Starting phenix.real_space_refine on Wed Mar 20 15:03:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dvq_30875/03_2024/7dvq_30875_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dvq_30875/03_2024/7dvq_30875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dvq_30875/03_2024/7dvq_30875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dvq_30875/03_2024/7dvq_30875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dvq_30875/03_2024/7dvq_30875_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dvq_30875/03_2024/7dvq_30875_neut_updated.pdb" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 7 6.06 5 P 290 5.49 5 Mg 5 5.21 5 S 360 5.16 5 C 61627 2.51 5 N 17965 2.21 5 O 19650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A TYR 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1093": "OD1" <-> "OD2" Residue "A ARG 1310": "NH1" <-> "NH2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A TYR 1371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A TYR 1432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A GLU 1504": "OE1" <-> "OE2" Residue "A ARG 1523": "NH1" <-> "NH2" Residue "A GLU 2141": "OE1" <-> "OE2" Residue "A PHE 2267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2303": "OE1" <-> "OE2" Residue "A ARG 2310": "NH1" <-> "NH2" Residue "A ARG 2330": "NH1" <-> "NH2" Residue "A GLU 2331": "OE1" <-> "OE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "C ARG 803": "NH1" <-> "NH2" Residue "C ARG 854": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 1090": "NH1" <-> "NH2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "v ARG 5": "NH1" <-> "NH2" Residue "v ARG 19": "NH1" <-> "NH2" Residue "v ARG 20": "NH1" <-> "NH2" Residue "v ARG 38": "NH1" <-> "NH2" Residue "v ARG 41": "NH1" <-> "NH2" Residue "v ARG 50": "NH1" <-> "NH2" Residue "v ARG 63": "NH1" <-> "NH2" Residue "v ARG 187": "NH1" <-> "NH2" Residue "v GLU 223": "OE1" <-> "OE2" Residue "1 ARG 108": "NH1" <-> "NH2" Residue "1 ARG 115": "NH1" <-> "NH2" Residue "1 ARG 123": "NH1" <-> "NH2" Residue "1 ARG 124": "NH1" <-> "NH2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 ARG 157": "NH1" <-> "NH2" Residue "1 ARG 166": "NH1" <-> "NH2" Residue "1 ARG 169": "NH1" <-> "NH2" Residue "1 ARG 451": "NH1" <-> "NH2" Residue "1 ARG 495": "NH1" <-> "NH2" Residue "1 ARG 517": "NH1" <-> "NH2" Residue "1 ARG 590": "NH1" <-> "NH2" Residue "1 ARG 614": "NH1" <-> "NH2" Residue "1 ARG 684": "NH1" <-> "NH2" Residue "1 GLU 691": "OE1" <-> "OE2" Residue "1 ARG 736": "NH1" <-> "NH2" Residue "1 ARG 767": "NH1" <-> "NH2" Residue "1 ARG 822": "NH1" <-> "NH2" Residue "1 GLU 870": "OE1" <-> "OE2" Residue "1 ARG 939": "NH1" <-> "NH2" Residue "1 TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 1019": "NH1" <-> "NH2" Residue "1 ARG 1027": "NH1" <-> "NH2" Residue "1 ARG 1045": "NH1" <-> "NH2" Residue "1 ARG 1053": "NH1" <-> "NH2" Residue "1 ARG 1106": "NH1" <-> "NH2" Residue "1 PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 1180": "NH1" <-> "NH2" Residue "1 TYR 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 1245": "NH1" <-> "NH2" Residue "2 ARG 515": "NH1" <-> "NH2" Residue "2 PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 530": "NH1" <-> "NH2" Residue "2 ARG 554": "NH1" <-> "NH2" Residue "3 GLU 136": "OE1" <-> "OE2" Residue "3 GLU 186": "OE1" <-> "OE2" Residue "3 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 274": "NH1" <-> "NH2" Residue "3 ARG 275": "NH1" <-> "NH2" Residue "3 PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 326": "NH1" <-> "NH2" Residue "3 ARG 429": "NH1" <-> "NH2" Residue "3 ARG 464": "NH1" <-> "NH2" Residue "3 GLU 469": "OE1" <-> "OE2" Residue "3 GLU 492": "OE1" <-> "OE2" Residue "3 ARG 528": "NH1" <-> "NH2" Residue "3 GLU 644": "OE1" <-> "OE2" Residue "3 ARG 718": "NH1" <-> "NH2" Residue "3 GLU 740": "OE1" <-> "OE2" Residue "3 PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 815": "NH1" <-> "NH2" Residue "3 ARG 895": "NH1" <-> "NH2" Residue "3 GLU 982": "OE1" <-> "OE2" Residue "3 ARG 999": "NH1" <-> "NH2" Residue "3 GLU 1007": "OE1" <-> "OE2" Residue "3 ARG 1013": "NH1" <-> "NH2" Residue "3 ARG 1079": "NH1" <-> "NH2" Residue "3 TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 19": "NH1" <-> "NH2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "5 ARG 85": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 57": "NH1" <-> "NH2" Residue "6 ARG 102": "NH1" <-> "NH2" Residue "L ARG 12": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ARG 83": "NH1" <-> "NH2" Residue "J ARG 262": "NH1" <-> "NH2" Residue "J GLU 266": "OE1" <-> "OE2" Residue "J GLU 284": "OE1" <-> "OE2" Residue "J GLU 321": "OE1" <-> "OE2" Residue "J GLU 358": "OE1" <-> "OE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 387": "OE1" <-> "OE2" Residue "J GLU 400": "OE1" <-> "OE2" Residue "P ARG 187": "NH1" <-> "NH2" Residue "R ARG 134": "NH1" <-> "NH2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R ARG 148": "NH1" <-> "NH2" Residue "R GLU 208": "OE1" <-> "OE2" Residue "R ARG 325": "NH1" <-> "NH2" Residue "R ARG 410": "NH1" <-> "NH2" Residue "R ARG 438": "NH1" <-> "NH2" Residue "R ARG 449": "NH1" <-> "NH2" Residue "T PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 248": "OE1" <-> "OE2" Residue "X GLU 251": "OE1" <-> "OE2" Residue "X ARG 253": "NH1" <-> "NH2" Residue "X TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 285": "NH1" <-> "NH2" Residue "X ARG 343": "NH1" <-> "NH2" Residue "X GLU 372": "OE1" <-> "OE2" Residue "Y TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 69": "NH1" <-> "NH2" Residue "Y ARG 105": "NH1" <-> "NH2" Residue "Y TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 129": "NH1" <-> "NH2" Residue "Z ARG 533": "NH1" <-> "NH2" Residue "Z ARG 536": "NH1" <-> "NH2" Residue "Z ARG 540": "NH1" <-> "NH2" Residue "9 ARG 35": "NH1" <-> "NH2" Residue "9 GLU 81": "OE1" <-> "OE2" Residue "9 ARG 86": "NH1" <-> "NH2" Residue "9 ARG 120": "NH1" <-> "NH2" Residue "9 ARG 142": "NH1" <-> "NH2" Residue "9 GLU 148": "OE1" <-> "OE2" Residue "9 ARG 205": "NH1" <-> "NH2" Residue "9 GLU 258": "OE1" <-> "OE2" Residue "z PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 154": "NH1" <-> "NH2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M ARG 154": "NH1" <-> "NH2" Residue "M ARG 179": "NH1" <-> "NH2" Residue "M ARG 190": "NH1" <-> "NH2" Residue "M PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 223": "NH1" <-> "NH2" Residue "V ARG 457": "NH1" <-> "NH2" Residue "V ARG 501": "NH1" <-> "NH2" Residue "0 ARG 32": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 75": "OE1" <-> "OE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 99906 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 18354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2223, 18354 Classifications: {'peptide': 2223} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 4, 'PTRANS': 120, 'TRANS': 2098} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1898 Classifications: {'RNA': 90} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 35, 'rna3p_pyr': 40} Link IDs: {'rna2p': 15, 'rna3p': 74} Chain breaks: 2 Chain: "C" Number of atoms: 7125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7125 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 846} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 9215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1803, 9215 Classifications: {'peptide': 1803} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1535} Link IDs: {'PTRANS': 81, 'TRANS': 1721} Chain breaks: 1 Unresolved chain link angles: 79 Unresolved non-hydrogen bonds: 5580 Unresolved non-hydrogen angles: 7148 Unresolved non-hydrogen dihedrals: 4628 Unresolved non-hydrogen chiralities: 534 Planarities with less than four sites: {'GLN:plan1': 83, 'ASP:plan': 89, 'TYR:plan': 59, 'ASN:plan1': 70, 'TRP:plan': 18, 'HIS:plan': 52, 'PHE:plan': 65, 'GLU:plan': 125, 'ARG:plan': 87} Unresolved non-hydrogen planarities: 2969 Chain: "E" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2337 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 399 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 316 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "b" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 405 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "c" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "d" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 480 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "f" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 361 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "e" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "g" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 363 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "F" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1294 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 32, 'rna3p_pyr': 21} Link IDs: {'rna2p': 7, 'rna3p': 52} Chain breaks: 1 Chain: "G" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1303 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 12, 'rna3p_pur': 14, 'rna3p_pyr': 33} Link IDs: {'rna2p': 16, 'rna3p': 46} Chain breaks: 1 Chain: "H" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1350 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 7, 'rna3p_pur': 34, 'rna3p_pyr': 19} Link IDs: {'rna2p': 10, 'rna3p': 52} Chain breaks: 1 Chain: "h" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 392 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 126 Chain: "i" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 422 Classifications: {'peptide': 86} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 139 Chain: "j" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 406 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "k" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 422 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 144 Chain: "m" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 361 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "l" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 391 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "n" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 334 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "v" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 963 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Chain: "1" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7879 Classifications: {'peptide': 986} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 932} Chain breaks: 3 Chain: "2" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1674 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 194} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "3" Number of atoms: 9352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1193, 9352 Classifications: {'peptide': 1193} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1132} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 383 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 4, 'TRANS': 73} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 135 Chain: "5" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 906 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "6" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "7" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 669 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "L" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "J" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 3457 Classifications: {'peptide': 522} Incomplete info: {'backbone_only': 9, 'truncation_to_alanine': 262} Link IDs: {'PTRANS': 12, 'TRANS': 509} Chain breaks: 19 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1121 Unresolved non-hydrogen angles: 1424 Unresolved non-hydrogen dihedrals: 952 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 17, 'PHE:plan': 16, 'GLU:plan': 44, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 698 Chain: "P" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 384 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "R" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1923 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 223} Chain breaks: 5 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2507 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 306} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1271 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 145} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Y" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1095 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 136} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "Z" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1129 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 131} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "9" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 2691 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 22, 'TRANS': 386} Chain breaks: 3 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 631 Unresolved non-hydrogen angles: 804 Unresolved non-hydrogen dihedrals: 532 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 13, 'TYR:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 12, 'GLU:plan': 11, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 363 Chain: "z" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1400 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain: "x" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 3007 Classifications: {'peptide': 599} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 499} Link IDs: {'PTRANS': 28, 'TRANS': 570} Chain breaks: 11 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 1847 Unresolved non-hydrogen angles: 2374 Unresolved non-hydrogen dihedrals: 1522 Unresolved non-hydrogen chiralities: 182 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 23, 'TYR:plan': 23, 'ASN:plan1': 14, 'TRP:plan': 4, 'HIS:plan': 13, 'PHE:plan': 26, 'GLU:plan': 46, 'ARG:plan': 43} Unresolved non-hydrogen planarities: 1028 Chain: "y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "M" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1572 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "U" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 193 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "V" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3008 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 235} Link IDs: {'PTRANS': 14, 'TRANS': 453} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 843 Unresolved non-hydrogen angles: 1068 Unresolved non-hydrogen dihedrals: 685 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 17, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 11, 'GLU:plan': 23, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 443 Chain: "8" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1011 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "0" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 770 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "I" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 1 Chain: "K" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1314 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 12, 'TRANS': 175} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 39 Unusual residues: {' K': 2, ' MG': 4, 'G5J': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "v" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "0" 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: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 48767 SG CYS v 44 178.636 77.689 183.175 1.00 26.97 S ATOM 48786 SG CYS v 47 182.083 77.041 184.619 1.00 37.41 S ATOM 69735 SG CYS 6 23 164.793 121.789 208.736 1.00 22.26 S ATOM 69759 SG CYS 6 26 165.287 118.344 209.346 1.00 23.62 S ATOM 70006 SG CYS 6 58 165.808 120.411 212.253 1.00 22.59 S ATOM 70027 SG CYS 6 61 168.211 120.963 209.475 1.00 28.41 S ATOM 69648 SG CYS 6 11 173.598 116.660 224.189 1.00 13.91 S ATOM 69911 SG CYS 6 46 171.644 119.186 226.231 1.00 22.59 S ATOM 69934 SG CYS 6 49 172.420 119.898 222.756 1.00 27.92 S ATOM 70205 SG CYS 6 85 169.960 117.149 223.561 1.00 15.57 S ATOM 69786 SG CYS 6 30 161.112 108.992 215.559 1.00 15.44 S ATOM 69807 SG CYS 6 33 161.568 105.955 213.508 1.00 35.11 S ATOM 70102 SG CYS 6 72 158.594 106.114 215.545 1.00 17.24 S ATOM 70126 SG CYS 6 75 161.825 105.612 217.226 1.00 35.11 S ATOM 91626 SG CYS M 202 146.353 119.019 169.082 1.00 17.07 S ATOM 91701 SG CYS M 211 149.941 118.227 168.861 1.00 9.58 S ATOM 91740 SG CYS M 217 148.528 120.877 166.591 1.00 14.03 S ATOM 96655 SG CYS 0 3 128.928 119.054 199.744 1.00 40.19 S ATOM 96679 SG CYS 0 6 128.873 115.847 201.458 1.00 40.79 S ATOM 97274 SG CYS 0 83 129.458 115.920 197.708 1.00 35.26 S ATOM 97293 SG CYS 0 86 126.096 116.786 199.047 1.00 39.60 S ATOM 97085 SG CYS 0 58 126.262 106.173 190.082 1.00 36.07 S ATOM 97110 SG CYS 0 61 127.309 103.743 187.395 1.00 38.40 S ATOM 97202 SG CYS 0 73 129.753 106.143 188.490 1.00 28.40 S ATOM 97221 SG CYS 0 76 126.951 107.471 186.618 1.00 29.71 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N HIS D1502 " occ=0.92 ... (3 atoms not shown) pdb=" CB HIS D1502 " occ=0.92 Time building chain proxies: 40.48, per 1000 atoms: 0.41 Number of scatterers: 99906 At special positions: 0 Unit cell: (278.218, 252.437, 316.889, 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 7 29.99 K 2 19.00 S 360 16.00 P 290 15.00 Mg 5 11.99 O 19650 8.00 N 17965 7.00 C 61627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A2216 " - pdb=" SG CYS A2223 " distance=2.76 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 32.63 Conformation dependent library (CDL) restraints added in 13.