 " --> pdb=" O GLN 7 616 " (cutoff:3.500A) Processing helix chain '7' and resid 633 through 644 Processing helix chain '7' and resid 656 through 658 No H-bonds generated for 'chain '7' and resid 656 through 658' Processing helix chain '7' and resid 680 through 690 Processing helix chain '7' and resid 714 through 729 removed outlier: 3.694A pdb=" N TYR 7 717 " --> pdb=" O GLN 7 714 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR 7 718 " --> pdb=" O GLU 7 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER 7 719 " --> pdb=" O MET 7 716 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA 7 724 " --> pdb=" O LYS 7 721 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU 7 726 " --> pdb=" O GLN 7 723 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL 7 727 " --> pdb=" O ALA 7 724 " (cutoff:3.500A) Processing helix chain '7' and resid 742 through 744 No H-bonds generated for 'chain '7' and resid 742 through 744' Processing helix chain '7' and resid 753 through 765 removed outlier: 3.541A pdb=" N ARG 7 757 " --> pdb=" O PRO 7 753 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU 7 758 " --> pdb=" O ARG 7 754 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU 7 765 " --> pdb=" O GLN 7 761 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 27 removed outlier: 4.213A pdb=" N MET 5 27 " --> pdb=" O ILE 5 23 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 62 Processing helix chain '2' and resid 10 through 13 No H-bonds generated for 'chain '2' and resid 10 through 13' Processing helix chain '2' and resid 19 through 26 Processing helix chain '2' and resid 29 through 38 removed outlier: 3.791A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 52 Processing helix chain '2' and resid 59 through 65 Processing helix chain '2' and resid 71 through 83 Processing helix chain '2' and resid 102 through 112 removed outlier: 3.589A pdb=" N LEU 2 108 " --> pdb=" O PHE 2 104 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG 2 109 " --> pdb=" O LYS 2 105 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN 2 110 " --> pdb=" O ILE 2 106 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA 2 111 " --> pdb=" O SER 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 193 Processing helix chain '2' and resid 197 through 210 removed outlier: 3.822A pdb=" N GLN 2 206 " --> pdb=" O THR 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 230 removed outlier: 3.580A pdb=" N GLY 2 229 " --> pdb=" O ILE 2 225 " (cutoff:3.500A) Processing helix chain '2' and resid 244 through 256 Processing helix chain '2' and resid 263 through 265 No H-bonds generated for 'chain '2' and resid 263 through 265' Processing helix chain '2' and resid 273 through 279 Processing helix chain '2' and resid 354 through 362 removed outlier: 3.883A pdb=" N ALA 2 358 " --> pdb=" O PRO 2 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 388 removed outlier: 3.567A pdb=" N ARG 2 385 " --> pdb=" O GLU 2 381 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA 2 386 " --> pdb=" O SER 2 382 " (cutoff:3.500A) Processing helix chain '2' and resid 395 through 402 removed outlier: 3.699A pdb=" N GLU 2 401 " --> pdb=" O ILE 2 397 " (cutoff:3.500A) Processing helix chain '2' and resid 405 through 407 No H-bonds generated for 'chain '2' and resid 405 through 407' Processing helix chain '2' and resid 409 through 413 Processing helix chain '2' and resid 435 through 449 Processing helix chain '2' and resid 465 through 478 Processing helix chain '2' and resid 495 through 506 removed outlier: 3.652A pdb=" N VAL 2 501 " --> pdb=" O GLY 2 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 138 removed outlier: 3.990A pdb=" N GLN X 136 " --> pdb=" O THR X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 151 removed outlier: 4.182A pdb=" N LEU X 148 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 165 Processing helix chain 'X' and resid 189 through 198 Processing helix chain 'X' and resid 208 through 212 Processing helix chain 'X' and resid 217 through 223 Processing helix chain 'X' and resid 257 through 263 Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 removed outlier: 3.930A pdb=" N SER O 136 " --> pdb=" O SER O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 220 through 228 removed outlier: 3.503A pdb=" N TYR O 224 " --> pdb=" O ARG O 220 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE O 227 " --> pdb=" O ILE O 223 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 236 Processing helix chain 'W' and resid 5 through 20 removed outlier: 4.222A pdb=" N LYS W 14 " --> pdb=" O LYS W 10 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE W 15 " --> pdb=" O ASN W 11 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL W 16 " --> pdb=" O LEU