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 86 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 3 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 6 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 83 " pdb=" ZN 0 201 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 73 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 61 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 76 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 58 " pdb=" ZN 6 201 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 61 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 23 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 26 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 58 " pdb=" ZN 6 202 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 49 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 46 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 85 " pdb=" ZN 6 203 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 33 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 72 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 75 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 30 " pdb=" ZN M 500 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 211 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 217 " pdb="ZN ZN M 500 " - pdb=" NE2 HIS M 221 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 202 " pdb=" ZN v 300 " pdb="ZN ZN v 300 " - pdb=" ND1 HIS v 68 " pdb="ZN ZN v 300 " - pdb=" SG CYS v 44 " pdb="ZN ZN v 300 " - pdb=" NE2 HIS v 62 " pdb="ZN ZN v 300 " - pdb=" SG CYS v 47 " Number of angles added : 35 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25132 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 478 helices and 122 sheets defined 38.2% alpha, 15.0% beta 75 base pairs and 141 stacking pairs defined. Time for finding SS restraints: 39.14 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 84 through 105 removed outlier: 4.612A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 201 through 204 No H-bonds generated for 'chain 'A' and resid 201 through 204' Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 398 through 406 removed outlier: 3.780A pdb=" N LEU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 431 No H-bonds generated for 'chain 'A' and resid 428 through 431' Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 489 through 510 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 542 through 565 removed outlier: 3.542A pdb=" N SER A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 585 through 588 No H-bonds generated for 'chain 'A' and resid 585 through 588' Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 596 through 616 removed outlier: 3.518A pdb=" N HIS A 610 " --> pdb=" O ASP A 607 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR A 614 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 660 removed outlier: 3.549A pdb=" N TRP A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 674 through 696 removed outlier: 3.776A pdb=" N VAL A 677 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU A 678 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 679 " --> pdb=" O ARG A 676 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 685 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 686 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 695 " --> pdb=" O ASP A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'A' and resid 733 through 763 removed outlier: 3.567A pdb=" N GLU A 759 " --> pdb=" O HIS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 796 Processing helix chain 'A' and resid 803 through 819 Processing helix chain 'A' and resid 835 through 850 removed outlier: 4.217A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 874 through 887 Processing helix chain 'A' and resid 913 through 933 Processing helix chain 'A' and resid 948 through 960 Processing helix chain 'A' and resid 990 through 997 Processing helix chain 'A' and resid 1003 through 1012 Processing helix chain 'A' and resid 1037 through 1052 removed outlier: 3.568A pdb=" N VAL A1047 " --> pdb=" O TYR A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1062 Processing helix chain 'A' and resid 1077 through 1082 Processing helix chain 'A' and resid 1103 through 1116 Processing helix chain 'A' and resid 1124 through 1127 No H-bonds generated for 'chain 'A' and resid 1124 through 1127' Processing helix chain 'A' and resid 1144 through 1160 Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'A' and resid 1199 through 1201 No H-bonds generated for 'chain 'A' and resid 1199 through 1201' Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1234 through 1250 removed outlier: 3.544A pdb=" N ALA A1250 " --> pdb=" O GLN A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1278 removed outlier: 7.544A pdb=" N GLU A1276 " --> pdb=" O THR A1272 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA A1277 " --> pdb=" O TYR A1273 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL A1278 " --> pdb=" O PHE A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1302 Processing helix chain 'A' and resid 1313 through 1317 removed outlier: 3.876A pdb=" N TYR A1317 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1322 No H-bonds generated for 'chain 'A' and resid 1320 through 1322' Processing helix chain 'A' and resid 1340 through 1343 No H-bonds generated for 'chain 'A' and resid 1340 through 1343' Processing helix chain 'A' and resid 1368 through 1371 Processing helix chain 'A' and resid 1375 through 1398 Processing helix chain 'A' and resid 1410 through 1413 removed outlier: 4.501A pdb=" N ASP A1413 " --> pdb=" O ASP A1410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1410 through 1413' Processing helix chain 'A' and resid 1419 through 1422 Processing helix chain 'A' and resid 1427 through 1432 removed outlier: 4.500A pdb=" N TYR A1432 " --> pdb=" O HIS A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1445 removed outlier: 4.759A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1477 removed outlier: 3.927A pdb=" N THR A1472 " --> pdb=" O ASN A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1487 removed outlier: 4.499A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1493 No H-bonds generated for 'chain 'A' and resid 1490 through 1493' Processing helix chain 'A' and resid 1498 through 1500 No H-bonds generated for 'chain 'A' and resid 1498 through 1500' Processing helix chain 'A' and resid 1529 through 1537 Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1567 through 1576 removed outlier: 3.749A pdb=" N ILE A1571 " --> pdb=" O PRO A1567 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1600 removed outlier: 3.828A pdb=" N GLN A1599 " --> pdb=" O GLN A1595 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1618 through 1620 No H-bonds generated for 'chain 'A' and resid 1618 through 1620' Processing helix chain 'A' and resid 1676 through 1689 removed outlier: 3.728A pdb=" N THR A1689 " --> pdb=" O LEU A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1736 Processing helix chain 'A' and resid 1738 through 1751 Processing helix chain 'A' and resid 1766 through 1772 removed outlier: 3.585A pdb=" N LEU A1771 " --> pdb=" O ASN A1767 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE A1772 " --> pdb=" O TYR A1768 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1827 Processing helix chain 'A' and resid 1833 through 1851 removed outlier: 4.344A pdb=" N LYS A1838 " --> pdb=" O GLY A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1854 through 1856 No H-bonds generated for 'chain 'A' and resid 1854 through 1856' Processing helix chain 'A' and resid 1866 through 1875 removed outlier: 3.693A pdb=" N ASP A1870 " --> pdb=" O GLY A1867 " (cutoff:3.500A) Proline residue: A1871 - end of helix Processing helix chain 'A' and resid 1894 through 1898 Processing helix chain 'A' and resid 1900 through 1907 Processing helix chain 'A' and resid 1923 through 1926 No H-bonds generated for 'chain 'A' and resid 1923 through 1926' Processing helix chain 'A' and resid 1929 through 1945 Processing helix chain 'A' and resid 1947 through 1954 Processing helix chain 'A' and resid 1973 through 1995 Processing helix chain 'A' and resid 2004 through 2012 Processing helix chain 'A' and resid 2070 through 2088 removed outlier: 3.804A pdb=" N ARG A2074 " --> pdb=" O LYS A2070 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A2081 " --> pdb=" O ALA A2077 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN A2082 " --> pdb=" O ILE A2078 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A2083 " --> pdb=" O SER A2079 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS A2084 " --> pdb=" O ALA A2080 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A2085 " --> pdb=" O ALA A2081 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A2086 " --> pdb=" O ASN A2082 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A2087 " --> pdb=" O LEU A2083 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN A2088 " --> pdb=" O HIS A2084 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2117 Processing helix chain 'A' and resid 2167 through 2171 removed outlier: 4.061A pdb=" N GLU A2171 " --> pdb=" O TYR A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2202 removed outlier: 3.651A pdb=" N ASP A2202 " --> pdb=" O LYS A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2232 through 2240 Processing helix chain 'A' and resid 2253 through 2255 No H-bonds generated for 'chain 'A' and resid 2253 through 2255' Processing helix chain 'A' and resid 2307 through 2309 No H-bonds generated for 'chain 'A' and resid 2307 through 2309' Processing helix chain 'A' and resid 2311 through 2314 No H-bonds generated for 'chain 'A' and resid 2311 through 2314' Processing helix chain 'A' and resid 2321 through 2325 Processing helix chain 'C' and resid 69 through 72 No H-bonds generated for 'chain 'C' and resid 69 through 72' Processing helix chain 'C' and resid 116 through 125 Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 209 through 220 removed outlier: 4.751A pdb=" N ASP C 213 " --> pdb=" O ASN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 260 through 265 removed outlier: 4.298A pdb=" N LEU C 265 " --> pdb=" O ARG C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 292 Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.947A pdb=" N ARG C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 428 through 437 Processing helix chain 'C' and resid 441 through 452 removed outlier: 4.580A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 460 through 467 Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 597 through 613 Proline residue: C 601 - end of helix Processing helix chain 'C' and resid 634 through 646 Processing helix chain 'C' and resid 694 through 702 removed outlier: 4.582A pdb=" N GLU C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 722 Processing helix chain 'C' and resid 726 through 729 No H-bonds generated for 'chain 'C' and resid 726 through 729' Processing helix chain 'C' and resid 753 through 776 removed outlier: 4.710A pdb=" N ALA C 757 " --> pdb=" O VAL C 754 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 759 " --> pdb=" O LYS C 756 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLY C 760 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP C 764 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER C 765 " --> pdb=" O VAL C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 803 No H-bonds generated for 'chain 'C' and resid 800 through 803' Processing helix chain 'C' and resid 808 through 822 Processing helix chain 'C' and resid 840 through 853 removed outlier: 4.925A pdb=" N SER C 844 " --> pdb=" O ASP C 841 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU C 850 " --> pdb=" O TYR C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 889 Processing helix chain 'C' and resid 926 through 941 removed outlier: 3.938A pdb=" N LEU C 929 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA C 930 " --> pdb=" O PRO C 927 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG C 931 " --> pdb=" O HIS C 928 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE C 935 " --> pdb=" O GLU C 932 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 941 " --> pdb=" O ARG C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 124 removed outlier: 4.018A pdb=" N THR D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 144 Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.737A pdb=" N LEU D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 177 removed outlier: 4.196A pdb=" N HIS D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL D 171 " --> pdb=" O THR D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 494 removed outlier: 5.461A pdb=" N ARG D 490 " --> pdb=" O SER D 486 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA D 491 " --> pdb=" O LYS D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 3.932A pdb=" N LEU D 514 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG D 519 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE D 521 " --> pdb=" O LEU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 561 removed outlier: 3.673A pdb=" N LYS D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR D 561 " --> pdb=" O LYS D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 582 No H-bonds generated for 'chain 'D' and resid 580 through 582' Processing helix chain 'D' and resid 590 through 599 Processing helix chain 'D' and resid 617 through 621 Processing helix chain 'D' and resid 623 through 642 Proline residue: D 626 - end of helix removed outlier: 3.835A pdb=" N VAL D 632 " --> pdb=" O GLU D 629 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 633 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 664 Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 678 through 680 No H-bonds generated for 'chain 'D' and resid 678 through 680' Processing helix chain 'D' and resid 697 through 716 removed outlier: 3.528A pdb=" N GLN D 702 " --> pdb=" O ILE D 698 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 744 removed outlier: 3.964A pdb=" N ARG D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 766 Processing helix chain 'D' and resid 773 through 779 Proline residue: D 779 - end of helix Processing helix chain 'D' and resid 787 through 789 No H-bonds generated for 'chain 'D' and resid 787 through 789' Processing helix chain 'D' and resid 792 through 802 removed outlier: 3.536A pdb=" N LEU D 800 " --> pdb=" O LEU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 817 Processing helix chain 'D' and resid 846 through 853 Processing helix chain 'D' and resid 873 through 883 removed outlier: 4.439A pdb=" N GLN D 877 " --> pdb=" O GLY D 874 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR D 879 " --> pdb=" O LEU D 876 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 882 " --> pdb=" O TYR D 879 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 883 " --> pdb=" O LEU D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 906 Proline residue: D 898 - end of helix Processing helix chain 'D' and resid 913 through 922 removed outlier: 3.721A pdb=" N TYR D 922 " --> pdb=" O ASN D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 931 Processing helix chain 'D' and resid 933 through 936 No H-bonds generated for 'chain 'D' and resid 933 through 936' Processing helix chain 'D' and resid 940 through 945 Processing helix chain 'D' and resid 950 through 966 Processing helix chain 'D' and resid 983 through 991 Processing helix chain 'D' and resid 995 through 1004 removed outlier: 3.738A pdb=" N GLN D 999 " --> pdb=" O ASN D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1020 removed outlier: 3.852A pdb=" N ARG D1016 " --> pdb=" O ILE D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1024 No H-bonds generated for 'chain 'D' and resid 1022 through 1024' Processing helix chain 'D' and resid 1031 through 1042 removed outlier: 3.867A pdb=" N LEU D1035 " --> pdb=" O GLU D1032 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU D1037 " --> pdb=" O LYS D1034 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN D1038 " --> pdb=" O LEU D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1067 Processing helix chain 'D' and resid 1075 through 1102 removed outlier: 3.750A pdb=" N GLY D1089 " --> pdb=" O THR D1085 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG D1090 " --> pdb=" O GLN D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1105 through 1120 Processing helix chain 'D' and resid 1128 through 1131 Processing helix chain 'D' and resid 1137 through 1145 Processing helix chain 'D' and resid 1150 through 1152 No H-bonds generated for 'chain 'D' and resid 1150 through 1152' Processing helix chain 'D' and resid 1158 through 1162 removed outlier: 3.877A pdb=" N GLY D1162 " --> pdb=" O HIS D1158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1158 through 1162' Processing helix chain 'D' and resid 1168 through 1180 removed outlier: 4.723A pdb=" N LYS D1172 " --> pdb=" O LYS D1169 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE D1174 " --> pdb=" O GLY D1171 " (cutoff:3.500A) Processing helix chain 'D' and resid 1315 through 1320 removed outlier: 4.447A pdb=" N LEU D1320 " --> pdb=" O ALA D1316 " (cutoff:3.500A) Processing helix chain 'D' and resid 1330 through 1339 removed outlier: 4.789A pdb=" N ASN D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR D1338 " --> pdb=" O GLN D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1356 through 1370 removed outlier: 3.576A pdb=" N ALA D1363 " --> pdb=" O CYS D1359 " (cutoff:3.500A) Processing helix chain 'D' and resid 1383 through 1396 removed outlier: 3.773A pdb=" N ASP D1392 " --> pdb=" O GLN D1388 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D1395 " --> pdb=" O MET D1391 " (cutoff:3.500A) Processing helix chain 'D' and resid 1412 through 1418 Processing helix chain 'D' and resid 1431 through 1437 removed outlier: 3.664A pdb=" N LEU D1435 " --> pdb=" O LYS D1431 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER D1436 " --> pdb=" O TRP D1432 " (cutoff:3.500A) Processing helix chain 'D' and resid 1443 through 1446 No H-bonds generated for 'chain 'D' and resid 1443 through 1446' Processing helix chain 'D' and resid 1456 through 1460 Processing helix chain 'D' and resid 1465 through 1480 Processing helix chain 'D' and resid 1497 through 1504 Processing helix chain 'D' and resid 1508 through 1510 No H-bonds generated for 'chain 'D' and resid 1508 through 1510' Processing helix chain 'D' and resid 1535 through 1541 Processing helix chain 'D' and resid 1543 through 1553 removed outlier: 3.626A pdb=" N TYR D1547 " --> pdb=" O ALA D1543 " (cutoff:3.500A) Processing helix chain 'D' and resid 1568 through 1582 Processing helix chain 'D' and resid 1594 through 1603 removed outlier: 3.603A pdb=" N ILE D1598 " --> pdb=" O GLU D1594 " (cutoff:3.500A) Proline residue: D1599 - end of helix removed outlier: 4.739A pdb=" N LYS D1603 " --> pdb=" O PRO D1599 " (cutoff:3.500A) Processing helix chain 'D' and resid 1607 through 1615 removed outlier: 3.544A pdb=" N GLU D1611 " --> pdb=" O SER D1607 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN D1615 " --> pdb=" O GLU D1611 " (cutoff:3.500A) Processing helix chain 'D' and resid 1626 through 1637 Processing helix chain 'D' and resid 1648 through 1651 Processing helix chain 'D' and resid 1681 through 1690 Processing helix chain 'D' and resid 1711 through 1717 Processing helix chain 'D' and resid 1733 through 1741 Processing helix chain 'D' and resid 1748 through 1757 removed outlier: 3.617A pdb=" N TRP D1757 " --> pdb=" O ASP D1753 " (cutoff:3.500A) Processing helix chain 'D' and resid 1759 through 1765 removed outlier: 4.502A pdb=" N THR D1765 " --> pdb=" O TYR D1761 " (cutoff:3.500A) Processing helix chain 'D' and resid 1778 through 1798 Processing helix chain 'D' and resid 1814 through 1822 Processing helix chain 'D' and resid 1826 through 1835 Processing helix chain 'D' and resid 1842 through 1850 removed outlier: 3.679A pdb=" N GLU D1847 " --> pdb=" O ARG D1843 " (cutoff:3.500A) Processing helix chain 'D' and resid 1855 through 1857 No H-bonds generated for 'chain 'D' and resid 1855 through 1857' Processing helix chain 'D' and resid 1866 through 1874 removed outlier: 3.655A pdb=" N LYS D1874 " --> pdb=" O GLN D1870 " (cutoff:3.500A) Processing helix chain 'D' and resid 1887 through 1899 Processing helix chain 'D' and resid 1906 through 1933 removed outlier: 3.747A pdb=" N ASP D1911 " --> pdb=" O GLU D1907 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D1918 " --> pdb=" O GLU D1914 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE D1920 " --> pdb=" O LEU D1916 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG D1921 " --> pdb=" O SER D1917 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D1922 " --> pdb=" O LYS D1918 " (cutoff:3.500A) Processing helix chain 'D' and resid 1936 through 1951 Processing helix chain 'D' and resid 1959 through 1962 removed outlier: 3.940A pdb=" N GLN D1962 " --> pdb=" O TYR D1959 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1959 through 1962' Processing helix chain 'D' and resid 1968 through 1977 removed outlier: 3.680A pdb=" N LYS D1972 " --> pdb=" O SER D1968 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG D1973 " --> pdb=" O GLU D1969 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2013 removed outlier: 3.715A pdb=" N PHE D2010 " --> pdb=" O ASP D2006 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 65 through 67 No H-bonds generated for 'chain 'a' and resid 65 through 67' Processing helix chain 'a' and resid 75 through 78 No H-bonds generated for 'chain 'a' and resid 75 through 78' Processing helix chain 'b' and resid 74 through 76 No H-bonds generated for 'chain 'b' and resid 74 through 76' Processing helix chain 'c' and resid 3 through 10 removed outlier: 3.959A pdb=" N LEU c 10 " --> pdb=" O PHE c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 64 No H-bonds generated for 'chain 'c' and resid 62 through 64' Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 28 through 38 removed outlier: 3.634A pdb=" N GLN d 34 " --> pdb=" O VAL d 31 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL d 36 " --> pdb=" O THR d 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS d 37 " --> pdb=" O GLN d 34 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN d 38 " --> pdb=" O SER d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 105 No H-bonds generated for 'chain 'd' and resid 103 through 105' Processing helix chain 'f' and resid 7 through 14 Processing helix chain 'f' and resid 66 through 68 No H-bonds generated for 'chain 'f' and resid 66 through 68' Processing helix chain 'e' and resid 17 through 27 Processing helix chain 'e' and resid 81 through 83 No H-bonds generated for 'chain 'e' and resid 81 through 83' Processing helix chain 'g' and resid 10 through 12 No H-bonds generated for 'chain 'g' and resid 10 through 12' Processing helix chain 'g' and resid 64 through 66 No H-bonds generated for 'chain 'g' and resid 64 through 66' Processing helix chain 'h' and resid 5 through 13 Processing helix chain 'h' and resid 65 through 67 No H-bonds generated for 'chain 'h' and resid 65 through 67' Processing helix chain 'i' and resid 7 through 12 removed outlier: 4.671A pdb=" N HIS i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 76 No H-bonds generated for 'chain 'i' and resid 74 through 76' Processing helix chain 'j' and resid 3 through 10 removed outlier: 3.957A pdb=" N LEU j 10 " --> pdb=" O PHE j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 62 through 64 No H-bonds generated for 'chain 'j' and resid 62 through 64' Processing helix chain 'j' and resid 76 through 80 Processing helix chain 'k' and resid 21 through 26 Processing helix chain 'k' and resid 28 through 38 removed outlier: 3.637A pdb=" N GLN k 34 " --> pdb=" O VAL k 31 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL k 36 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS k 37 " --> pdb=" O GLN k 34 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN k 38 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 103 through 105 No H-bonds generated for 'chain 'k' and resid 103 through 105' Processing helix chain 'm' and resid 7 through 14 Processing helix chain 'm' and resid 66 through 68 No H-bonds generated for 'chain 'm' and resid 66 through 68' Processing helix chain 'l' and resid 17 through 27 Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' Processing helix chain 'n' and resid 10 through 12 No H-bonds generated for 'chain 'n' and resid 10 through 12' Processing helix chain 'n' and resid 64 through 66 No H-bonds generated for 'chain 'n' and resid 64 through 66' Processing helix chain 'v' and resid 10 through 28 removed outlier: 4.144A pdb=" N TYR v 28 " --> pdb=" O LEU v 24 " (cutoff:3.500A) Processing helix chain 'v' and resid 56 through 63 Processing helix chain 'v' and resid 66 through 73 Processing helix chain 'v' and resid 184 through 198 Processing helix chain '1' and resid 88 through 92 Processing helix chain '1' and resid 103 through 106 removed outlier: 4.386A pdb=" N GLU 1 106 " --> pdb=" O PRO 1 103 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 103 through 106' Processing helix chain '1' and resid 120 through 124 Processing helix chain '1' and resid 137 through 140 No H-bonds generated for 'chain '1' and resid 137 through 140' Processing helix chain '1' and resid 152 through 175 removed outlier: 3.791A pdb=" N GLU 1 174 " --> pdb=" O GLN 1 170 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS 1 175 " --> pdb=" O GLN 1 171 " (cutoff:3.500A) Processing helix chain '1' and resid 401 through 407 removed outlier: 3.792A pdb=" N ASP 1 405 " --> pdb=" O ASP 1 401 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA 1 406 " --> pdb=" O GLU 1 402 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET 1 407 " --> pdb=" O GLU 1 403 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 401 through 407' Processing helix chain '1' and resid 452 through 455 No H-bonds generated for 'chain '1' and resid 452 through 455' Processing helix chain '1' and resid 469 through 471 No H-bonds generated for 'chain '1' and resid 469 through 471' Processing helix chain '1' and resid 476 through 478 No H-bonds generated for 'chain '1' and resid 476 through 478' Processing helix chain '1' and resid 489 through 506 Processing helix chain '1' and resid 509 through 521 Processing helix chain '1' and resid 523 through 526 No H-bonds generated for 'chain '1' and resid 523 through 526' Processing helix chain '1' and resid 528 through 539 removed outlier: 3.985A pdb=" N GLN 1 534 " --> pdb=" O PRO 1 530 " (cutoff:3.500A) Proline residue: 1 537 - end of helix Processing helix chain '1' and resid 546 through 562 removed outlier: 3.913A pdb=" N TYR 1 561 " --> pdb=" O ASP 1 557 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS 1 562 " --> pdb=" O ARG 1 558 " (cutoff:3.500A) Processing helix chain '1' and resid 568 through 583 removed outlier: 5.103A pdb=" N HIS 1 572 " --> pdb=" O PRO 1 569 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS 1 573 " --> pdb=" O TYR 1 570 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL 1 576 " --> pdb=" O LYS 1 573 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLU 1 579 " --> pdb=" O VAL 1 576 " (cutoff:3.500A) Proline residue: 1 580 - end of helix Processing helix chain '1' and resid 587 through 604 Processing helix chain '1' and resid 606 through 617 Proline residue: 1 615 - end of helix Processing helix chain '1' and resid 622 through 639 removed outlier: 3.808A pdb=" N ALA 1 633 " --> pdb=" O ALA 1 629 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL 1 634 " --> pdb=" O ARG 1 630 " (cutoff:3.500A) Processing helix chain '1' and resid 641 through 652 Proline residue: 1 646 - end of helix Processing helix chain '1' and resid 658 through 693 removed outlier: 7.294A pdb=" N CYS 1 677 " --> pdb=" O ILE 1 673 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA 1 678 " --> pdb=" O LEU 1 674 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE 1 679 " --> pdb=" O MET 1 675 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU 1 680 " --> pdb=" O GLY 1 676 " (cutoff:3.500A) Proline residue: 1 681 - end of helix removed outlier: 5.065A pdb=" N ARG 1 684 " --> pdb=" O LEU 1 680 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER 1 685 " --> pdb=" O PRO 1 681 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU 1 688 " --> pdb=" O ARG 1 684 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE 1 689 " --> pdb=" O SER 1 685 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS 1 692 " --> pdb=" O GLU 1 688 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY 1 693 " --> pdb=" O ILE 1 689 " (cutoff:3.500A) Processing helix chain '1' and resid 699 through 715 Processing helix chain '1' and resid 728 through 737 Processing helix chain '1' and resid 742 through 755 Proline residue: 1 755 - end of helix Processing helix chain '1' and resid 759 through 777 removed outlier: 3.659A pdb=" N TYR 1 764 " --> pdb=" O GLU 1 760 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG 1 767 " --> pdb=" O ASN 1 763 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU 1 768 " --> pdb=" O TYR 1 764 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG 1 775 " --> pdb=" O LEU 1 771 " (cutoff:3.500A) Processing helix chain '1' and resid 782 through 797 removed outlier: 3.909A pdb=" N LYS 1 790 " --> pdb=" O LYS 1 786 " (cutoff:3.500A) Processing helix chain '1' and resid 803 through 809 Processing helix chain '1' and resid 811 through 817 Processing helix chain '1' and resid 827 through 844 removed outlier: 3.743A pdb=" N LYS 1 843 " --> pdb=" O GLU 1 839 " (cutoff:3.500A) Processing helix chain '1' and resid 846 through 857 removed outlier: 4.000A pdb=" N ARG 1 852 " --> pdb=" O GLU 1 848 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE 1 853 " --> pdb=" O ILE 1 849 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP 1 855 " --> pdb=" O SER 1 851 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP 1 856 " --> pdb=" O ARG 1 852 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU 1 857 " --> pdb=" O ILE 1 853 " (cutoff:3.500A) Processing helix chain '1' and resid 862 through 878 Processing helix chain '1' and resid 886 through 902 removed outlier: 3.709A pdb=" N GLU 1 890 " --> pdb=" O HIS 1 886 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN 1 891 " --> pdb=" O LYS 1 887 " (cutoff:3.500A) Processing helix chain '1' and resid 909 through 941 removed outlier: 6.284A pdb=" N LYS 1 923 " --> pdb=" O ASN 1 919 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG 1 924 " --> pdb=" O ALA 1 920 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL 1 925 " --> pdb=" O LEU 1 921 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS 1 926 " --> pdb=" O GLY 1 922 " (cutoff:3.500A) Proline residue: 1 927 - end of helix Proline residue: 1 930 - end of helix removed outlier: 4.594A pdb=" N ASN 1 941 " --> pdb=" O LEU 1 937 " (cutoff:3.500A) Processing helix chain '1' and resid 945 through 964 removed outlier: 5.512A pdb=" N VAL 1 960 " --> pdb=" O SER 1 956 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL 1 961 " --> pdb=" O ARG 1 957 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET 1 962 " --> pdb=" O THR 1 958 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS 1 963 " --> pdb=" O ALA 1 959 " (cutoff:3.500A) Processing helix chain '1' and resid 968 through 983 removed outlier: 3.905A pdb=" N GLU 1 980 " --> pdb=" O VAL 1 976 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR 1 981 " --> pdb=" O VAL 1 977 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU 1 982 " --> pdb=" O LEU 1 978 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLY 1 983 " --> pdb=" O TYR 1 979 " (cutoff:3.500A) Processing helix chain '1' and resid 987 through 1004 Processing helix chain '1' and resid 1013 through 1020 Proline residue: 11018 - end of helix Processing helix chain '1' and resid 1029 through 1045 removed outlier: 3.566A pdb=" N LEU 11038 " --> pdb=" O ASN 11034 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP 11044 " --> pdb=" O GLY 11040 " (cutoff:3.500A) Processing helix chain '1' and resid 1047 through 1049 No H-bonds generated for 'chain '1' and resid 1047 through 1049' Processing helix chain '1' and resid 1052 through 1063 removed outlier: 3.944A pdb=" N LEU 11063 " --> pdb=" O CYS 11059 " (cutoff:3.500A) Processing helix chain '1' and resid 1065 through 1067 No H-bonds generated for 'chain '1' and resid 1065 through 1067' Processing helix chain '1' and resid 1071 through 1088 removed outlier: 3.653A pdb=" N GLY 11082 " --> pdb=" O VAL 11078 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA 11087 " --> pdb=" O TYR 11083 " (cutoff:3.500A) Processing helix chain '1' and resid 1090 through 1102 removed outlier: 3.680A pdb=" N THR 11096 " --> pdb=" O ASP 11092 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU 11101 " --> pdb=" O LEU 11097 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS 11102 " --> pdb=" O LEU 11098 " (cutoff:3.500A) Processing helix chain '1' and resid 1106 through 1122 Processing helix chain '1' and resid 1125 through 1137 Proline residue: 11130 - end of helix removed outlier: 3.717A pdb=" N TYR 11136 " --> pdb=" O LEU 11132 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG 11137 " --> pdb=" O MET 11133 " (cutoff:3.500A) Processing helix chain '1' and resid 1141 through 1164 removed outlier: 7.068A pdb=" N GLU 11160 " --> pdb=" O GLU 11156 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N MET 11161 " --> pdb=" O TYR 11157 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY 11162 " --> pdb=" O ILE 11158 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS 11163 " --> pdb=" O GLY 11159 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASP 11164 " --> pdb=" O GLU 11160 " (cutoff:3.500A) Processing helix chain '1' and resid 1166 through 1177 Proline residue: 11171 - end of helix Processing helix chain '1' and resid 1182 through 1198 removed outlier: 3.539A pdb=" N GLY 11198 " --> pdb=" O HIS 11194 " (cutoff:3.500A) Processing helix chain '1' and resid 1205 through 1220 removed outlier: 3.820A pdb=" N TYR 11214 " --> pdb=" O HIS 11210 " (cutoff:3.500A) Proline residue: 11217 - end of helix removed outlier: 5.353A pdb=" N PHE 11220 " --> pdb=" O TRP 11216 " (cutoff:3.500A) Processing helix chain '1' and resid 1224 through 1241 removed outlier: 3.957A pdb=" N VAL 11239 " --> pdb=" O GLU 11235 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA 11240 " --> pdb=" O GLY 11236 " (cutoff:3.500A) Processing helix chain '1' and resid 1243 through 1253 removed outlier: 5.186A pdb=" N GLN 11252 " --> pdb=" O GLN 11248 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY 11253 " --> pdb=" O TYR 11249 " (cutoff:3.500A) Processing helix chain '1' and resid 1259 through 1275 removed outlier: 3.722A pdb=" N VAL 11264 " --> pdb=" O LYS 11260 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER 11271 " --> pdb=" O LYS 11267 " (cutoff:3.500A) Processing helix chain '1' and resid 1279 through 1282 removed outlier: 3.642A pdb=" N ALA 11282 " --> pdb=" O ALA 11279 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1279 through 1282' Processing helix chain '2' and resid 462 through 468 Processing helix chain '2' and resid 479 through 481 No H-bonds generated for 'chain '2' and resid 479 through 481' Processing helix chain '2' and resid 485 through 492 Processing helix chain '2' and resid 502 through 505 removed outlier: 3.983A pdb=" N CYS 2 505 " --> pdb=" O ARG 2 502 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 502 through 505' Processing helix chain '2' and resid 514 through 518 Processing helix chain '2' and resid 526 through 531 removed outlier: 4.207A pdb=" N THR 2 531 " --> pdb=" O PHE 2 527 " (cutoff:3.500A) Processing helix chain '2' and resid 533 through 544 Processing helix chain '2' and resid 549 through 554 Processing helix chain '2' and resid 568 through 576 removed outlier: 3.631A pdb=" N PHE 2 575 " --> pdb=" O LEU 2 571 " (cutoff:3.500A) Processing helix chain '2' and resid 612 through 616 Processing helix chain '2' and resid 632 through 639 removed outlier: 5.078A pdb=" N GLN 2 637 " --> pdb=" O ILE 2 634 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR 2 639 " --> pdb=" O MET 2 636 " (cutoff:3.500A) Processing helix chain '2' and resid 692 through 702 removed outlier: 3.764A pdb=" N THR 2 696 " --> pdb=" O ALA 2 692 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 194 No H-bonds generated for 'chain '3' and resid 192 through 194' Processing helix chain '3' and resid 199 through 203 Processing helix chain '3' and resid 430 through 432 No H-bonds generated for 'chain '3' and resid 430 through 432' Processing helix chain '3' and resid 809 through 826 removed outlier: 3.572A pdb=" N VAL 3 824 " --> pdb=" O ALA 3 820 " (cutoff:3.500A) Processing helix chain '3' and resid 835 through 844 Processing helix chain '3' and resid 849 through 852 No H-bonds generated for 'chain '3' and resid 849 through 852' Processing helix chain '3' and resid 1135 through 1151 removed outlier: 3.951A pdb=" N SER 31150 " --> pdb=" O MET 31146 " (cutoff:3.500A) Processing helix chain '3' and resid 1160 through 1163 No H-bonds generated for 'chain '3' and resid 1160 through 1163' Processing helix chain '3' and resid 1176 through 1182 removed outlier: 3.734A pdb=" N GLN 31181 " --> pdb=" O ASP 31177 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE 31182 " --> pdb=" O LEU 31178 " (cutoff:3.500A) Processing helix chain '3' and resid 1187 through 1196 removed outlier: 4.086A pdb=" N GLU 31196 " --> pdb=" O ASN 31192 " (cutoff:3.500A) Processing helix chain '3' and resid 1201 through 1215 removed outlier: 3.779A pdb=" N ILE 31211 " --> pdb=" O LYS 31207 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG 31212 " --> pdb=" O LEU 31208 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 34 Processing helix chain '4' and resid 64 through 76 removed outlier: 4.254A pdb=" N ILE 4 71 " --> pdb=" O ALA 4 67 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS 4 72 " --> pdb=" O ASP 4 68 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN 4 75 " --> pdb=" O ILE 4 71 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET 4 76 " --> pdb=" O LYS 4 72 " (cutoff:3.500A) Processing helix chain '5' and resid 32 through 39 Processing helix chain '5' and resid 67 through 77 Processing helix chain '5' and resid 103 through 117 Processing helix chain '6' and resid 24 through 26 No H-bonds generated for 'chain '6' and resid 24 through 26' Processing helix chain '6' and resid 47 through 50 Processing helix chain '6' and resid 52 through 54 No H-bonds generated for 'chain '6' and resid 52 through 54' Processing helix chain '6' and resid 73 through 77 Processing helix chain '6' and resid 80 through 82 No H-bonds generated for 'chain '6' and resid 80 through 82' Processing helix chain '6' and resid 92 through 105 removed outlier: 3.557A pdb=" N THR 6 96 " --> pdb=" O GLY 6 92 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 17 Processing helix chain '7' and resid 28 through 45 Processing helix chain '7' and resid 47 through 56 Processing helix chain '7' and resid 61 through 71 Processing helix chain 'L' and resid 13 through 26 Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'L' and resid 43 through 52 Processing helix chain 'L' and resid 65 through 77 Processing helix chain 'L' and resid 82 through 89 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 93 through 108 Processing helix chain 'J' and resid 217 through 238 removed outlier: 3.797A pdb=" N ASN J 238 " --> pdb=" O ASN J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 255 removed outlier: 3.904A pdb=" N LYS J 247 " --> pdb=" O SER J 243 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR J 248 " --> pdb=" O ASN J 244 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA J 249 " --> pdb=" O TRP J 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 271 Processing helix chain 'J' and resid 277 through 288 Processing helix chain 'J' and resid 293 through 305 Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.722A pdb=" N MET J 319 " --> pdb=" O LYS J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 339 removed outlier: 3.922A pdb=" N GLU J 338 " --> pdb=" O GLU J 334 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP J 339 " --> pdb=" O ARG J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 355 removed outlier: 3.555A pdb=" N HIS J 347 " --> pdb=" O GLU J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 360 through 371 removed outlier: 3.949A pdb=" N THR J 364 " --> pdb=" O ASP J 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 376 through 389 Processing helix chain 'J' and resid 393 through 405 Processing helix chain 'J' and resid 413 through 426 Processing helix chain 'J' and resid 429 through 442 Processing helix chain 'J' and resid 451 through 466 Processing helix chain 'J' and resid 478 through 489 Proline residue: J 488 - end of helix Processing helix chain 'J' and resid 496 through 512 removed outlier: 3.998A pdb=" N VAL J 501 " --> pdb=" O TYR J 497 " (cutoff:3.500A) Processing helix chain 'J' and resid 521 through 533 Processing helix chain 'J' and resid 538 through 545 removed outlier: 3.749A pdb=" N LEU J 542 " --> pdb=" O ILE J 538 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR J 543 " --> pdb=" O ASN J 539 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU J 544 " --> pdb=" O TYR J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 561 through 568 Proline residue: J 566 - end of helix Processing helix chain 'J' and resid 574 through 581 Processing helix chain 'J' and resid 595 through 603 Processing helix chain 'J' and resid 610 through 623 Processing helix chain 'J' and resid 633 through 643 Proline residue: J 637 - end of helix Processing helix chain 'J' and resid 649 through 659 removed outlier: 3.814A pdb=" N LEU J 653 " --> pdb=" O LEU J 649 " (cutoff:3.500A) Processing helix chain 'J' and resid 667 through 678 removed outlier: 3.901A pdb=" N ARG J 671 " --> pdb=" O ILE J 667 " (cutoff:3.500A) Proline residue: J 675 - end of helix Processing helix chain 'J' and resid 684 through 694 Processing helix chain 'J' and resid 700 through 708 removed outlier: 3.617A pdb=" N HIS J 708 " --> pdb=" O GLN J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 730 Processing helix chain 'J' and resid 743 through 755 Processing helix chain 'J' and resid 766 through 775 Processing helix chain 'J' and resid 782 through 799 Processing helix chain 'P' and resid 200 through 202 No H-bonds generated for 'chain 'P' and resid 200 through 202' Processing helix chain 'P' and resid 218 through 227 Processing helix chain 'R' and resid 129 through 132 No H-bonds generated for 'chain 'R' and resid 129 through 132' Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 239 through 245 Processing helix chain 'R' and resid 282 through 336 Processing helix chain 'R' and resid 409 through 411 No H-bonds generated for 'chain 'R' and resid 409 through 411' Processing helix chain 'R' and resid 455 through 458 No H-bonds generated for 'chain 'R' and resid 455 through 458' Processing helix chain 'R' and resid 463 through 469 Processing helix chain 'T' and resid 460 through 462 No H-bonds generated for 'chain 'T' and resid 460 through 462' Processing helix chain 'X' and resid 230 through 235 removed outlier: 3.731A pdb=" N ASP X 235 " --> pdb=" O ALA X 231 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 20 Processing helix chain 'Y' and resid 24 through 26 No H-bonds generated for 'chain 'Y' and resid 24 through 26' Processing helix chain 'Y' and resid 28 through 32 Processing helix chain 'Y' and resid 49 through 59 removed outlier: 5.044A pdb=" N GLN Y 58 " --> pdb=" O CYS Y 54 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR Y 59 " --> pdb=" O VAL Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 97 Processing helix chain 'Y' and resid 127 through 133 Processing helix chain 