W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 34 removed outlier: 3.950A pdb=" N LEU W 27 " --> pdb=" O GLY W 23 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA W 31 " --> pdb=" O LEU W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 46 removed outlier: 3.535A pdb=" N GLN W 45 " --> pdb=" O ASP W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 63 Proline residue: W 56 - end of helix removed outlier: 3.574A pdb=" N ALA W 59 " --> pdb=" O GLY W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 91 through 115 removed outlier: 3.623A pdb=" N TRP W 100 " --> pdb=" O ASP W 96 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL W 105 " --> pdb=" O LYS W 101 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL W 106 " --> pdb=" O VAL W 102 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN W 107 " --> pdb=" O HIS W 103 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP W 112 " --> pdb=" O ARG W 108 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU W 113 " --> pdb=" O LEU W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 138 removed outlier: 3.717A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 165 through 190 removed outlier: 3.855A pdb=" N GLN W 169 " --> pdb=" O ASN W 165 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP W 170 " --> pdb=" O LYS W 166 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS W 171 " --> pdb=" O GLU W 167 " (cutoff:3.500A) Proline residue: W 181 - end of helix removed outlier: 4.275A pdb=" N ASP W 184 " --> pdb=" O GLN W 180 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER W 185 " --> pdb=" O PRO W 181 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'Q' and resid 139 through 141 removed outlier: 3.691A pdb=" N HIS Q 140 " --> pdb=" O VAL Q 351 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'Q' and resid 362 through 365 Processing sheet with id= C, first strand: chain 'Q' and resid 374 through 376 Processing sheet with id= D, first strand: chain 'R' and resid 104 through 107 removed outlier: 4.186A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL R 68 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU R 221 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU R 70 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLN R 223 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG R 72 " --> pdb=" O GLN R 223 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N MET R 225 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 2 through 13 Processing sheet with id= F, first strand: chain 'G' and resid 85 through 87 removed outlier: 3.690A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 44 through 49 removed outlier: 6.499A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'M' and resid 34 through 37 Processing sheet with id= I, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= J, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.464A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 348 through 352 Processing sheet with id= L, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.252A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 375 through 379 Processing sheet with id= N, first strand: chain 'A' and resid 404 through 407 removed outlier: 3.894A pdb=" N ARG A 407 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 849 through 851 removed outlier: 3.549A pdb=" N THR A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= Q, first strand: chain 'A' and resid 1225 through 1228 removed outlier: 4.167A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 1281 through 1288 removed outlier: 4.019A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= T, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.679A pdb=" N LEU B 128 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= V, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= W, first strand: chain 'B' and resid 498 through 500 removed outlier: 6.685A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 223 through 227 removed outlier: 6.938A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 578 through 580 Processing sheet with id= Z, first strand: chain 'B' and resid 634 through 638 Processing sheet with id= AA, first strand: chain 'B' and resid 640 through 642 Processing sheet with id= AB, first strand: chain 'B' and resid 793 through 796 removed outlier: 5.869A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 1086 through 1092 removed outlier: 4.352A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 840 through 842 removed outlier: 6.410A pdb=" N ILE B 992 " --> pdb=" O MET B 841 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= AF, first strand: chain 'B' and resid 979 through 981 Processing sheet with id= AG, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id= AH, first