'Z' and resid 481 through 499 Processing helix chain 'Z' and resid 501 through 519 Processing helix chain 'Z' and resid 529 through 536 Processing helix chain 'Z' and resid 544 through 556 removed outlier: 4.442A pdb=" N ASN Z 547 " --> pdb=" O PRO Z 544 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU Z 556 " --> pdb=" O LYS Z 553 " (cutoff:3.500A) Processing helix chain 'Z' and resid 593 through 615 removed outlier: 4.091A pdb=" N LYS Z 605 " --> pdb=" O LEU Z 601 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA Z 606 " --> pdb=" O ALA Z 602 " (cutoff:3.500A) Processing helix chain '9' and resid 15 through 21 Processing helix chain '9' and resid 63 through 72 Proline residue: 9 68 - end of helix Processing helix chain '9' and resid 85 through 87 No H-bonds generated for 'chain '9' and resid 85 through 87' Processing helix chain '9' and resid 128 through 135 Processing helix chain '9' and resid 152 through 154 No H-bonds generated for 'chain '9' and resid 152 through 154' Processing helix chain '9' and resid 202 through 214 Processing helix chain '9' and resid 220 through 224 Processing helix chain '9' and resid 245 through 251 Processing helix chain '9' and resid 301 through 312 Processing helix chain '9' and resid 388 through 390 No H-bonds generated for 'chain '9' and resid 388 through 390' Processing helix chain '9' and resid 404 through 412 Processing helix chain '9' and resid 437 through 455 removed outlier: 3.524A pdb=" N ALA 9 443 " --> pdb=" O GLU 9 439 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN 9 447 " --> pdb=" O ALA 9 443 " (cutoff:3.500A) Processing helix chain 'z' and resid 34 through 45 Processing helix chain 'z' and resid 121 through 123 No H-bonds generated for 'chain 'z' and resid 121 through 123' Processing helix chain 'z' and resid 135 through 145 removed outlier: 3.925A pdb=" N VAL z 138 " --> pdb=" O GLY z 135 " (cutoff:3.500A) Processing helix chain 'x' and resid 387 through 398 removed outlier: 4.613A pdb=" N SER x 398 " --> pdb=" O ALA x 394 " (cutoff:3.500A) Processing helix chain 'x' and resid 400 through 414 removed outlier: 4.094A pdb=" N GLU x 406 " --> pdb=" O PHE x 402 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU x 407 " --> pdb=" O PRO x 403 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA x 410 " --> pdb=" O GLU x 406 " (cutoff:3.500A) Processing helix chain 'x' and resid 428 through 439 Proline residue: x 433 - end of helix removed outlier: 3.977A pdb=" N GLU x 438 " --> pdb=" O GLN x 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU x 439 " --> pdb=" O TYR x 435 " (cutoff:3.500A) Processing helix chain 'x' and resid 455 through 468 removed outlier: 3.515A pdb=" N MET x 459 " --> pdb=" O ARG x 455 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA x 463 " --> pdb=" O MET x 459 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG x 467 " --> pdb=" O ALA x 463 " (cutoff:3.500A) Processing helix chain 'x' and resid 498 through 507 Processing helix chain 'x' and resid 522 through 524 No H-bonds generated for 'chain 'x' and resid 522 through 524' Processing helix chain 'x' and resid 527 through 542 removed outlier: 3.599A pdb=" N ASP x 538 " --> pdb=" O GLY x 534 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG x 541 " --> pdb=" O LYS x 537 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE x 542 " --> pdb=" O ASP x 538 " (cutoff:3.500A) Processing helix chain 'x' and resid 558 through 563 removed outlier: 4.118A pdb=" N PHE x 563 " --> pdb=" O ARG x 559 " (cutoff:3.500A) Processing helix chain 'x' and resid 592 through 605 removed outlier: 3.953A pdb=" N SER x 598 " --> pdb=" O ALA x 594 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU x 600 " --> pdb=" O VAL x 596 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN x 601 " --> pdb=" O VAL x 597 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL x 604 " --> pdb=" O LEU x 600 " (cutoff:3.500A) Processing helix chain 'x' and resid 618 through 635 removed outlier: 3.878A pdb=" N ALA x 623 " --> pdb=" O GLU x 619 " (cutoff:3.500A) Processing helix chain 'x' and resid 653 through 660 removed outlier: 4.337A pdb=" N ARG x 658 " --> pdb=" O ASP x 654 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE x 659 " --> pdb=" O MET x 655 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE x 660 " --> pdb=" O GLN x 656 " (cutoff:3.500A) Processing helix chain 'x' and resid 675 through 679 removed outlier: 4.316A pdb=" N THR x 679 " --> pdb=" O ILE x 676 " (cutoff:3.500A) Processing helix chain 'x' and resid 716 through 727 removed outlier: 3.640A pdb=" N ALA x 723 " --> pdb=" O ALA x 719 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY x 724 " --> pdb=" O ASN x 720 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG x 725 " --> pdb=" O GLN x 721 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA x 726 " --> pdb=" O ARG x 722 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLY x 727 " --> pdb=" O ALA x 723 " (cutoff:3.500A) Processing helix chain 'x' and resid 740 through 744 removed outlier: 3.544A pdb=" N GLN x 744 " --> pdb=" O ALA x 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 740 through 744' Processing helix chain 'x' and resid 754 through 756 No H-bonds generated for 'chain 'x' and resid 754 through 756' Processing helix chain 'x' and resid 761 through 770 Processing helix chain 'x' and resid 786 through 798 Processing helix chain 'x' and resid 810 through 817 removed outlier: 3.570A pdb=" N ALA x 816 " --> pdb=" O GLY x 812 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU x 817 " --> pdb=" O ARG x 813 " (cutoff:3.500A) Processing helix chain 'x' and resid 822 through 830 Processing helix chain 'x' and resid 837 through 847 removed outlier: 3.829A pdb=" N ALA x 845 " --> pdb=" O LEU x 841 " (cutoff:3.500A) Processing helix chain 'x' and resid 866 through 871 removed outlier: 3.970A pdb=" N ASN x 870 " --> pdb=" O ASN x 866 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE x 871 " --> pdb=" O ALA x 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 866 through 871' Processing helix chain 'x' and resid 878 through 888 Processing helix chain 'x' and resid 905 through 924 Processing helix chain 'x' and resid 935 through 946 removed outlier: 3.579A pdb=" N LYS x 941 " --> pdb=" O ILE x 937 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA x 942 " --> pdb=" O ARG x 938 " (cutoff:3.500A) Processing helix chain 'x' and resid 1005 through 1011 Processing helix chain 'x' and resid 1013 through 1016 No H-bonds generated for 'chain 'x' and resid 1013 through 1016' Processing helix chain 'M' and resid 130 through 145 Processing helix chain 'M' and resid 203 through 207 Processing helix chain 'M' and resid 214 through 216 No H-bonds generated for 'chain 'M' and resid 214 through 216' Processing helix chain 'M' and resid 229 through 238 Processing helix chain 'M' and resid 243 through 245 No H-bonds generated for 'chain 'M' and resid 243 through 245' Processing helix chain 'M' and resid 283 through 292 Processing helix chain 'U' and resid 2 through 4 No H-bonds generated for 'chain 'U' and resid 2 through 4' Processing helix chain 'V' and resid 150 through 172 Processing helix chain 'V' and resid 178 through 187 removed outlier: 3.538A pdb=" N GLN V 187 " --> pdb=" O GLN V 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 194 through 207 Processing helix chain 'V' and resid 209 through 225 removed outlier: 5.211A pdb=" N HIS V 213 " --> pdb=" O ILE V 210 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN V 223 " --> pdb=" O ALA V 220 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 246 Processing helix chain 'V' and resid 250 through 265 Processing helix chain 'V' and resid 272 through 283 Processing helix chain 'V' and resid 287 through 307 removed outlier: 3.578A pdb=" N GLU V 299 " --> pdb=" O GLY V 295 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU V 302 " --> pdb=" O LYS V 298 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LYS V 303 " --> pdb=" O GLU V 299 " (cutoff:3.500A) Processing helix chain 'V' and resid 309 through 324 Processing helix chain 'V' and resid 330 through 344 Processing helix chain 'V' and resid 362 through 364 No H-bonds generated for 'chain 'V' and resid 362 through 364' Processing helix chain 'V' and resid 380 through 383 Processing helix chain 'V' and resid 391 through 405 removed outlier: 3.570A pdb=" N GLU V 404 " --> pdb=" O ALA V 400 " (cutoff:3.500A) Processing helix chain 'V' and resid 450 through 465 Processing helix chain 'V' and resid 469 through 479 removed outlier: 3.547A pdb=" N MET V 479 " --> pdb=" O LYS V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 483 through 499 removed outlier: 4.519A pdb=" N LYS V 487 " --> pdb=" O SER V 484 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS V 490 " --> pdb=" O LYS V 487 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS V 496 " --> pdb=" O ILE V 493 " (cutoff:3.500A) Processing helix chain 'V' and resid 505 through 517 Processing helix chain 'V' and resid 519 through 538 removed outlier: 3.713A pdb=" N LYS V 530 " --> pdb=" O GLU V 526 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR V 535 " --> pdb=" O GLU V 531 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS V 537 " --> pdb=" O TYR V 533 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG V 538 " --> pdb=" O ASP V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 541 through 556 Processing helix chain 'V' and resid 562 through 567 Processing helix chain 'V' and resid 577 through 594 Processing helix chain 'V' and resid 596 through 603 Processing helix chain 'V' and resid 611 through 613 No H-bonds generated for 'chain 'V' and resid 611 through 613' Processing helix chain 'V' and resid 621 through 634 Processing helix chain 'V' and resid 638 through 648 removed outlier: 4.686A pdb=" N GLU V 642 " --> pdb=" O LEU V 639 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU V 645 " --> pdb=" O GLU V 642 " (cutoff:3.500A) Processing helix chain '8' and resid 20 through 27 Processing helix chain '8' and resid 46 through 60 Proline residue: 8 50 - end of helix Processing helix chain '8' and resid 65 through 76 removed outlier: 3.623A pdb=" N GLU 8 76 " --> pdb=" O PHE 8 72 " (cutoff:3.500A) Processing helix chain '8' and resid 82 through 90 Processing helix chain '8' and resid 97 through 114 Proline residue: 8 107 - end of helix Processing helix chain '8' and resid 121 through 125 Processing helix chain '0' and resid 5 through 9 removed outlier: 4.250A pdb=" N LYS 0 8 " --> pdb=" O LYS 0 5 " (cutoff:3.500A) Processing helix chain '0' and resid 74 through 80 Processing helix chain 'I' and resid 59 through 67 removed outlier: 3.549A pdb=" N VAL I 63 " --> pdb=" O MET I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 107 Processing helix chain 'I' and resid 128 through 143 Processing helix chain 'K' and resid 13 through 26 Processing helix chain 'K' and resid 30 through 43 removed outlier: 3.625A pdb=" N VAL K 36 " --> pdb=" O ALA K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 56 removed outlier: 3.810A pdb=" N LEU K 56 " --> pdb=" O TYR K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 67 removed outlier: 3.823A pdb=" N SER K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 85 removed outlier: 3.589A pdb=" N ASN K 83 " --> pdb=" O GLY K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 97 Processing helix chain 'K' and resid 100 through 108 removed outlier: 3.837A pdb=" N CYS K 106 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU K 107 " --> pdb=" O ILE K 103 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER K 108 " --> pdb=" O ILE K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 124 Processing helix chain 'K' and resid 133 through 138 removed outlier: 3.646A pdb=" N THR K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA K 138 " --> pdb=" O PRO K 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 133 through 138' Processing helix chain 'K' and resid 140 through 149 Processing helix chain 'K' and resid 154 through 167 Processing helix chain 'K' and resid 170 through 185 Processing sheet with id= A, first strand: chain 'A' and resid 482 through 488 Processing sheet with id= B, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= C, first strand: chain 'A' and resid 516 through 518 Processing sheet with id= D, first strand: chain 'A' and resid 895 through 900 Processing sheet with id= E, first strand: chain 'A' and resid 1174 through 1178 removed outlier: 3.530A pdb=" N LEU A1087 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= G, first strand: chain 'A' and resid 1184 through 1189 removed outlier: 3.524A pdb=" N GLU A1223 " --> pdb=" O ASN A1218 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN A1227 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP A1214 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id= I, first strand: chain 'A' and resid 1711 through 1716 removed outlier: 8.502A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1637 through 1639 Processing sheet with id= K, first strand: chain 'A' and resid 1913 through 1918 removed outlier: 6.727A pdb=" N GLN A1860 " --> pdb=" O TRP A1778 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL A1780 " --> pdb=" O GLN A1860 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A1862 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A1883 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL A1863 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A1885 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1787 through 1791 removed outlier: 4.440A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 2090 through 2092 removed outlier: 6.866A pdb=" N CYS A2223 " --> pdb=" O TYR A2091 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU A2128 " --> pdb=" O LEU A2175 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP A2177 " --> pdb=" O GLY A2126 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY A2126 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A2131 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE A2142 " --> pdb=" O VAL A2131 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR A2103 " --> pdb=" O LYS A2140 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE A2142 " --> pdb=" O THR A2103 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE A2105 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N CYS A2144 " --> pdb=" O ILE A2105 " (cutoff:3.500A) removed outlier: 11.657A pdb=" N VAL A2146 " --> pdb=" O PRO A2107 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLN A2260 " --> pdb=" O TYR A2104 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A2106 " --> pdb=" O GLN A2260 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A2262 " --> pdb=" O LEU A2106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 2144 through 2146 removed outlier: 6.450A pdb=" N PHE A2270 " --> pdb=" O ILE A2145 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 2150 through 2152 Processing sheet with id= P, first strand: chain 'A' and resid 2228 through 2230 Processing sheet with id= Q, first strand: chain 'C' and resid 316 through 318 removed outlier: 9.272A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 348 through 350 Processing sheet with id= S, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.784A pdb=" N HIS C 477 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL C 496 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 480 through 483 Processing sheet with id= U, first strand: chain 'C' and resid 530 through 533 removed outlier: 4.227A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.927A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 662 through 666 removed outlier: 5.504A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER C 897 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.641A pdb=" N ILE C 688 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE C 791 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLU C 690 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N PHE C 789 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 734 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP C 747 " --> pdb=" O ILE C 732 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE C 732 " --> pdb=" O ASP C 747 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 831 through 838 removed outlier: 6.706A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 435 through 438 removed outlier: 3.771A pdb=" N ILE D 692 " --> pdb=" O THR D 871 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 826 " --> pdb=" O GLU D 866 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 499 through 502 removed outlier: 3.660A pdb=" N LEU D 499 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 501 " --> pdb=" O GLY D 650 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE D 586 " --> pdb=" O TYR D 540 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 721 through 723 Processing sheet with id= AC, first strand: chain 'D' and resid 832 through 835 Processing sheet with id= AD, first strand: chain 'D' and resid 970 through 972 Processing sheet with id= AE, first strand: chain 'D' and resid 1250 through 1257 removed outlier: 5.934A pdb=" N LYS D1199 " --> pdb=" O PRO D1192 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLU D1201 " --> pdb=" O LEU D1190 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU D1190 " --> pdb=" O GLU D1201 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR D1203 " --> pdb=" O VAL D1188 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL D1188 " --> pdb=" O THR D1203 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR D1205 " --> pdb=" O LEU D1186 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU D1186 " --> pdb=" O THR D1205 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 1279 through 1285 Processing sheet with id= AG, first strand: chain 'D' and resid 1511 through 1513 removed outlier: 6.011A pdb=" N PHE D1347 " --> pdb=" O PHE D1512 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 1523 through 1530 removed outlier: 6.605A pdb=" N GLY D1700 " --> pdb=" O GLU D1524 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N HIS D1526 " --> pdb=" O GLY D1700 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS D1702 " --> pdb=" O HIS D1526 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLN D1528 " --> pdb=" O CYS D1702 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE D1704 " --> pdb=" O GLN D1528 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE D1530 " --> pdb=" O ILE D1704 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS D1706 " --> pdb=" O PHE D1530 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET D1664 " --> pdb=" O PHE D1562 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 1668 through 1670 Processing sheet with id= AJ, first strand: chain 'D' and resid 1802 through 1805 Processing sheet with id= AK, first strand: chain 'D' and resid 2017 through 2023 Processing sheet with id= AL, first strand: chain 'D' and resid 2118 through 2124 removed outlier: 3.767A pdb=" N HIS D2102 " --> pdb=" O VAL D2124 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP D2070 " --> pdb=" O LEU D2076 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU D2076 " --> pdb=" O ASP D2070 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 90 through 94 Processing sheet with id= AN, first strand: chain 'E' and resid 112 through 117 removed outlier: 6.575A pdb=" N ALA E 127 " --> pdb=" O MET E 113 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU E 115 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE E 125 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR E 117 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N MET E 123 " --> pdb=" O TYR E 117 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL E 133 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 145 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP E 137 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG E 143 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 154 through 159 removed outlier: 6.998A pdb=" N GLY E 170 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS E 157 " --> pdb=" O CYS E 168 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N CYS E 168 " --> pdb=" O CYS E 157 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN E 188 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 196 through 201 removed outlier: 6.709A pdb=" N GLY E 211 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL E 199 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE E 209 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE E 201 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN E 207 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP E 221 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU E 227 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 275 through 277 removed outlier: 3.596A pdb=" N LYS E 275 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY E 240 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 291 through 293 removed outlier: 6.363A pdb=" N ASP E 313 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE E 319 " --> pdb=" O ASP E 313 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'E' and resid 351 through 355 Processing sheet with id= AT, first strand: chain 'a' and resid 55 through 58 Processing sheet with id= AU, first strand: chain 'a' and resid 60 through 63 removed outlier: 6.828A pdb=" N SER a 44 " --> pdb=" O LEU a 32 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU a 32 " --> pdb=" O SER a 44 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'b' and resid 64 through 68 removed outlier: 6.214A pdb=" N CYS b 45 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG b 18 " --> pdb=" O VAL b 82 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL b 82 " --> pdb=" O ARG b 18 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE b 20 " --> pdb=" O MET b 80 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N MET b 80 " --> pdb=" O ILE b 20 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'b' and resid 70 through 72 removed outlier: 3.689A pdb=" N ALA b 33 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS b 43 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N PHE b 31 " --> pdb=" O CYS b 43 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'c' and resid 53 through 55 Processing sheet with id= AY, first strand: chain 'c' and resid 57 through 60 removed outlier: 6.029A pdb=" N LYS c 41 " --> pdb=" O ILE c 29 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE c 29 " --> pdb=" O LYS c 41 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'd' and resid 89 through 96 Processing sheet with id= BA, first strand: chain 'd' and resid 98 through 101 removed outlier: 6.580A pdb=" N GLU d 68 " --> pdb=" O VAL d 56 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL d 56 " --> pdb=" O GLU d 68 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'f' and resid 57 through 60 removed outlier: 3.572A pdb=" N GLY f 57 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N THR f 47 " --> pdb=" O LEU f 59 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'f' and resid 62 through 64 removed outlier: 3.672A pdb=" N SER f 35 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA f 45 " --> pdb=" O LEU f 33 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU f 33 " --> pdb=" O ALA f 45 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'e' and resid 70 through 75 removed outlier: 5.727A pdb=" N ALA e 61 " --> pdb=" O LEU e 74 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N MET e 41 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU e 35 " --> pdb=" O MET e 41 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG e 30 " --> pdb=" O VAL e 90 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'e' and resid 77 through 79 removed outlier: 3.790A pdb=" N GLY e 49 " --> pdb=" O VAL e 57 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP e 59 " --> pdb=" O ILE e 47 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE e 47 " --> pdb=" O ASP e 59 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'g' and resid 67 through 72 removed outlier: 6.921A pdb=" N LYS g 20 " --> pdb=" O ILE g 68 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU g 70 " --> pdb=" O SER g 18 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER g 18 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA g 72 " --> pdb=" O LYS g 16 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LYS g 16 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL g 41 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'g' and resid 45 through 48 removed outlier: 6.476A pdb=" N GLU g 47 " --> pdb=" O ASN g 56 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASN g 56 " --> pdb=" O GLU g 47 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'h' and resid 55 through 58 Processing sheet with id= BI, first strand: chain 'h' and resid 60 through 63 removed outlier: 6.830A pdb=" N SER h 44 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU h 32 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'i' and resid 64 through 68 removed outlier: 6.215A pdb=" N CYS i 45 " --> pdb=" O LEU i 67 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG i 18 " --> pdb=" O VAL i 82 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL i 82 " --> pdb=" O ARG i 18 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE i 20 " --> pdb=" O MET i 80 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N MET i 80 " --> pdb=" O ILE i 20 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'i' and resid 70 through 72 removed outlier: 3.687A pdb=" N ALA i 33 " --> pdb=" O ILE i 41 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS i 43 " --> pdb=" O PHE i 31 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N PHE i 31 " --> pdb=" O CYS i 43 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'j' and resid 53 through 55 Processing sheet with id= BM, first strand: chain 'j' and resid 57 through 60 removed outlier: 6.031A pdb=" N LYS j 41 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE j 29 " --> pdb=" O LYS j 41 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'k' and resid 90 through 96 Processing sheet with id= BO, first strand: chain 'k' and resid 98 through 101 removed outlier: 6.582A pdb=" N GLU k 68 " --> pdb=" O VAL k 56 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL k 56 " --> pdb=" O GLU k 68 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'm' and resid 57 through 60 removed outlier: 3.571A pdb=" N GLY m 57 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR m 47 " --> pdb=" O LEU m 59 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'm' and resid 62 through 64 removed outlier: 3.670A pdb=" N SER m 35 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA m 45 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU m 33 " --> pdb=" O ALA m 45 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'l' and resid 70 through 75 removed outlier: 5.722A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG l 30 " --> pdb=" O VAL l 90 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'l' and resid 77 through 79 removed outlier: 3.790A pdb=" N GLY l 49 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP l 59 " --> pdb=" O ILE l 47 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE l 47 " --> pdb=" O ASP l 59 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'n' and resid 67 through 72 removed outlier: 6.919A pdb=" N LYS n 20 " --> pdb=" O ILE n 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU n 70 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER n 18 " --> pdb=" O LEU n 70 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA n 72 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LYS n 16 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'n' and resid 45 through 47 removed outlier: 6.477A pdb=" N GLU n 47 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASN n 56 " --> pdb=" O GLU n 47 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'v' and resid 34 through 36 Processing sheet with id= BW, first strand: chain '3' and resid 1173 through 1175 removed outlier: 6.779A pdb=" N LEU 3 3 " --> pdb=" O ILE 31174 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE 31126 " --> pdb=" O LEU 3 8 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLU 31115 " --> pdb=" O PRO 31131 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER 31103 " --> pdb=" O THR 31120 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain '3' and resid 16 through 20 removed outlier: 6.361A pdb=" N ARG 3 42 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N THR 3 52 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain '3' and resid 62 through 68 removed outlier: 6.935A pdb=" N GLY 3 81 " --> pdb=" O ARG 3 63 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU 3 65 " --> pdb=" O VAL 3 79 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL 3 79 " --> pdb=" O LEU 3 65 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA 3 67 " --> pdb=" O TYR 3 77 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR 3 77 " --> pdb=" O ALA 3 67 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER 3 82 " --> pdb=" O ARG 3 86 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG 3 86 " --> pdb=" O SER 3 82 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU 3 91 " --> pdb=" O LYS 3 101 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS 3 101 " --> pdb=" O GLU 3 91 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLN 3 93 " --> pdb=" O PHE 3 99 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE 3 99 " --> pdb=" O GLN 3 93 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain '3' and resid 120 through 123 Processing sheet with id= CA, first strand: chain '3' and resid 144 through 146 Processing sheet with id= CB, first strand: chain '3' and resid 165 through 167 removed outlier: 6.563A pdb=" N GLU 3 212 " --> pdb=" O ARG 3 222 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG 3 222 " --> pdb=" O GLU 3 212 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP 3 214 " --> pdb=" O VAL 3 220 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL 3 220 " --> pdb=" O ASP 3 214 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain '3' and resid 170 through 173 removed outlier: 4.476A pdb=" N MET 3 181 " --> pdb=" O VAL 3 173 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain '3' and resid 267 through 270 removed outlier: 3.742A pdb=" N PHE 3 234 " --> pdb=" O CYS 3 251 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain '3' and resid 287 through 294 removed outlier: 6.907A pdb=" N GLN 3 304 " --> pdb=" O VAL 3 288 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER 3 290 " --> pdb=" O LEU 3 302 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU 3 302 " --> pdb=" O SER 3 290 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR 3 292 " --> pdb=" O PHE 3 300 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE 3 300 " --> pdb=" O THR 3 292 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE 3 299 " --> pdb=" O LEU 3 315 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU 3 315 " --> pdb=" O PHE 3 299 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP 3 309 " --> pdb=" O THR 3 305 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS 3 312 " --> pdb=" O TYR 3 329 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N TYR 3 329 " --> pdb=" O LYS 3 312 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR 3 314 " --> pdb=" O LEU 3 327 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU 3 327 " --> pdb=" O THR 3 314 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU 3 316 " --> pdb=" O ILE 3 325 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE 3 325 " --> pdb=" O GLU 3 316 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain '3' and resid 336 through 342 removed outlier: 7.093A pdb=" N ALA 3 350 " --> pdb=" O ALA 3 337 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET 3 339 " --> pdb=" O PHE 3 348 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE 3 348 " --> pdb=" O MET 3 339 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL 3 341 " --> pdb=" O PHE 3 346 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE 3 346 " --> pdb=" O VAL 3 341 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN 3 360 " --> pdb=" O LEU 3 397 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU 3 397 " --> pdb=" O GLN 3 360 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain '3' and resid 774 through 780 Processing sheet with id= CH, first strand: chain '3' and resid 482 through 486 removed outlier: 3.546A pdb=" N ALA 3 458 " --> pdb=" O SER 3 477 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain '3' and resid 533 through 537 Processing sheet with id= CJ, first strand: chain '3' and resid 574 through 576 removed outlier: 3.754A pdb=" N GLU 3 562 " --> pdb=" O LEU 3 558 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS 3 546 " --> pdb=" O ALA 3 557 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain '3' and resid 587 through 592 removed outlier: 6.960A pdb=" N GLY 3 608 " --> pdb=" O VAL 3 588 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET 3 590 " --> pdb=" O ALA 3 606 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA 3 606 " --> pdb=" O MET 3 590 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU 3 592 " --> pdb=" O PHE 3 604 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N PHE 3 604 " --> pdb=" O LEU 3 592 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER 3 629 " --> pdb=" O ILE 3 616 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N SER 3 618 " --> pdb=" O PRO 3 627 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain '3' and resid 689 through 693 removed outlier: 3.942A pdb=" N ARG 3 676 " --> pdb=" O ARG 3 690 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL 3 673 " --> pdb=" O LEU 3 669 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU 3 669 " --> pdb=" O VAL 3 673 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET 3 645 " --> pdb=" O PHE 3 662 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER 3 639 " --> pdb=" O GLY 3 668 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain '3' and resid 700 through 703 Processing sheet with id= CN, first strand: chain '3' and resid 741 through 745 removed outlier: 3.743A pdb=" N ALA 3 448 " --> pdb=" O ILE 3 764 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA 3 766 " --> pdb=" O GLU 3 446 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLU 3 446 " --> pdb=" O ALA 3 766 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain '3' and resid 784 through 790 removed outlier: 3.587A pdb=" N THR 3 784 " --> pdb=" O THR 3 802 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE 3 800 " --> pdb=" O ARG 3 786 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE 3 788 " --> pdb=" O ILE 3 798 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE 3 798 " --> pdb=" O PHE 3 788 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE 3 790 " --> pdb=" O ASN 3 796 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN 3 796 " --> pdb=" O ILE 3 790 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN 3 870 " --> pdb=" O THR 3 876 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR 3 876 " --> pdb=" O ASN 3 870 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain '3' and resid 886 through 895 removed outlier: 6.565A pdb=" N GLY 3 908 " --> pdb=" O PHE 3 889 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL 3 891 " --> pdb=" O LEU 3 906 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU 3 906 " --> pdb=" O VAL 3 891 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL 3 893 " --> pdb=" O TYR 3 904 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TYR 3 904 " --> pdb=" O VAL 3 893 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP 3 903 " --> pdb=" O LEU 3 930 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS 3 941 " --> pdb=" O THR 3 927 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS 3 929 " --> pdb=" O PHE 3 939 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N PHE 3 939 " --> pdb=" O LYS 3 929 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL 3 931 " --> pdb=" O LEU 3 937 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU 3 937 " --> pdb=" O VAL 3 931 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain '3' and resid 977 through 980 removed outlier: 3.867A pdb=" N ALA 3 951 " --> pdb=" O GLY 3 962 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain '3' and resid 990 through 996 removed outlier: 6.491A pdb=" N SER 31003 " --> pdb=" O SER 3 991 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE 3 993 " --> pdb=" O ILE 31001 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE 31001 " --> pdb=" O ILE 3 993 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR 3 995 " --> pdb=" O ARG 3 999 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG 3 999 " --> pdb=" O THR 3 995 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG 31013 " --> pdb=" O ILE 31023 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE 31023 " --> pdb=" O ARG 31013 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS 31015 " --> pdb=" O LEU 31021 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU 31021 " --> pdb=" O LYS 31015 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain '3' and resid 1033 through 1038 removed outlier: 6.788A pdb=" N ALA 31047 " --> pdb=" O THR 31034 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA 31036 " --> pdb=" O ALA 31045 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA 31045 " --> pdb=" O ALA 31036 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU 31038 " --> pdb=" O THR 31043 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR 31043 " --> pdb=" O LEU 31038 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN 31052 " --> pdb=" O ASP 31048 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG 31057 " --> pdb=" O VAL 31091 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL 31091 " --> pdb=" O ARG 31057 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain '4' and resid 41 through 44 Processing sheet with id= CU, first strand: chain '5' and resid 88 through 91 Processing sheet with id= CV, first strand: chain '6' and resid 39 through 42 removed outlier: 6.303A pdb=" N TYR 6 71 " --> pdb=" O CYS 6 40 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'T' and resid 207 through 212 removed outlier: 6.634A pdb=" N GLY T 222 " --> pdb=" O ARG T 208 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE T 210 " --> pdb=" O VAL T 220 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL T 220 " --> pdb=" O ILE T 210 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL T 212 " --> pdb=" O TRP T 218 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TRP T 218 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASP T 232 " --> pdb=" O LEU T 238 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU T 238 " --> pdb=" O ASP T 232 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'T' and resid 249 through 254 removed outlier: 6.570A pdb=" N CYS T 264 " --> pdb=" O ARG T 250 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL T 252 " --> pdb=" O PHE T 262 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE T 262 " --> pdb=" O VAL T 252 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL T 254 " --> pdb=" O TYR T 260 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR T 260 " --> pdb=" O VAL T 254 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL T 270 " --> pdb=" O TYR T 284 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG T 282 " --> pdb=" O CYS T 272 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP T 274 " --> pdb=" O VAL T 280 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL T 280 " --> pdb=" O ASP T 274 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'T' and resid 291 through 296 removed outlier: 6.687A pdb=" N CYS T 306 " --> pdb=" O TYR T 292 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU T 294 " --> pdb=" O VAL T 304 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL T 304 " --> pdb=" O LEU T 294 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU T 296 " --> pdb=" O VAL T 302 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL T 302 " --> pdb=" O LEU T 296 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR T 311 " --> pdb=" O SER T 307 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS T 324 " --> pdb=" O ILE T 314 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP T 316 " --> pdb=" O SER T 322 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER T 322 " --> pdb=" O ASP T 316 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'T' and resid 333 through 338 removed outlier: 6.751A pdb=" N GLY T 348 " --> pdb=" O ALA T 334 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL T 336 " --> pdb=" O ILE T 346 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE T 346 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE T 345 " --> pdb=" O TRP T 357 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'T' and