strand: chain 'C' and resid 228 through 233 removed outlier: 6.385A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 97 through 104 removed outlier: 5.522A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AK, first strand: chain 'E' and resid 78 through 82 removed outlier: 6.756A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AM, first strand: chain 'H' and resid 100 through 103 removed outlier: 6.540A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 58 through 60 Processing sheet with id= AO, first strand: chain 'I' and resid 26 through 28 Processing sheet with id= AP, first strand: chain 'I' and resid 83 through 87 Processing sheet with id= AQ, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AR, first strand: chain '0' and resid 2 through 4 Processing sheet with id= AS, first strand: chain '0' and resid 455 through 459 removed outlier: 3.723A pdb=" N SER 0 73 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 205 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER 0 209 " --> pdb=" O LEU 0 108 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain '0' and resid 417 through 419 removed outlier: 4.565A pdb=" N LEU 0 417 " --> pdb=" O THR 0 438 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR 0 438 " --> pdb=" O LEU 0 417 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '0' and resid 492 through 494 removed outlier: 8.141A pdb=" N GLY 0 677 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain '0' and resid 537 through 541 removed outlier: 5.860A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain '4' and resid 234 through 236 removed outlier: 4.088A pdb=" N VAL 4 234 " --> pdb=" O ILE 4 210 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR 4 27 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU 4 177 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 179 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N CYS 4 181 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA 4 78 " --> pdb=" O ILE 4 30 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain '6' and resid 178 through 183 removed outlier: 6.681A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY 6 170 " --> pdb=" O LEU 6 126 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG 6 260 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ILE 6 234 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LYS 6 262 " --> pdb=" O ILE 6 234 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '6' and resid 346 through 348 Processing sheet with id= AZ, first strand: chain '7' and resid 453 through 456 removed outlier: 6.617A pdb=" N PHE 7 484 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU 7 410 " --> pdb=" O PHE 7 484 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE 7 486 " --> pdb=" O LEU 7 410 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU 7 511 " --> pdb=" O LEU 7 487 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '7' and resid 552 through 559 removed outlier: 7.221A pdb=" N ALA 7 703 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA 7 555 " --> pdb=" O ALA 7 703 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE 7 705 " --> pdb=" O ALA 7 555 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL 7 557 " --> pdb=" O PHE 7 705 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N SER 7 707 " --> pdb=" O VAL 7 557 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS 7 559 " --> pdb=" O SER 7 707 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL 7 709 " --> pdb=" O CYS 7 559 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '5' and resid 8 through 11 Processing sheet with id= BC, first strand: chain 'U' and resid 243 through 245 removed outlier: 3.537A pdb=" N THR U 268 " --> pdb=" O LEU U 243 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'U' and resid 278 through 281 removed outlier: 3.586A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'V' and resid 110 through 116 removed outlier: 3.597A pdb=" N LEU V 111 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL V 80 " --> pdb=" O LEU V 111 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR V 68 " --> pdb=" O ILE V 79 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'V' and resid 83 through 86 Processing sheet with id= BG, first strand: chain 'O' and resid 120 through 123 removed outlier: 4.364A pdb=" N ASP O 154 " --> pdb=" O THR O 75 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'O' and resid 111 through 116 removed outlier: 3.896A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE O 106 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN O 95 " --> pdb=" O PHE O 99 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA O 101 " --> pdb=" O GLU O 93 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU O 93 " --> pdb=" O ALA O 101 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'O' and resid 194 through 197 removed outlier: 3.736A pdb=" N VAL O 203 " --> pdb=" O THR O 215 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR O 215 " --> pdb=" O VAL O 203 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'O' and resid 66 through 71 removed outlier: 6.250A pdb=" N VAL O 161 " --> pdb=" O GLN O 68 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE O 70 " --> pdb=" O ASN O 159 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASN O 159 " --> pdb=" O ILE O 70 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'W' and resid 68 through 74 removed outlier: 3.799A pdb=" N GLU W 74 " --> pdb=" O VAL W 82 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL W 82 " --> pdb=" O GLU W 74 " (cutoff:3.500A) 2068 hydrogen bonds defined for protein. 5823 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 22.32 Time building geometry restraints manager: 23.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 26228 1.42 - 1.64: 37198 1.64 - 1.85: 532 1.85 - 2.07: 0 2.07 - 2.29: 12 Bond restraints: 63970 Sorted by residual: bond pdb=" CA GLU B 687 " pdb=" C GLU B 687 " ideal model delta sigma weight residual 1.523 1.396 0.127 1.41e-02 5.03e+03 8.08e+01 bond pdb=" CA HIS A 786 " pdb=" C HIS A 786 " ideal model delta sigma weight residual 1.523 1.374 0.150 1.80e-02 3.09e+03 6.90e+01 bond pdb=" C VAL A 512 " pdb=" N SER A 513 " ideal model delta sigma weight residual 1.331 1.213 0.118 2.07e-02 2.33e+03 3.24e+01 bond pdb=" CA HIS A 118 " pdb=" C HIS A 118 " ideal model delta sigma weight residual 1.522 1.456 0.066 1.43e-02 4.89e+03 2.12e+01 bond pdb=" CA ILE B 992 " pdb=" CB ILE B 992 " ideal model delta sigma weight residual 1.553 1.520 0.033 7.40e-03 1.83e+04 2.03e+01 ... (remaining 63965 not shown) Histogram of bond angle deviations from ideal: 73.57 - 85.67: 12 85.67 - 97.78: 23 97.78 - 109.88: 12472 109.88 - 121.98: 62129 121.98 - 134.09: 12123 Bond angle restraints: 86759 Sorted by residual: angle pdb=" C2' G P 9 " pdb=" C1' G P 9 " pdb=" N9 G P 9 " ideal model delta sigma weight residual 112.00 121.54 -9.54 1.50e+00 4.44e-01 4.04e+01 angle pdb=" C GLY A1123 " pdb=" N HIS A1124 " pdb=" CA HIS A1124 " ideal model delta sigma weight residual 121.70 133.01 -11.31 1.80e+00 3.09e-01 3.95e+01 angle pdb=" C GLU M 268 " pdb=" N ILE M 269 " pdb=" CA ILE M 269 " ideal model delta sigma weight residual 121.97 133.27 -11.30 1.80e+00 3.09e-01 3.94e+01 angle pdb=" C MET A1444 " pdb=" N ILE A1445 " pdb=" CA ILE A1445 " ideal model delta sigma weight residual 121.70 132.76 -11.06 1.80e+00 3.09e-01 3.77e+01 angle pdb=" N VAL H 57 " pdb=" CA VAL H 57 " pdb=" C VAL H 57 " ideal model delta sigma weight residual 107.75 116.54 -8.79 1.46e+00 4.69e-01 3.62e+01 ... (remaining 86754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.75: 36666 32.75 - 65.51: 1690 65.51 - 98.26: 98 98.26 - 131.02: 0 131.02 - 163.77: 1 Dihedral angle restraints: 38455 sinusoidal: 15636 harmonic: 22819 Sorted by residual: dihedral pdb=" CA SER B 838 " pdb=" C SER B 838 " pdb=" N MET B 839 " pdb=" CA MET B 839 " ideal model delta harmonic sigma weight residual -180.00 -105.65 -74.35 0 5.00e+00 4.00e-02 2.21e+02 dihedral pdb=" CA ASP B 837 " pdb=" C ASP B 837 " pdb=" N SER B 838 " pdb=" CA SER B 838 " ideal model delta harmonic sigma weight residual -180.00 -115.48 -64.52 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CA ALA M 270 " pdb=" C ALA M 270 " pdb=" N GLY M 271 " pdb=" CA GLY M 271 " ideal model delta harmonic sigma weight residual -180.00 -117.46 -62.54 0 5.00e+00 4.00e-02 1.56e+02 ... (remaining 38452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 7653 0.064 - 0.128: 1900 0.128 - 0.192: 208 0.192 - 0.257: 17 0.257 - 0.321: 6 Chirality restraints: 9784 Sorted by residual: chirality pdb=" CA HIS A 786 " pdb=" N HIS A 786 " pdb=" C HIS A 786 " pdb=" CB HIS A 786 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA MET A1444 " pdb=" N MET A1444 " pdb=" C MET A1444 " pdb=" CB MET A1444 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA GLU B 687 " pdb=" N GLU B 687 " pdb=" C GLU B 687 " pdb=" CB GLU B 687 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 9781 not shown) Planarity restraints: 10970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR M 200 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C THR M 200 " -0.061 2.00e-02 2.50e+03 pdb=" O THR M 200 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS M 201 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 567 " 0.058 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 568 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 410 " -0.057 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO B 411 