resid 377 through 380 removed outlier: 3.582A pdb=" N ALA T 377 " --> pdb=" O GLY T 390 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS T 399 " --> pdb=" O PHE T 405 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE T 405 " --> pdb=" O LYS T 399 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'T' and resid 416 through 421 removed outlier: 6.949A pdb=" N GLY T 430 " --> pdb=" O ASN T 417 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU T 419 " --> pdb=" O VAL T 428 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL T 428 " --> pdb=" O LEU T 419 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL T 421 " --> pdb=" O VAL T 426 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL T 426 " --> pdb=" O VAL T 421 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR T 435 " --> pdb=" O ALA T 431 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN T 448 " --> pdb=" O LEU T 438 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP T 440 " --> pdb=" O ASN T 446 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASN T 446 " --> pdb=" O ASP T 440 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'T' and resid 194 through 200 removed outlier: 6.862A pdb=" N VAL T 488 " --> pdb=" O TYR T 197 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL T 199 " --> pdb=" O ILE T 486 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE T 486 " --> pdb=" O VAL T 199 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'X' and resid 259 through 264 removed outlier: 3.688A pdb=" N PHE X 264 " --> pdb=" O GLU X 366 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU X 366 " --> pdb=" O PHE X 264 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'X' and resid 280 through 283 Processing sheet with id= DF, first strand: chain 'X' and resid 337 through 339 Processing sheet with id= DG, first strand: chain 'Y' and resid 108 through 111 Processing sheet with id= DH, first strand: chain '9' and resid 52 through 54 Processing sheet with id= DI, first strand: chain '9' and resid 125 through 127 removed outlier: 6.442A pdb=" N ALA 9 118 " --> pdb=" O THR 9 157 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR 9 157 " --> pdb=" O ALA 9 118 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain '9' and resid 430 through 435 removed outlier: 6.250A pdb=" N TYR 9 281 " --> pdb=" O PHE 9 434 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLU 9 294 " --> pdb=" O VAL 9 400 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL 9 400 " --> pdb=" O GLU 9 294 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU 9 366 " --> pdb=" O PHE 9 397 " (cutoff:3.500A) Processing sheet with id= DK, first strand: chain 'z' and resid 56 through 58 removed outlier: 3.917A pdb=" N ARG z 56 " --> pdb=" O GLN z 64 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU z 98 " --> pdb=" O THR z 116 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET z 101 " --> pdb=" O ILE z 129 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE z 129 " --> pdb=" O MET z 101 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU z 16 " --> pdb=" O VAL z 166 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL z 166 " --> pdb=" O LEU z 16 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS z 18 " --> pdb=" O CYS z 164 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N CYS z 164 " --> pdb=" O LYS z 18 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'x' and resid 569 through 571 removed outlier: 9.632A pdb=" N PHE x 570 " --> pdb=" O VAL x 417 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE x 419 " --> pdb=" O PHE x 570 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL x 548 " --> pdb=" O LEU x 418 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE x 420 " --> pdb=" O VAL x 548 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL x 550 " --> pdb=" O ILE x 420 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU x 549 " --> pdb=" O VAL x 517 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG x 494 " --> pdb=" O ILE x 448 " (cutoff:3.500A) Processing sheet with id= DM, first strand: chain 'x' and resid 479 through 481 Processing sheet with id= DN, first strand: chain 'x' and resid 579 through 583 removed outlier: 7.110A pdb=" N GLY x 732 " --> pdb=" O ASP x 580 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N PHE x 582 " --> pdb=" O GLY x 732 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS x 734 " --> pdb=" O PHE x 582 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP x 610 " --> pdb=" O ILE x 687 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL x 689 " --> pdb=" O ASP x 610 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU x 612 " --> pdb=" O VAL x 689 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP x 691 " --> pdb=" O LEU x 612 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE x 614 " --> pdb=" O ASP x 691 " (cutoff:3.500A) Processing sheet with id= DO, first strand: chain 'x' and resid 694 through 701 removed outlier: 3.565A pdb=" N CYS x 695 " --> pdb=" O THR x 712 " (cutoff:3.500A) Processing sheet with id= DP, first strand: chain 'x' and resid 984 through 986 Processing sheet with id= DQ, first strand: chain 'x' and resid 988 through 991 removed outlier: 3.544A pdb=" N GLU x 988 " --> pdb=" O ARG x 998 " (cutoff:3.500A) Processing sheet with id= DR, first strand: chain 'I' and resid 118 through 121 removed outlier: 5.534A pdb=" N GLU I 88 " --> pdb=" O GLY I 52 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN I 74 " --> pdb=" O LYS I 93 " (cutoff:3.500A) 4075 hydrogen bonds defined for protein. 10944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 184 hydrogen bonds 344 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 141 stacking parallelities Total time for adding SS restraints: 69.87 Time building geometry restraints manager: 35.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 17194 1.30 - 1.43: 28131 1.43 - 1.56: 55655 1.56 - 1.69: 639 1.69 - 1.82: 568 Bond restraints: 102187 Sorted by residual: bond pdb=" CA TYR A 515 " pdb=" C TYR A 515 " ideal model delta sigma weight residual 1.523 1.411 0.112 1.56e-02 4.11e+03 5.20e+01 bond pdb=" CA ASP A 797 " pdb=" C ASP A 797 " ideal model delta sigma weight residual 1.524 1.409 0.115 1.66e-02 3.63e+03 4.83e+01 bond pdb=" CA GLU x 926 " pdb=" CB GLU x 926 " ideal model delta sigma weight residual 1.531 1.448 0.083 1.45e-02 4.76e+03 3.26e+01 bond pdb=" O2G G5J F 207 " pdb=" PG G5J F 207 " ideal model delta sigma weight residual 1.495 1.605 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" O1B G5J F 207 " pdb=" PB G5J F 207 " ideal model delta sigma weight residual 1.492 1.601 -0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 102182 not shown) Histogram of bond angle deviations from ideal: 92.47 - 101.66: 492 101.66 - 110.86: 38283 110.86 - 120.05: 56117 120.05 - 129.24: 44666 129.24 - 138.43: 830 Bond angle restraints: 140388 Sorted by residual: angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 111.36 122.12 -10.76 1.09e+00 8.42e-01 9.74e+01 angle pdb=" N ILE 6 60 " pdb=" CA ILE 6 60 " pdb=" C ILE 6 60 " ideal model delta sigma weight residual 110.62 119.46 -8.84 1.02e+00 9.61e-01 7.50e+01 angle pdb=" N VAL R 405 " pdb=" CA VAL R 405 " pdb=" C VAL R 405 " ideal model delta sigma weight residual 109.30 120.62 -11.32 1.31e+00 5.83e-01 7.47e+01 angle pdb=" N PHE R 412 " pdb=" CA PHE R 412 " pdb=" C PHE R 412 " ideal model delta sigma weight residual 110.53 121.25 -10.72 1.29e+00 6.01e-01 6.91e+01 angle pdb=" C PRO 2 642 " pdb=" N PRO 2 643 " pdb=" CA PRO 2 643 " ideal model delta sigma weight residual 119.05 128.21 -9.16 1.11e+00 8.12e-01 6.81e+01 ... (remaining 140383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 59990 35.84 - 71.67: 1479 71.67 - 107.51: 119 107.51 - 143.35: 13 143.35 - 179.18: 7 Dihedral angle restraints: 61608 sinusoidal: 22891 harmonic: 38717 Sorted by residual: dihedral pdb=" C4' G F 51 " pdb=" C3' G F 51 " pdb=" C2' G F 51 " pdb=" C1' G F 51 " ideal model delta sinusoidal sigma weight residual -35.00 34.95 -69.95 1 8.00e+00 1.56e-02 9.86e+01 dihedral pdb=" C5' G F 51 " pdb=" C4' G F 51 " pdb=" C3' G F 51 " pdb=" O3' G F 51 " ideal model delta sinusoidal sigma weight residual 147.00 79.46 67.54 1 8.00e+00 1.56e-02 9.27e+01 dihedral pdb=" O4' G F 51 " pdb=" C4' G F 51 " pdb=" C3' G F 51 " pdb=" C2' G F 51 " ideal model delta sinusoidal sigma weight residual 24.00 -38.29 62.29 1 8.00e+00 1.56e-02 8.02e+01 ... (remaining 61605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.994: 16412 0.994 - 1.989: 0 1.989 - 2.983: 0 2.983 - 3.978: 0 3.978 - 4.972: 2 Chirality restraints: 16414 Sorted by residual: chirality pdb=" C2 IHP A3000 " pdb=" C1 IHP A3000 " pdb=" C3 IHP A3000 " pdb=" O12 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.52 2.45 -4.97 2.00e-01 2.50e+01 6.18e+02 chirality pdb=" C3 IHP A3000 " pdb=" C2 IHP A3000 " pdb=" C4 IHP A3000 " pdb=" O13 IHP A3000 " both_signs ideal model delta sigma weight residual False -2.34 2.46 -4.80 2.00e-01 2.50e+01 5.75e+02 chirality pdb=" C3' U G -11 " pdb=" C4' U G -11 " pdb=" O3' U G -11 " pdb=" C2' U G -11 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 16411 not shown) Planarity restraints: 17507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U H 79 " 0.073 2.00e-02 2.50e+03 3.49e-02 2.74e+01 pdb=" N1 U H 79 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U H 79 " -0.011 2.00e-02 2.50e+03 pdb=" O2 U H 79 " -0.018 2.00e-02 2.50e+03 pdb=" N3 U H 79 " -0.012 2.00e-02 2.50e+03 pdb=" C4 U H 79 " 0.012 2.00e-02 2.50e+03 pdb=" O4 U H 79 " 0.035 2.00e-02 2.50e+03 pdb=" C5 U H 79 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U H 79 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G H 81 " 0.048 2.00e-02 2.50e+03 2.79e-02 2.34e+01 pdb=" N9 G H 81 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G H 81 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G H 81 " -0.011 2.00e-02 2.50e+03 pdb=" C5 G H 81 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G H 81 " 0.023 2.00e-02 2.50e+03 pdb=" O6 G H 81 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G H 81 " 0.032 2.00e-02 2.50e+03 pdb=" C2 G H 81 " -0.063 2.00e-02 2.50e+03 pdb=" N2 G H 81 " 0.014 2.00e-02 2.50e+03 pdb=" N3 G H 81 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G H 81 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 831 " -0.030 2.00e-02 2.50e+03 3.38e-02 2.28e+01 pdb=" CG TYR C 831 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR C 831 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR C 831 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C 831 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR C 831 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C 831 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 831 " 0.000 2.00e-02 2.50e+03 ... (remaining 17504 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.62: 1333 2.62 - 3.25: 101332 3.25 - 3.88: 188749 3.88 - 4.51: 256773 4.51 - 5.14: 392967 Nonbonded interactions: 941154 Sorted by model distance: nonbonded pdb=" OP1 G F 43 " pdb="MG MG F 204 " model vdw 1.987 2.170 nonbonded pdb=" O2B GTP C1500 " pdb="MG MG C1501 " model vdw 2.064 2.170 nonbonded pdb=" O1G GTP C1500 " pdb="MG MG C1501 " model vdw 2.066 2.170 nonbonded pdb=" O2' C G 206 " pdb=" OP2 A G 207 " model vdw 2.072 2.440 nonbonded pdb=" OG1 THR C 143 " pdb="MG MG C1501 " model vdw 2.073 2.170 ... (remaining 941149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and ((resid 4 and (name CA or name C or name O )) or resid 5 through \ 56 or (resid 57 and (name N or name CA or name C or name O )) or resid 58 throug \ h 85)) selection = chain 'h' } ncs_group { reference = (chain 'b' and (resid 8 through 56 or (resid 57 and (name N or name CA or name C \ or name O )) or resid 58 through 84 or (resid 85 and (name N or name CA or name \ C or name O )) or resid 86 through 89)) selection = (chain 'i' and resid 8 through 89) } ncs_group { reference = chain 'c' selection = chain 'j' } ncs_group { reference = (chain 'd' and (resid 20 through 76 or resid 89 through 116)) selection = chain 'k' } ncs_group { reference = chain 'e' selection = chain 'l' } ncs_group { reference = chain 'f' selection = chain 'm' } ncs_group { reference = (chain 'g' and (resid 4 through 48 or resid 54 through 76)) selection = chain 'n' } 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 51.010 Check model and map are aligned: 1.150 Set scattering table: 0.770 Process input model: 277.860 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.460 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:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 359.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.021 0.211 102187 Z= 1.390 Angle : 1.366 15.897 140388 Z= 0.836 Chirality : 0.104 4.972 16414 Planarity : 0.008 0.091 17507 Dihedral : 15.161 179.182 36473 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 3.57 % Allowed : 5.47 % Favored : 90.96 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.07), residues: 13107 helix: -1.18 (0.07), residues: 5010 sheet: -0.33 (0.10), residues: 2167 loop : -1.12 (0.07), residues: 5930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.005 TRP C 772 HIS 0.040 0.004 HIS T 412 PHE 0.076 0.005 PHE 2 575 TYR 0.080 0.005 TYR C 831 ARG 0.038 0.003 ARG A1787 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2044 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1763 time to evaluate : 8.460 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: A 147 MET cc_start: 0.8701 (mmp) cc_final: 0.8308 (mmp) REVERT: A 151 MET cc_start: 0.8875 (mtt) cc_final: 0.8674 (mtt) REVERT: A 258 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8941 (t80) REVERT: A 426 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8216 (mp) REVERT: A 474 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7842 (mtt180) REVERT: A 546 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8658 (tt) REVERT: A 591 MET cc_start: 0.8632 (ttm) cc_final: 0.8336 (ttm) REVERT: A 976 MET cc_start: 0.8926 (tpp) cc_final: 0.8536 (tpt) REVERT: A 1061 MET cc_start: 0.9270 (mtt) cc_final: 0.9066 (mtp) REVERT: A 1231 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8563 (ttt90) REVERT: A 1370 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8203 (mmp-170) REVERT: A 1425 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8516 (tppt) REVERT: A 1482 GLU cc_start: 0.7843 (tp30) cc_final: 0.7497 (tp30) REVERT: A 2014 MET cc_start: 0.8019 (mmt) cc_final: 0.7765 (mmt) REVERT: A 2087 THR cc_start: 0.6058 (OUTLIER) cc_final: 0.5627 (p) REVERT: C 714 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 726 LEU cc_start: 0.7802 (tp) cc_final: 0.7487 (tt) REVERT: E 176 VAL cc_start: 0.6261 (t) cc_final: 0.5812 (p) REVERT: E 232 ARG cc_start: 0.2843 (mmm160) cc_final: 0.2457 (mmm-85) REVERT: v 1 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6332 (tmt) REVERT: 1 407 MET cc_start: 0.8325 (mtp) cc_final: 0.8105 (mtp) REVERT: 1 457 ASN cc_start: 0.8195 (p0) cc_final: 0.7836 (t0) REVERT: 1 688 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7719 (mt-10) REVERT: 1 783 GLU cc_start: 0.7922 (pt0) cc_final: 0.7652 (pm20) REVERT: 1 869 MET cc_start: 0.9009 (tpt) cc_final: 0.8754 (tpt) REVERT: 1 1119 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8699 (t) REVERT: 1 1133 MET cc_start: 0.8810 (mtm) cc_final: 0.8560 (mtm) REVERT: 2 484 ASP cc_start: 0.8513 (t70) cc_final: 0.8311 (t70) REVERT: 2 549 MET cc_start: 0.8062 (tpp) cc_final: 0.7834 (tpt) REVERT: 3 136 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: 3 298 MET cc_start: 0.7284 (ppp) cc_final: 0.7057 (ptt) REVERT: 3 377 MET cc_start: 0.7896 (mtp) cc_final: 0.7633 (mtt) REVERT: 3 686 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8208 (mt) REVERT: 3 690 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8121 (mtp85) REVERT: 3 743 SER cc_start: 0.8345 (m) cc_final: 0.8114 (m) REVERT: 3 982 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6747 (tt0) REVERT: 5 65 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7705 (mt-10) REVERT: 5 80 PHE cc_start: 0.7745 (t80) cc_final: 0.7375 (t80) REVERT: 5 104 LYS cc_start: 0.8425 (ttpp) cc_final: 0.8221 (mppt) REVERT: 5 107 GLU cc_start: 0.8500 (tp30) cc_final: 0.8248 (tp30) REVERT: 6 36 TYR cc_start: 0.8948 (m-80) cc_final: 0.8549 (m-80) REVERT: J 226 ARG cc_start: 0.6144 (ptp-170) cc_final: 0.5593 (ptt90) REVERT: J 360 ASP cc_start: 0.3957 (OUTLIER) cc_final: 0.3176 (t70) REVERT: J 378 ASN cc_start: 0.5341 (m-40) cc_final: 0.5064 (m-40) REVERT: J 386 GLU cc_start: 0.4496 (mm-30) cc_final: 0.3141 (pp20) REVERT: J 417 VAL cc_start: 0.4562 (t) cc_final: 0.4273 (m) REVERT: R 230 MET cc_start: 0.7151 (tpp) cc_final: 0.6878 (mmm) REVERT: R 325 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7712 (mtm110) REVERT: T 384 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7758 (m90) REVERT: X 270 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6584 (mt) REVERT: X 292 ILE cc_start: 0.8521 (mt) cc_final: 0.8317 (mt) REVERT: X 353 LYS cc_start: 0.7189 (mttt) cc_final: 0.6779 (mmmt) REVERT: Y 105 ARG cc_start: 0.8551 (mtp85) cc_final: 0.8223 (mtp85) REVERT: x 1032 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8532 (tttt) REVERT: M 194 ARG cc_start: 0.8558 (ptm-80) cc_final: 0.8275 (ptt90) REVERT: M 249 TYR cc_start: 0.8870 (m-80) cc_final: 0.8638 (m-80) REVERT: 8 37 LYS cc_start: 0.8514 (ttpp) cc_final: 0.8213 (tmmt) REVERT: 8 47 VAL cc_start: 0.9165 (p) cc_final: 0.8964 (t) REVERT: 0 53 ASN cc_start: 0.8678 (m110) cc_final: 0.8477 (m110) REVERT: K 22 THR cc_start: 0.7510 (p) cc_final: 0.7158 (t) outliers start: 281 outliers final: 90 residues processed: 1976 average time/residue: 1.8642 time to fit residues: 4981.9807 Evaluate side-chains 1312 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1205 time to evaluate : 8.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1231 ARG Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain A residue 1425 LYS Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1762 TYR Chi-restraints excluded: chain A residue 1764 SER Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1921 ASP Chi-restraints excluded: chain A residue 2073 TRP Chi-restraints excluded: chain A residue 2074 ARG Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 683 ASN Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 1090 ARG Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 219 SER Chi-restraints excluded: chain 1 residue 563 LEU Chi-restraints excluded: chain 1 residue 564 ASP Chi-restraints excluded: chain 1 residue 677 CYS Chi-restraints excluded: chain 1 residue 872 ILE Chi-restraints excluded: chain 1 residue 883 ASP Chi-restraints excluded: chain 1 residue 936 VAL Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1024 LEU Chi-restraints excluded: chain 1 residue 1038 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1058 ILE Chi-restraints excluded: chain 1 residue 1119 VAL Chi-restraints excluded: chain 1 residue 1128 VAL Chi-restraints excluded: chain 1 residue 1226 VAL Chi-restraints excluded: chain 1 residue 1227 ILE Chi-restraints excluded: chain 1 residue 1239 VAL Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 577 LYS Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 2 residue 590 LEU Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 184 CYS Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 322 VAL Chi-restraints excluded: chain 3 residue 425 VAL Chi-restraints excluded: chain 3 residue 614 VAL Chi-restraints excluded: chain 3 residue 615 ARG Chi-restraints excluded: chain 3 residue 686 LEU Chi-restraints excluded: chain 3 residue 690 ARG Chi-restraints excluded: chain 3 residue 691 THR Chi-restraints excluded: chain 3 residue 943 THR Chi-restraints excluded: chain 3 residue 982 GLU Chi-restraints excluded: chain 3 residue 1007 GLU Chi-restraints excluded: chain 3 residue 1064 ASP Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 95 LYS Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain J residue 360 ASP Chi-restraints excluded: chain R residue 237 MET Chi-restraints excluded: chain R residue 384 GLU Chi-restraints excluded: chain R residue 410 ARG Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain T residue 384 HIS Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain T residue 456 PRO Chi-restraints excluded: chain X residue 264 PHE Chi-restraints excluded: chain X residue 270 LEU Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Z residue 526 ILE Chi-restraints excluded: chain 9 residue 220 ILE Chi-restraints excluded: chain 9 residue 224 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 226 TYR Chi-restraints excluded: chain U residue 20 GLN Chi-restraints excluded: chain V residue 467 LEU Chi-restraints excluded: chain V residue 536 ILE Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain 0 residue 100 SER Chi-restraints excluded: chain I residue 31 ARG Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 105 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1339 random chunks: chunk 1130 optimal weight: 20.0000 chunk 1014 optimal weight: 0.8980 chunk 563 optimal weight: 1.9990 chunk 346 optimal weight: 6.9990 chunk 684 optimal weight: 6.9990 chunk 542 optimal weight: 2.9990 chunk 1049 optimal weight: 0.9980 chunk 406 optimal weight: 0.0070 chunk 638 optimal weight: 20.0000 chunk 781 optimal weight: 0.0270 chunk 1215 optimal weight: 9.