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " -0.047 5.00e-02 4.00e+02 ... (remaining 10967 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 729 2.39 - 3.02: 43380 3.02 - 3.65: 103069 3.65 - 4.27: 150216 4.27 - 4.90: 239034 Nonbonded interactions: 536428 Sorted by model distance: nonbonded pdb=" CB CYS 0 156 " pdb=" S1 SF4 0 801 " model vdw 1.769 3.040 nonbonded pdb=" NE2 GLN A 68 " pdb=" ND1 HIS A 80 " model vdw 1.921 3.200 nonbonded pdb=" O SER G 95 " pdb=" OH TYR G 130 " model vdw 1.993 2.440 nonbonded pdb=" O GLY A1423 " pdb=" ND2 ASN A1427 " model vdw 1.994 2.520 nonbonded pdb=" N ASP B 188 " pdb=" OD1 ASP B 188 " model vdw 1.999 2.520 ... (remaining 536423 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 20.130 Check model and map are aligned: 0.750 Set scattering table: 0.440 Process input model: 159.480 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5119 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 : 0.015 0.150 63970 Z= 1.002 Angle : 1.087 14.680 86759 Z= 0.598 Chirality : 0.054 0.321 9784 Planarity : 0.005 0.087 10970 Dihedral : 17.003 163.775 23825 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.63 % Favored : 89.14 % Rotamer: Outliers : 12.47 % Allowed : 13.20 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.30 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.09), residues: 7759 helix: -0.50 (0.09), residues: 2926 sheet: -1.49 (0.17), residues: 940 loop : -2.14 (0.09), residues: 3893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 146 HIS 0.016 0.002 HIS A 587 PHE 0.031 0.002 PHE B 963 TYR 0.027 0.002 TYR A 303 ARG 0.013 0.001 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 783 poor density : 231 time to evaluate : 5.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 783 outliers final: 376 residues processed: 997 average time/residue: 0.5818 time to fit residues: 1014.1714 Evaluate side-chains 593 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 217 time to evaluate : 5.792 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 376 outliers final: 1 residues processed: 376 average time/residue: 0.5042 time to fit residues: 356.4207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 642 optimal weight: 30.0000 chunk 576 optimal weight: 50.0000 chunk 320 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 389 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 596 optimal weight: 20.0000 chunk 230 optimal weight: 0.9990 chunk 362 optimal weight: 0.9990 chunk 443 optimal weight: 9.9990 chunk 691 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN A 64 ASN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 700 ASN A 706 HIS ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN A1078 GLN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN A1265 ASN A1278 ASN A1390 ASN B 481 GLN B 761 HIS ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1193 GLN E 5 ASN H 128 ASN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 503 GLN ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 500 GLN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4954 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 63970 Z= 0.302 Angle : 0.704 13.617 86759 Z= 0.371 Chirality : 0.045 0.345 9784 Planarity : 0.005 0.083 10970 Dihedral : 12.240 167.314 9631 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.27 % Favored : 91.60 % Rotamer: Outliers : 2.48 % Allowed : 18.51 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.13 % Twisted Proline : 0.30 % Twisted General : 0.20 % 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: -1.61 (0.09), residues: 7759 helix: 0.04 (0.09), residues: 3032 sheet: -1.27 (0.17), residues: 911 loop : -1.96 (0.10), residues: 3816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 656 HIS 0.013 0.001 HIS 6 381 PHE 0.038 0.002 PHE A 219 TYR 0.023 0.002 TYR A 852 ARG 0.010 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 225 time to evaluate : 5.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 156 outliers final: 54 residues processed: 364 average time/residue: 0.5531 time to fit residues: 358.7458 Evaluate side-chains 271 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 217 time to evaluate : 5.896 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 54 outliers final: 1 residues processed: 54 average time/residue: 0.4698 time to fit residues: 54.3808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 384 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 575 optimal weight: 50.0000 chunk 470 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 692 optimal weight: 30.0000 chunk 747 optimal weight: 10.0000 chunk 616 optimal weight: 10.0000 chunk 686 optimal weight: 30.0000 chunk 236 optimal weight: 0.9980 chunk 555 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 283 GLN ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 707 ASN ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 226 GLN ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 405 HIS ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN W 107 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5003 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 63970 Z= 0.362 Angle : 0.680 11.884 86759 Z= 0.357 Chirality : 0.045 0.261 9784 Planarity : 0.004 0.081 10970 Dihedral : 12.251 165.667 9631 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.71 % Favored : 91.13 % Rotamer: Outliers : 2.74 % Allowed : 19.46 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.30 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.09), residues: 7759 helix: 0.27 (0.09), residues: 3038 sheet: -1.23 (0.17), residues: 930 loop : -1.88 (0.10), residues: 3791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 350 HIS 0.011 0.001 HIS A 587 PHE 0.042 0.002 PHE 0 656 TYR 0.020 0.001 TYR 1 630 ARG 0.008 0.000 ARG Q 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 223 time to evaluate : 5.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 74 residues processed: 379 average time/residue: 0.6078 time to fit residues: 412.7043 Evaluate side-chains 291 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 217 time to evaluate : 6.090 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 2 residues processed: 74 average time/residue: 0.5376 time to fit residues: 81.8044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 684 optimal weight: 7.9990 chunk 520 optimal weight: 8.9990 chunk 359 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 464 optimal weight: 30.0000 chunk 694 optimal weight: 50.0000 chunk 735 optimal weight: 20.0000 chunk 363 optimal weight: 2.9990 chunk 658 optimal weight: 0.6980 chunk 198 optimal weight: 9.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN A 736 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 ASN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 283 GLN ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 302 ASN ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 93 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 63970 Z= 0.271 Angle : 0.628 12.921 86759 Z= 0.327 Chirality : 0.043 0.238 9784 Planarity : 0.004 0.083 10970 Dihedral : 12.172 160.433 9631 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.98 % Favored : 91.88 % Rotamer: Outliers : 2.20 % Allowed : 20.07 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.30 % Twisted General : 0.16 % 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: -1.21 (0.10), residues: 7759 helix: 0.46 (0.09), residues: 3029 sheet: -1.14 (0.17), residues: 924 loop : -1.79 (0.10), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Q 350 HIS 0.014 0.001 HIS B 110 PHE 0.026 0.001 PHE A 219 TYR 0.020 0.001 TYR 1 630 ARG 0.009 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 221 time to evaluate : 7.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 60 residues processed: 346 average time/residue: 0.5763 time to fit residues: 357.5480 Evaluate side-chains 277 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 217 time to evaluate : 5.855 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 2 residues processed: 60 average time/residue: 0.4789 time to fit residues: 61.9032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 612 optimal weight: 20.0000 chunk 417 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 547 optimal weight: 20.0000 chunk 303 optimal weight: 5.9990 chunk 627 optimal weight: 50.0000 chunk 508 optimal weight: 20.0000 chunk 0 optimal weight: 80.0000 chunk 375 optimal weight: 6.9990 chunk 660 optimal weight: 0.1980 chunk 185 optimal weight: 0.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS K 104 ASN ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4942 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 63970 Z= 0.217 Angle : 0.597 10.973 86759 Z= 0.311 Chirality : 0.042 0.237 9784 Planarity : 0.004 0.082 10970 Dihedral : 12.070 160.504 9631 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.96 % Favored : 91.91 % Rotamer: Outliers : 1.18 % Allowed : 21.20 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.30 % Twisted General : 0.13 % 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: -1.07 (0.10), residues: 7759 helix: 0.63 (0.10), residues: 3033 sheet: -1.07 (0.17), residues: 937 loop : -1.75 (0.10), residues: 3789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Q 350 HIS 0.010 0.001 HIS B 110 PHE 0.036 0.001 PHE 0 656 TYR 0.020 0.001 TYR 1 630 ARG 0.006 0.000 ARG B 857 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 220 time to evaluate : 5.