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN A 579 GLN A 601 GLN A 675 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN A1450 GLN A2166 HIS ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN C 163 GLN C 245 HIS C 548 ASN ** C 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 706 GLN E 225 ASN E 257 ASN 1 148 ASN 1 473 GLN 1 659 GLN 1 778 GLN 1 912 ASN 11209 ASN 11252 GLN 2 490 HIS ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 304 GLN 31192 ASN 5 25 ASN 5 47 GLN 5 72 ASN 5 76 HIS ** 5 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 238 ASN J 250 GLN J 275 ASN ** J 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 291 GLN J 294 HIS ** J 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 389 HIS R 279 HIS R 403 ASN R 453 ASN ** T 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 66 ASN Z 503 GLN Z 519 GLN M 198 GLN V 440 GLN 8 74 GLN 8 88 ASN ** 8 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 74 GLN I 15 HIS I 110 GLN K 35 GLN K 49 ASN K 55 GLN K 96 HIS ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 102187 Z= 0.189 Angle : 0.588 10.824 140388 Z= 0.317 Chirality : 0.043 0.305 16414 Planarity : 0.005 0.063 17507 Dihedral : 13.503 179.139 18680 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.93 % Favored : 98.05 % Rotamer: Outliers : 4.01 % Allowed : 13.44 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.07), residues: 13107 helix: 0.35 (0.07), residues: 5043 sheet: 0.08 (0.11), residues: 2106 loop : -0.59 (0.08), residues: 5958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A2206 HIS 0.025 0.001 HIS K 124 PHE 0.029 0.002 PHE Y 56 TYR 0.026 0.002 TYR J 349 ARG 0.008 0.001 ARG 1 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1760 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1444 time to evaluate : 8.524 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: A 61 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7899 (mtp) REVERT: A 147 MET cc_start: 0.8558 (mmp) cc_final: 0.7967 (mmp) REVERT: A 426 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8553 (mp) REVERT: A 591 MET cc_start: 0.8631 (ttm) cc_final: 0.8252 (ttm) REVERT: A 1370 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8101 (mmp-170) REVERT: A 1675 ASP cc_start: 0.8254 (t0) cc_final: 0.8051 (t0) REVERT: A 2087 THR cc_start: 0.5967 (OUTLIER) cc_final: 0.5088 (p) REVERT: A 2284 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6658 (ptp) REVERT: A 2303 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5287 (pp20) REVERT: C 673 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7323 (mmtm) REVERT: C 726 LEU cc_start: 0.7852 (tp) cc_final: 0.7489 (tt) REVERT: E 176 VAL cc_start: 0.6222 (t) cc_final: 0.5851 (p) REVERT: E 192 ASN cc_start: 0.0888 (OUTLIER) cc_final: 0.0499 (m-40) REVERT: E 232 ARG cc_start: 0.3094 (mmm160) cc_final: 0.2668 (mmm160) REVERT: E 315 THR cc_start: 0.3626 (m) cc_final: 0.3260 (p) REVERT: v 188 ARG cc_start: 0.6918 (tmm-80) cc_final: 0.6429 (mtm110) REVERT: 1 164 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7216 (tm-30) REVERT: 1 457 ASN cc_start: 0.8124 (p0) cc_final: 0.7868 (t0) REVERT: 1 869 MET cc_start: 0.8932 (tpt) cc_final: 0.8612 (tpt) REVERT: 1 1058 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.7908 (mt) REVERT: 2 484 ASP cc_start: 0.8377 (t70) cc_final: 0.8043 (t70) REVERT: 2 577 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8527 (mtpp) REVERT: 3 131 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.6838 (tmt) REVERT: 3 138 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8434 (mm-40) REVERT: 3 377 MET cc_start: 0.7767 (mtp) cc_final: 0.7516 (mtt) REVERT: 3 461 THR cc_start: 0.6991 (m) cc_final: 0.6770 (t) REVERT: 3 669 LEU cc_start: 0.8238 (mt) cc_final: 0.7852 (mt) REVERT: 3 1192 ASN cc_start: 0.7486 (m110) cc_final: 0.7098 (m-40) REVERT: 5 46 ARG cc_start: 0.8168 (tpt90) cc_final: 0.7967 (mmm160) REVERT: 5 65 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7767 (mt-10) REVERT: 5 80 PHE cc_start: 0.7742 (t80) cc_final: 0.7511 (t80) REVERT: 5 84 ASN cc_start: 0.8006 (t0) cc_final: 0.6515 (t0) REVERT: 5 111 LYS cc_start: 0.8287 (tppt) cc_final: 0.8062 (ttmt) REVERT: 6 55 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8162 (tm-30) REVERT: 6 57 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7549 (mmt180) REVERT: L 76 LYS cc_start: 0.8752 (tppp) cc_final: 0.8469 (tptt) REVERT: J 226 ARG cc_start: 0.6113 (ptp-170) cc_final: 0.5474 (ptt90) REVERT: J 291 GLN cc_start: 0.5284 (tp40) cc_final: 0.4945 (tm130) REVERT: J 337 MET cc_start: 0.4366 (tpp) cc_final: 0.4072 (tpp) REVERT: J 360 ASP cc_start: 0.4132 (OUTLIER) cc_final: 0.3693 (t70) REVERT: J 379 TRP cc_start: 0.5565 (m100) cc_final: 0.5210 (m100) REVERT: J 386 GLU cc_start: 0.4461 (mm-30) cc_final: 0.3362 (pp20) REVERT: R 142 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: R 230 MET cc_start: 0.7049 (tpp) cc_final: 0.6811 (mmm) REVERT: R 325 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7801 (mtm110) REVERT: X 262 TYR cc_start: 0.7829 (m-80) cc_final: 0.7212 (m-80) REVERT: X 264 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.5121 (p90) REVERT: 9 209 GLN cc_start: 0.8011 (tt0) cc_final: 0.7784 (tm-30) REVERT: z 86 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: x 1028 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8302 (mmtp) REVERT: M 147 LYS cc_start: 0.8103 (mtmm) cc_final: 0.7851 (mtmm) REVERT: V 449 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7507 (mm-30) REVERT: V 530 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8452 (tmtt) REVERT: 8 19 ASN cc_start: 0.8573 (t0) cc_final: 0.8148 (t0) REVERT: K 22 THR cc_start: 0.7622 (p) cc_final: 0.7328 (t) REVERT: K 112 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5903 (tt0) REVERT: K 149 SER cc_start: 0.4881 (OUTLIER) cc_final: 0.4648 (p) outliers start: 316 outliers final: 111 residues processed: 1627 average time/residue: 1.7773 time to fit residues: 3963.6691 Evaluate side-chains 1372 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1240 time to evaluate : 8.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1649 LYS Chi-restraints excluded: chain A residue 1655 THR Chi-restraints excluded: chain A residue 1762 TYR Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1897 LEU Chi-restraints excluded: chain A residue 1921 ASP Chi-restraints excluded: chain A residue 2073 TRP Chi-restraints excluded: chain A residue 2074 ARG Chi-restraints excluded: chain A residue 2087 THR Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2303 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 191 ASP Chi-restraints excluded: chain v residue 216 GLU Chi-restraints excluded: chain 1 residue 414 VAL Chi-restraints excluded: chain 1 residue 479 LEU Chi-restraints excluded: chain 1 residue 494 GLU Chi-restraints excluded: chain 1 residue 563 LEU Chi-restraints excluded: chain 1 residue 564 ASP Chi-restraints excluded: chain 1 residue 883 ASP Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1058 ILE Chi-restraints excluded: chain 1 residue 1127 THR Chi-restraints excluded: chain 1 residue 1128 VAL Chi-restraints excluded: chain 1 residue 1226 VAL Chi-restraints excluded: chain 1 residue 1239 VAL Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 577 LYS Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 2 residue 698 THR Chi-restraints excluded: chain 3 residue 131 MET Chi-restraints excluded: chain 3 residue 138 GLN Chi-restraints excluded: chain 3 residue 159 GLU Chi-restraints excluded: chain 3 residue 322 VAL Chi-restraints excluded: chain 3 residue 425 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 590 MET Chi-restraints excluded: chain 3 residue 605 LEU Chi-restraints excluded: chain 3 residue 610 VAL Chi-restraints excluded: chain 3 residue 614 VAL Chi-restraints excluded: chain 3 residue 691 THR Chi-restraints excluded: chain 3 residue 699 VAL Chi-restraints excluded: chain 3 residue 722 SER Chi-restraints excluded: chain 3 residue 773 VAL Chi-restraints excluded: chain 3 residue 909 VAL Chi-restraints excluded: chain 3 residue 943 THR Chi-restraints excluded: chain 3 residue 1007 GLU Chi-restraints excluded: chain 3 residue 1064 ASP Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 5 residue 31 THR Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 74 CYS Chi-restraints excluded: chain 5 residue 85 ARG Chi-restraints excluded: chain 6 residue 57 ARG Chi-restraints excluded: chain 6 residue 95 LYS Chi-restraints excluded: chain 6 residue 96 THR Chi-restraints excluded: chain L residue 98 GLU Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 360 ASP Chi-restraints excluded: chain J residue 365 ILE Chi-restraints excluded: chain R residue 142 GLU Chi-restraints excluded: chain R residue 237 MET Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain R residue 303 GLU Chi-restraints excluded: chain R residue 384 GLU Chi-restraints excluded: chain R residue 418 MET Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain T residue 384 HIS Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain X residue 257 LYS Chi-restraints excluded: chain X residue 264 PHE Chi-restraints excluded: chain Y residue 54 CYS Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 85 GLU Chi-restraints excluded: chain Y residue 112 VAL Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 82 LYS Chi-restraints excluded: chain z residue 86 GLU Chi-restraints excluded: chain z residue 148 ASP Chi-restraints excluded: chain z residue 172 ASP Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain U residue 20 GLN Chi-restraints excluded: chain V residue 449 GLU Chi-restraints excluded: chain V residue 467 LEU Chi-restraints excluded: chain V residue 530 LYS Chi-restraints excluded: chain V residue 536 ILE Chi-restraints excluded: chain V residue 607 THR Chi-restraints excluded: chain I residue 31 ARG Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 149 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1339 random chunks: chunk 675 optimal weight: 0.1980 chunk 377 optimal weight: 0.0040 chunk 1012 optimal weight: 5.9990 chunk 827 optimal weight: 4.9990 chunk 335 optimal weight: 9.9990 chunk 1218 optimal weight: 0.9990 chunk 1315 optimal weight: 7.9990 chunk 1084 optimal weight: 3.9990 chunk 1208 optimal weight: 6.9990 chunk 415 optimal weight: 10.0000 chunk 977 optimal weight: 6.9990 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 579 GLN C 163 GLN C 437 HIS C 706 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 148 ASN 1 518 GLN 2 695 GLN ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 670 GLN 5 25 ASN 5 72 ASN 5 76 HIS 5 84 ASN J 250 GLN ** J 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 394 HIS R 279 HIS R 453 ASN T 446 ASN ** X 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 591 ASN ** 9 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 ASN ** V 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 485 GLN 8 74 GLN ** 8 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 102187 Z= 0.269 Angle : 0.557 10.393 140388 Z= 0.297 Chirality : 0.043 0.250 16414 Planarity : 0.004 0.056 17507 Dihedral : 13.064 179.045 18566 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.34 % Favored : 97.63 % Rotamer: Outliers : 4.23 % Allowed : 15.58 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.07), residues: 13107 helix: 0.87 (0.07), residues: 5069 sheet: 0.18 (0.11), residues: 2096 loop : -0.45 (0.08), residues: 5942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 293 HIS 0.023 0.001 HIS R 279 PHE 0.027 0.002 PHE Y 56 TYR 0.028 0.002 TYR E 194 ARG 0.010 0.001 ARG Z 565 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1298 time to evaluate : 9.244 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: A 61 MET cc_start: 0.8162 (mtp) cc_final: 0.7779 (mtp) REVERT: A 147 MET cc_start: 0.8501 (mmp) cc_final: 0.7994 (mmp) REVERT: A 426 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8882 (mt) REVERT: A 480 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8062 (tttm) REVERT: A 591 MET cc_start: 0.8619 (ttm) cc_final: 0.8176 (ttm) REVERT: A 1370 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8082 (mmp-170) REVERT: A 2284 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6565 (ptp) REVERT: A 2303 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5619 (pp20) REVERT: C 329 ASP cc_start: 0.7618 (t0) cc_final: 0.7409 (t0) REVERT: C 726 LEU cc_start: 0.7729 (tp) cc_final: 0.7375 (tt) REVERT: C 822 MET cc_start: 0.8083 (mmm) cc_final: 0.7848 (mmm) REVERT: D 102 TYR cc_start: 0.4822 (t80) cc_final: 0.4019 (m-10) REVERT: E 176 VAL cc_start: 0.6066 (t) cc_final: 0.5661 (p) REVERT: E 315 THR cc_start: 0.3783 (m) cc_final: 0.3405 (p) REVERT: v 1 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7318 (ttm) REVERT: v 73 GLN cc_start: 0.6813 (pp30) cc_final: 0.6514 (pp30) REVERT: v 188 ARG cc_start: 0.7016 (tmm-80) cc_final: 0.6240 (mtm110) REVERT: 1 118 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7036 (tp30) REVERT: 1 124 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7150 (ttp-110) REVERT: 1 164 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7420 (tm-30) REVERT: 1 395 ARG cc_start: 0.7916 (ptp90) cc_final: 0.7569 (ptp90) REVERT: 1 457 ASN cc_start: 0.8123 (p0) cc_final: 0.7824 (t0) REVERT: 1 688 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: 1 1053 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8216 (mtt180) REVERT: 1 1058 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8324 (mt) REVERT: 1 1239 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8876 (t) REVERT: 2 577 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8546 (mtpt) REVERT: 2 695 GLN cc_start: 0.8733 (tt0) cc_final: 0.8513 (tt0) REVERT: 3 1 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7746 (ttt) REVERT: 3 131 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.6791 (tmt) REVERT: 3 363 HIS cc_start: 0.7608 (OUTLIER) cc_final: 0.7000 (m90) REVERT: 3 471 ASP cc_start: 0.6826 (t70) cc_final: 0.6601 (t70) REVERT: 5 30 ILE cc_start: 0.8130 (tt) cc_final: 0.7734 (pt) REVERT: 5 46 ARG cc_start: 0.8279 (tpt90) cc_final: 0.7992 (mmm160) REVERT: 5 80 PHE cc_start: 0.7845 (t80) cc_final: 0.7483 (t80) REVERT: 5 84 ASN cc_start: 0.7767 (t0) cc_final: 0.6754 (t0) REVERT: 5 116 LYS cc_start: 0.8305 (ttmp) cc_final: 0.8040 (tttt) REVERT: 6 55 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8181 (tm-30) REVERT: J 226 ARG cc_start: 0.6014 (ptp-170) cc_final: 0.5508 (ptt90) REVERT: J 291 GLN cc_start: 0.5159 (tp40) cc_final: 0.4855 (tm130) REVERT: J 337 MET cc_start: 0.4280 (tpp) cc_final: 0.4051 (tpp) REVERT: J 375 ASP cc_start: 0.3185 (p0) cc_final: 0.2910 (p0) REVERT: J 381 LYS cc_start: 0.5772 (tppp) cc_final: 0.5558 (tppp) REVERT: J 386 GLU cc_start: 0.4231 (mm-30) cc_final: 0.3069 (pp20) REVERT: R 142 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: R 279 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7585 (m90) REVERT: R 325 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7708 (mtm110) REVERT: X 262 TYR cc_start: 0.7870 (m-80) cc_final: 0.7356 (m-80) REVERT: X 264 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.5566 (p90) REVERT: X 308 TYR cc_start: 0.8728 (m-80) cc_final: 0.8192 (m-80) REVERT: X 330 ASP cc_start: 0.7725 (t70) cc_final: 0.7407 (t70) REVERT: Z 517 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: 9 86 ARG cc_start: 0.6135 (OUTLIER) cc_final: 0.5547 (mmp-170) REVERT: 9 209 GLN cc_start: 0.8011 (tt0) cc_final: 0.7797 (tm-30) REVERT: U 1 MET cc_start: 0.7941 (ttp) cc_final: 0.7682 (mtm) REVERT: V 619 ASP cc_start: 0.7594 (p0) cc_final: 0.7370 (p0) REVERT: K 112 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5733 (tt0) REVERT: K 149 SER cc_start: 0.3744 (t) cc_final: 0.3395 (p) outliers start: 333 outliers final: 154 residues processed: 1509 average time/residue: 1.7640 time to fit residues: 3662.5673 Evaluate side-chains 1373 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1197 time to evaluate : 8.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1562 MET Chi-restraints excluded: chain A residue 1655 THR Chi-restraints excluded: chain A residue 1757 GLU Chi-restraints excluded: chain A residue 1762 TYR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1870 ASP Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 2073 TRP Chi-restraints excluded: chain A residue 2074 ARG Chi-restraints excluded: chain A residue 2139 VAL Chi-restraints excluded: chain A residue 2147 MET Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2273 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2303 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain v residue 1 MET Chi-restraints excluded: chain v residue 14 ASN Chi-restraints excluded: chain v residue 36 MET Chi-restraints excluded: chain 1 residue 118 GLU Chi-restraints excluded: chain 1 residue 124 ARG Chi-restraints excluded: chain 1 residue 166 ARG Chi-restraints excluded: chain 1 residue 479 LEU Chi-restraints excluded: chain 1 residue 482 VAL Chi-restraints excluded: chain 1 residue 563 LEU Chi-restraints excluded: chain 1 residue 688 GLU Chi-restraints excluded: chain 1 residue 690 ILE Chi-restraints excluded: chain 1 residue 883 ASP Chi-restraints excluded: chain 1 residue 936 VAL Chi-restraints excluded: chain 1 residue 1053 ARG Chi-restraints excluded: chain 1 residue 1058 ILE Chi-restraints excluded: chain 1 residue 1127 THR Chi-restraints excluded: chain 1 residue 1128 VAL Chi-restraints excluded: chain 1 residue 1226 VAL Chi-restraints excluded: chain 1 residue 1228 GLN Chi-restraints excluded: chain 1 residue 1239 VAL Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 577 LYS Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 2 residue 698 THR Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 131 MET Chi-restraints excluded: chain 3 residue 159 GLU Chi-restraints excluded: chain 3 residue 322 VAL Chi-restraints excluded: chain 3 residue 363 HIS Chi-restraints excluded: chain 3 residue 425 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 605 LEU Chi-restraints excluded: chain 3 residue 610 VAL Chi-restraints excluded: chain 3 residue 614 VAL Chi-restraints excluded: chain 3 residue 691 THR Chi-restraints excluded: chain 3 residue 699 VAL Chi-restraints excluded: chain 3 residue 722 SER Chi-restraints excluded: chain 3 residue 743 SER Chi-restraints excluded: chain 3 residue 770 LEU Chi-restraints excluded: chain 3 residue 909 VAL Chi-restraints excluded: chain 3 residue 943 THR Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1064 ASP Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 5 residue 31 THR Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 74 CYS Chi-restraints excluded: chain 5 residue 85 ARG Chi-restraints excluded: chain 5 residue 113 LEU Chi-restraints excluded: chain 6 residue 95 LYS Chi-restraints excluded: chain 7 residue 44 MET Chi-restraints excluded: chain 7 residue 71 LYS Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 346 TRP Chi-restraints excluded: chain R residue 142 GLU Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain R residue 303 GLU Chi-restraints excluded: chain R residue 384 GLU Chi-restraints excluded: chain R residue 418 MET Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain T residue 216 ASN Chi-restraints excluded: chain T residue 288 LEU Chi-restraints excluded: chain T residue 384 HIS Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain X residue 225 SER Chi-restraints excluded: chain X residue 254 ILE Chi-restraints excluded: chain X residue 257 LYS Chi-restraints excluded: chain X residue 264 PHE Chi-restraints excluded: chain X residue 294 ILE Chi-restraints excluded: chain X residue 364 SER Chi-restraints excluded: chain Y residue 46 