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 33 residues processed: 289 average time/residue: 0.5665 time to fit residues: 291.6785 Evaluate side-chains 251 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 218 time to evaluate : 5.769 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.5186 time to fit residues: 38.2864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 247 optimal weight: 3.9990 chunk 662 optimal weight: 50.0000 chunk 145 optimal weight: 0.9980 chunk 431 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 736 optimal weight: 50.0000 chunk 611 optimal weight: 40.0000 chunk 340 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 386 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 ASN ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4915 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 63970 Z= 0.186 Angle : 0.585 11.261 86759 Z= 0.302 Chirality : 0.042 0.242 9784 Planarity : 0.004 0.080 10970 Dihedral : 11.970 158.548 9631 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.62 % Favored : 92.25 % Rotamer: Outliers : 0.84 % Allowed : 21.31 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.92 (0.10), residues: 7759 helix: 0.79 (0.10), residues: 3035 sheet: -1.04 (0.17), residues: 929 loop : -1.70 (0.10), residues: 3795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 350 HIS 0.008 0.001 HIS A 587 PHE 0.037 0.001 PHE 0 656 TYR 0.019 0.001 TYR 1 630 ARG 0.005 0.000 ARG B 857 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 221 time to evaluate : 5.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 19 residues processed: 270 average time/residue: 0.5924 time to fit residues: 284.1097 Evaluate side-chains 237 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 218 time to evaluate : 5.804 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.4664 time to fit residues: 24.4997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 709 optimal weight: 9.9990 chunk 82 optimal weight: 0.0770 chunk 419 optimal weight: 6.9990 chunk 537 optimal weight: 50.0000 chunk 416 optimal weight: 0.5980 chunk 619 optimal weight: 20.0000 chunk 411 optimal weight: 4.9990 chunk 733 optimal weight: 20.0000 chunk 459 optimal weight: 8.9990 chunk 447 optimal weight: 50.0000 chunk 338 optimal weight: 6.9990 overall best weight: 3.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 HIS ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4952 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 63970 Z= 0.254 Angle : 0.597 11.069 86759 Z= 0.308 Chirality : 0.042 0.199 9784 Planarity : 0.004 0.080 10970 Dihedral : 12.003 160.109 9631 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.82 % Favored : 92.06 % Rotamer: Outliers : 0.80 % Allowed : 21.72 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.86 (0.10), residues: 7759 helix: 0.84 (0.10), residues: 3041 sheet: -1.03 (0.17), residues: 926 loop : -1.66 (0.10), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 350 HIS 0.007 0.001 HIS A 587 PHE 0.041 0.001 PHE 0 656 TYR 0.019 0.001 TYR 1 630 ARG 0.008 0.000 ARG A1100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 5.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 18 residues processed: 264 average time/residue: 0.6067 time to fit residues: 285.6996 Evaluate side-chains 238 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 5.786 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.5565 time to fit residues: 25.0908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 453 optimal weight: 50.0000 chunk 292 optimal weight: 8.9990 chunk 438 optimal weight: 50.0000 chunk 220 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 466 optimal weight: 9.9990 chunk 499 optimal weight: 0.8980 chunk 362 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 576 optimal weight: 50.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4984 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 63970 Z= 0.300 Angle : 0.630 11.052 86759 Z= 0.325 Chirality : 0.042 0.218 9784 Planarity : 0.004 0.081 10970 Dihedral : 12.092 163.190 9631 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.15 % Favored : 91.74 % Rotamer: Outliers : 0.86 % Allowed : 21.90 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.30 % Twisted General : 0.12 % 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: -0.85 (0.10), residues: 7759 helix: 0.84 (0.10), residues: 3046 sheet: -1.00 (0.17), residues: 913 loop : -1.65 (0.10), residues: 3800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 350 HIS 0.008 0.001 HIS A 587 PHE 0.040 0.001 PHE 0 656 TYR 0.020 0.001 TYR 1 630 ARG 0.005 0.000 ARG B 857 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 221 time to evaluate : 5.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 22 residues processed: 268 average time/residue: 0.5816 time to fit residues: 278.9128 Evaluate side-chains 242 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 5.830 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.5030 time to fit residues: 28.0918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 667 optimal weight: 30.0000 chunk 702 optimal weight: 4.9990 chunk 641 optimal weight: 30.0000 chunk 683 optimal weight: 6.9990 chunk 411 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 536 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 617 optimal weight: 30.0000 chunk 646 optimal weight: 40.0000 chunk 681 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4982 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 63970 Z= 0.279 Angle : 0.627 13.641 86759 Z= 0.321 Chirality : 0.042 0.258 9784 Planarity : 0.004 0.082 10970 Dihedral : 12.083 165.194 9631 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.89 % Favored : 92.00 % Rotamer: Outliers : 0.40 % Allowed : 22.36 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.30 % Twisted General : 0.11 % 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: -0.81 (0.10), residues: 7759 helix: 0.87 (0.10), residues: 3036 sheet: -0.95 (0.17), residues: 908 loop : -1.64 (0.10), residues: 3815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 350 HIS 0.009 0.001 HIS A 587 PHE 0.043 0.001 PHE 0 656 TYR 0.032 0.001 TYR W 21 ARG 0.006 0.000 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 5.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 241 average time/residue: 0.5928 time to fit residues: 253.9228 Evaluate side-chains 228 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 219 time to evaluate : 5.816 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.5596 time to fit residues: 16.4235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 448 optimal weight: 50.0000 chunk 722 optimal weight: 10.0000 chunk 441 optimal weight: 90.0000 chunk 342 optimal weight: 0.8980 chunk 502 optimal weight: 50.0000 chunk 758 optimal weight: 20.0000 chunk 697 optimal weight: 8.9990 chunk 603 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 466 optimal weight: 2.9990 chunk 370 optimal weight: 8.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5035 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 63970 Z= 0.370 Angle : 0.685 14.258 86759 Z= 0.351 Chirality : 0.044 0.250 9784 Planarity : 0.004 0.082 10970 Dihedral : 12.206 172.899 9631 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.47 % Favored : 91.40 % Rotamer: Outliers : 0.24 % Allowed : 22.69 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.89 (0.10), residues: 7759 helix: 0.80 (0.10), residues: 3011 sheet: -1.00 (0.18), residues: 893 loop : -1.65 (0.10), residues: 3855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 350 HIS 0.010 0.001 HIS A 587 PHE 0.040 0.002 PHE 0 656 TYR 0.038 0.001 TYR 7 613 ARG 0.015 0.000 ARG H 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 219 time to evaluate : 6.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 232 average time/residue: 0.6046 time to fit residues: 252.0092 Evaluate side-chains 228 residues out of total 7065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 219 time to evaluate : 6.538 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.5221 time to fit residues: 16.8122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 479 optimal weight: 30.0000 chunk 643 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 556 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 604 optimal weight: 30.0000 chunk 253 optimal weight: 0.9990 chunk 620 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.056894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.043177 restraints weight = 684502.981| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 6.81 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 333 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 337 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 63970 Z= 0.229 Angle : 0.621 11.865 86759 Z= 0.318 Chirality : 0.042 0.223 9784 Planarity : 0.004 0.082 10970 Dihedral : 12.125 174.217 9631 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.90 % Favored : 91.98 % Rotamer: Outliers : 0.13 % Allowed : 22.90 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.77 (0.10), residues: 7759 helix: 0.93 (0.10), residues: 3002 sheet: -0.95 (0.18), residues: 885 loop : -1.61 (0.10), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 350 HIS 0.007 0.001 HIS B 363 PHE 0.039 0.001 PHE 0 656 TYR 0.019 0.001 TYR 1 630 ARG 0.005 0.000 ARG B 857 =============================================================================== Job complete usr+sys time: 11538.24 seconds wall clock time: 206 minutes 29.72 seconds (12389.72 seconds total)