GLU Chi-restraints excluded: chain Y residue 54 CYS Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 85 GLU Chi-restraints excluded: chain Z residue 517 GLU Chi-restraints excluded: chain Z residue 610 LEU Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 82 LYS Chi-restraints excluded: chain 9 residue 86 ARG Chi-restraints excluded: chain z residue 27 GLU Chi-restraints excluded: chain z residue 86 GLU Chi-restraints excluded: chain z residue 89 SER Chi-restraints excluded: chain z residue 145 SER Chi-restraints excluded: chain z residue 148 ASP Chi-restraints excluded: chain z residue 156 HIS Chi-restraints excluded: chain z residue 172 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain V residue 467 LEU Chi-restraints excluded: chain V residue 519 LYS Chi-restraints excluded: chain V residue 536 ILE Chi-restraints excluded: chain V residue 555 LEU Chi-restraints excluded: chain V residue 563 SER Chi-restraints excluded: chain V residue 598 LYS Chi-restraints excluded: chain V residue 605 ASP Chi-restraints excluded: chain 8 residue 45 LEU Chi-restraints excluded: chain 8 residue 82 SER Chi-restraints excluded: chain 0 residue 52 LYS Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1339 random chunks: chunk 1203 optimal weight: 40.0000 chunk 915 optimal weight: 8.9990 chunk 632 optimal weight: 40.0000 chunk 134 optimal weight: 6.9990 chunk 581 optimal weight: 50.0000 chunk 817 optimal weight: 4.9990 chunk 1222 optimal weight: 4.9990 chunk 1294 optimal weight: 1.9990 chunk 638 optimal weight: 50.0000 chunk 1158 optimal weight: 4.9990 chunk 348 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN A 675 GLN A 775 ASN A1023 ASN A1282 GLN A2255 HIS C 297 ASN D 127 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 148 ASN ** 1 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 829 ASN 1 901 GLN 11134 ASN 11194 HIS ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 440 HIS 3 631 GLN 3 776 GLN 3 916 ASN 31192 ASN 5 25 ASN 5 72 ASN 5 76 HIS 5 93 ASN L 13 ASN J 250 GLN ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 279 HIS R 453 ASN T 344 GLN X 286 HIS Y 2 ASN ** V 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 74 GLN ** 8 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 GLN ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 102187 Z= 0.533 Angle : 0.689 12.449 140388 Z= 0.363 Chirality : 0.050 0.338 16414 Planarity : 0.006 0.077 17507 Dihedral : 13.177 178.131 18538 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.88 % Favored : 97.09 % Rotamer: Outliers : 5.31 % Allowed : 16.16 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.07), residues: 13107 helix: 0.67 (0.07), residues: 5065 sheet: -0.01 (0.11), residues: 2156 loop : -0.60 (0.08), residues: 5886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP J 313 HIS 0.029 0.002 HIS R 279 PHE 0.050 0.003 PHE C 228 TYR 0.038 0.003 TYR C 614 ARG 0.012 0.001 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1691 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 418 poor density : 1273 time to evaluate : 8.644 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: A 61 MET cc_start: 0.8216 (mtp) cc_final: 0.7816 (mtp) REVERT: A 71 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7968 (tpp-160) REVERT: A 420 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7366 (mtp85) REVERT: A 591 MET cc_start: 0.8661 (ttm) cc_final: 0.8281 (ttm) REVERT: A 1370 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8208 (mmp-170) REVERT: A 1533 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8097 (ttp-170) REVERT: A 1548 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.6237 (t80) REVERT: A 2112 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7373 (mppt) REVERT: A 2284 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6475 (ptp) REVERT: A 2303 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6075 (pp20) REVERT: C 329 ASP cc_start: 0.7596 (t0) cc_final: 0.7348 (t0) REVERT: C 733 TRP cc_start: 0.7930 (m-10) cc_final: 0.7598 (m100) REVERT: C 802 HIS cc_start: 0.7206 (t70) cc_final: 0.6997 (t70) REVERT: D 102 TYR cc_start: 0.4875 (t80) cc_final: 0.4108 (m-10) REVERT: D 154 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.5444 (ttt-90) REVERT: E 60 MET cc_start: 0.2083 (ptm) cc_final: 0.1536 (tmm) REVERT: E 74 PHE cc_start: 0.3876 (OUTLIER) cc_final: 0.3419 (t80) REVERT: E 143 ARG cc_start: 0.5993 (tmm-80) cc_final: 0.5768 (mtp180) REVERT: E 176 VAL cc_start: 0.5946 (t) cc_final: 0.5582 (p) REVERT: E 217 ILE cc_start: 0.3844 (OUTLIER) cc_final: 0.3485 (tt) REVERT: E 315 THR cc_start: 0.3813 (m) cc_final: 0.3418 (p) REVERT: v 73 GLN cc_start: 0.7139 (pp30) cc_final: 0.6578 (pp30) REVERT: v 188 ARG cc_start: 0.6645 (tmm-80) cc_final: 0.6255 (mtm110) REVERT: 1 124 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7046 (ttp-110) REVERT: 1 126 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8093 (mtm) REVERT: 1 164 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7441 (tm-30) REVERT: 1 457 ASN cc_start: 0.8208 (p0) cc_final: 0.7884 (t0) REVERT: 1 688 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: 1 942 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8443 (p0) REVERT: 1 1053 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8273 (mtt180) REVERT: 1 1227 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8841 (tp) REVERT: 2 549 MET cc_start: 0.7627 (tpt) cc_final: 0.7309 (tpt) REVERT: 3 331 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: 3 363 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7159 (m90) REVERT: 3 510 LEU cc_start: 0.7268 (pt) cc_final: 0.7052 (pp) REVERT: 3 620 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: 3 630 MET cc_start: 0.7017 (tpt) cc_final: 0.6753 (tpt) REVERT: 3 631 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7177 (pt0) REVERT: 3 821 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: 5 30 ILE cc_start: 0.8115 (tt) cc_final: 0.7322 (pt) REVERT: 5 80 PHE cc_start: 0.7844 (t80) cc_final: 0.7238 (t80) REVERT: 5 84 ASN cc_start: 0.7607 (t0) cc_final: 0.7321 (t0) REVERT: 6 57 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7487 (mmt180) REVERT: J 226 ARG cc_start: 0.5995 (ptp-170) cc_final: 0.5749 (ptt90) REVERT: J 291 GLN cc_start: 0.5604 (tp40) cc_final: 0.4857 (tm130) REVERT: J 337 MET cc_start: 0.4682 (tpp) cc_final: 0.4322 (tpp) REVERT: J 360 ASP cc_start: 0.5049 (t70) cc_final: 0.4799 (t70) REVERT: J 379 TRP cc_start: 0.5852 (m100) cc_final: 0.5587 (m100) REVERT: J 386 GLU cc_start: 0.4394 (mm-30) cc_final: 0.3362 (pp20) REVERT: R 142 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: R 230 MET cc_start: 0.7919 (mmm) cc_final: 0.7673 (mmm) REVERT: R 279 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.7165 (m90) REVERT: R 325 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7719 (mtm110) REVERT: T 360 VAL cc_start: 0.8605 (p) cc_final: 0.8346 (t) REVERT: X 262 TYR cc_start: 0.8018 (m-80) cc_final: 0.7644 (m-80) REVERT: X 264 PHE cc_start: 0.6624 (OUTLIER) cc_final: 0.5795 (p90) REVERT: X 296 HIS cc_start: 0.4512 (m-70) cc_final: 0.4299 (m-70) REVERT: X 301 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.4766 (mptt) REVERT: X 366 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6189 (mp0) REVERT: Z 508 GLN cc_start: 0.8159 (tp40) cc_final: 0.7957 (tp40) REVERT: Z 526 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8848 (pp) REVERT: Z 556 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5879 (pm20) REVERT: Z 574 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7874 (m110) REVERT: Z 609 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: 9 3 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.6844 (ptmm) REVERT: 9 35 ARG cc_start: 0.5458 (OUTLIER) cc_final: 0.2935 (tpp-160) REVERT: 9 86 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5682 (mmp-170) REVERT: V 467 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8541 (pt) REVERT: V 492 MET cc_start: 0.8318 (tpt) cc_final: 0.7990 (tpp) REVERT: 0 35 ASN cc_start: 0.8864 (m-40) cc_final: 0.8561 (t0) REVERT: K 112 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5824 (tt0) REVERT: K 149 SER cc_start: 0.3501 (OUTLIER) cc_final: 0.3160 (p) outliers start: 418 outliers final: 205 residues processed: 1550 average time/residue: 1.8080 time to fit residues: 3885.7858 Evaluate side-chains 1428 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1185 time to evaluate : 8.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1459 ARG Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1533 ARG Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1568 THR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1655 THR Chi-restraints excluded: chain A residue 1757 GLU Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1875 HIS Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1897 LEU Chi-restraints excluded: chain A residue 1993 LYS Chi-restraints excluded: chain A residue 2073 TRP Chi-restraints excluded: chain A residue 2074 ARG Chi-restraints excluded: chain A residue 2112 LYS Chi-restraints excluded: chain A residue 2139 VAL Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2303 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 683 ASN Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 766 ILE Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain v residue 14 ASN Chi-restraints excluded: chain v residue 36 MET Chi-restraints excluded: chain 1 residue 124 ARG Chi-restraints excluded: chain 1 residue 126 MET Chi-restraints excluded: chain 1 residue 482 VAL Chi-restraints excluded: chain 1 residue 543 THR Chi-restraints excluded: chain 1 residue 655 LYS Chi-restraints excluded: chain 1 residue 680 LEU Chi-restraints excluded: chain 1 residue 688 GLU Chi-restraints excluded: chain 1 residue 690 ILE Chi-restraints excluded: chain 1 residue 733 LYS Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 747 LEU Chi-restraints excluded: chain 1 residue 936 VAL Chi-restraints excluded: chain 1 residue 942 ASN Chi-restraints excluded: chain 1 residue 1044 ASP Chi-restraints excluded: chain 1 residue 1053 ARG Chi-restraints excluded: chain 1 residue 1128 VAL Chi-restraints excluded: chain 1 residue 1226 VAL Chi-restraints excluded: chain 1 residue 1227 ILE Chi-restraints excluded: chain 1 residue 1228 GLN Chi-restraints excluded: chain 1 residue 1239 VAL Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 577 LYS Chi-restraints excluded: chain 2 residue 580 THR Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 2 residue 590 LEU Chi-restraints excluded: chain 2 residue 698 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 3 residue 131 MET Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 320 ASP Chi-restraints excluded: chain 3 residue 322 VAL Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 363 HIS Chi-restraints excluded: chain 3 residue 425 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 3 residue 605 LEU Chi-restraints excluded: chain 3 residue 610 VAL Chi-restraints excluded: chain 3 residue 614 VAL Chi-restraints excluded: chain 3 residue 620 ASP Chi-restraints excluded: chain 3 residue 631 GLN Chi-restraints excluded: chain 3 residue 662 PHE Chi-restraints excluded: chain 3 residue 666 ASN Chi-restraints excluded: chain 3 residue 691 THR Chi-restraints excluded: chain 3 residue 697 ARG Chi-restraints excluded: chain 3 residue 699 VAL Chi-restraints excluded: chain 3 residue 722 SER Chi-restraints excluded: chain 3 residue 743 SER Chi-restraints excluded: chain 3 residue 770 LEU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 849 GLU Chi-restraints excluded: chain 3 residue 859 ASN Chi-restraints excluded: chain 3 residue 909 VAL Chi-restraints excluded: chain 3 residue 943 THR Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1028 THR Chi-restraints excluded: chain 3 residue 1052 ASN Chi-restraints excluded: chain 3 residue 1064 ASP Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 5 residue 31 THR Chi-restraints excluded: chain 5 residue 48 ILE Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 63 VAL Chi-restraints excluded: chain 5 residue 74 CYS Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 6 residue 57 ARG Chi-restraints excluded: chain 7 residue 44 MET Chi-restraints excluded: chain 7 residue 71 LYS Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 98 GLU Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 304 THR Chi-restraints excluded: chain J residue 346 TRP Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain R residue 142 GLU Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain R residue 303 GLU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 434 ASP Chi-restraints excluded: chain T residue 216 ASN Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 288 LEU Chi-restraints excluded: chain T residue 384 HIS Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain X residue 225 SER Chi-restraints excluded: chain X residue 254 ILE Chi-restraints excluded: chain X residue 257 LYS Chi-restraints excluded: chain X residue 264 PHE Chi-restraints excluded: chain X residue 301 LYS Chi-restraints excluded: chain X residue 329 ILE Chi-restraints excluded: chain X residue 363 SER Chi-restraints excluded: chain X residue 364 SER Chi-restraints excluded: chain X residue 366 GLU Chi-restraints excluded: chain Y residue 54 CYS Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 80 CYS Chi-restraints excluded: chain Y residue 85 GLU Chi-restraints excluded: chain Z residue 526 ILE Chi-restraints excluded: chain Z residue 556 GLU Chi-restraints excluded: chain Z residue 574 ASN Chi-restraints excluded: chain Z residue 609 GLU Chi-restraints excluded: chain Z residue 610 LEU Chi-restraints excluded: chain 9 residue 3 LYS Chi-restraints excluded: chain 9 residue 35 ARG Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 82 LYS Chi-restraints excluded: chain 9 residue 86 ARG Chi-restraints excluded: chain z residue 27 GLU Chi-restraints excluded: chain z residue 86 GLU Chi-restraints excluded: chain z residue 89 SER Chi-restraints excluded: chain z residue 145 SER Chi-restraints excluded: chain z residue 148 ASP Chi-restraints excluded: chain z residue 156 HIS Chi-restraints excluded: chain z residue 172 ASP Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain V residue 467 LEU Chi-restraints excluded: chain V residue 519 LYS Chi-restraints excluded: chain V residue 536 ILE Chi-restraints excluded: chain V residue 555 LEU Chi-restraints excluded: chain V residue 563 SER Chi-restraints excluded: chain V residue 574 THR Chi-restraints excluded: chain V residue 605 ASP Chi-restraints excluded: chain 8 residue 82 SER Chi-restraints excluded: chain 8 residue 85 MET Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 0 residue 65 VAL Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 126 SER Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 149 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1339 random chunks: chunk 1077 optimal weight: 0.7980 chunk 734 optimal weight: 0.3980 chunk 18 optimal weight: 0.0370 chunk 963 optimal weight: 20.0000 chunk 534 optimal weight: 50.0000 chunk 1104 optimal weight: 1.9990 chunk 894 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 660 optimal weight: 0.7980 chunk 1161 optimal weight: 40.0000 chunk 326 optimal weight: 9.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN A1282 GLN C 297 ASN C 807 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 12 GLN 1 518 GLN 1 829 ASN 2 695 GLN ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 264 GLN 3 575 ASN 3 916 ASN 31147 HIS 31192 ASN 5 72 ASN 5 76 HIS 5 93 ASN L 13 ASN J 250 GLN J 378 ASN R 279 HIS R 453 ASN T 344 GLN Z 507 GLN V 600 ASN 8 74 GLN ** 8 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 GLN ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 102187 Z= 0.157 Angle : 0.514 11.291 140388 Z= 0.271 Chirality : 0.041 0.231 16414 Planarity : 0.004 0.067 17507 Dihedral : 12.884 177.246 18518 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.99 % Rotamer: Outliers : 3.37 % Allowed : 18.77 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.07), residues: 13107 helix: 1.16 (0.07), residues: 5081 sheet: 0.12 (0.11), residues: 2116 loop : -0.41 (0.08), residues: 5910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 750 HIS 0.012 0.001 HIS R 279 PHE 0.024 0.001 PHE C 717 TYR 0.025 0.001 TYR A 351 ARG 0.012 0.000 ARG 9 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1554 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1289 time to evaluate : 9.274 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: A 61 MET cc_start: 0.8093 (mtp) cc_final: 0.7641 (mtp) REVERT: A 1370 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7988 (mmp-170) REVERT: A 1394 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: A 1548 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.6240 (t80) REVERT: A 2223 CYS cc_start: 0.3609 (OUTLIER) cc_final: 0.3052 (t) REVERT: A 2284 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6544 (ptt) REVERT: A 2303 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6089 (pp20) REVERT: A 2306 HIS cc_start: 0.7064 (t-90) cc_final: 0.6844 (t-170) REVERT: A 2331 GLU cc_start: 0.3400 (OUTLIER) cc_final: 0.3194 (pm20) REVERT: C 329 ASP cc_start: 0.7569 (t0) cc_final: 0.7341 (t0) REVERT: C 673 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6954 (mmtm) REVERT: C 733 TRP cc_start: 0.7778 (m-10) cc_final: 0.7564 (m100) REVERT: C 822 MET cc_start: 0.8093 (mmm) cc_final: 0.7861 (mmm) REVERT: D 102 TYR cc_start: 0.4800 (t80) cc_final: 0.3733 (m-10) REVERT: D 154 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.5348 (ttt-90) REVERT: E 60 MET cc_start: 0.2095 (ptm) cc_final: 0.1877 (tmm) REVERT: E 176 VAL cc_start: 0.6059 (t) cc_final: 0.5666 (p) REVERT: E 272 ARG cc_start: 0.1120 (OUTLIER) cc_final: -0.0059 (mtm-85) REVERT: E 315 THR cc_start: 0.3554 (m) cc_final: 0.3172 (p) REVERT: v 14 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8338 (m-40) REVERT: v 50 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8295 (mtt90) REVERT: v 188 ARG cc_start: 0.6596 (tmm-80) cc_final: 0.6287 (mtm110) REVERT: 1 118 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7148 (tp30) REVERT: 1 164 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7418 (tm-30) REVERT: 1 457 ASN cc_start: 0.8137 (p0) cc_final: 0.7833 (t0) REVERT: 1 547 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: 1 675 MET cc_start: 0.8252 (mmm) cc_final: 0.7983 (mtt) REVERT: 1 688 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: 1 1239 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8909 (t) REVERT: 1 1291 ASP cc_start: 0.7236 (t0) cc_final: 0.6754 (t0) REVERT: 2 484 ASP cc_start: 0.8182 (t70) cc_final: 0.7894 (t70) REVERT: 2 695 GLN cc_start: 0.8689 (tt0) cc_final: 0.8407 (tt0) REVERT: 3 131 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.6677 (tmt) REVERT: 3 331 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: 3 620 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: 3 705 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6884 (tpp-160) REVERT: 5 69 ASP cc_start: 0.8043 (p0) cc_final: 0.7586 (p0) REVERT: 5 72 ASN cc_start: 0.8360 (t0) cc_final: 0.7987 (m110) REVERT: 5 80 PHE cc_start: 0.7888 (t80) cc_final: 0.7586 (t80) REVERT: 5 84 ASN cc_start: 0.7652 (t0) cc_final: 0.7439 (t0) REVERT: 6 55 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8024 (tm-30) REVERT: 6 57 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7275 (mmt180) REVERT: J 226 ARG cc_start: 0.5965 (ptp-170) cc_final: 0.5601 (ptt90) REVERT: J 285 MET cc_start: 0.5849 (tmm) cc_final: 0.5344 (tpt) REVERT: J 291 GLN cc_start: 0.5525 (tp40) cc_final: 0.4792 (tm130) REVERT: J 337 MET cc_start: 0.4495 (tpp) cc_final: 0.3929 (tpp) REVERT: J 386 GLU cc_start: 0.4109 (mm-30) cc_final: 0.3184 (pp20) REVERT: P 218 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: R 230 MET cc_start: 0.7659 (mmm) cc_final: 0.7389 (mmm) REVERT: R 238 THR cc_start: 0.8810 (p) cc_final: 0.8583 (t) REVERT: R 279 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7355 (m90) REVERT: T 492 ASP cc_start: 0.7460 (t0) cc_final: 0.7202 (t0) REVERT: X 258 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6230 (mtt90) REVERT: X 262 TYR cc_start: 0.7928 (m-80) cc_final: 0.7620 (m-80) REVERT: X 366 GLU cc_start: 0.6511 (mm-30) cc_final: 0.6093 (mp0) REVERT: Z 526 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8724 (pp) REVERT: Z 565 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7733 (mtp180) REVERT: 9 86 ARG cc_start: 0.6057 (OUTLIER) cc_final: 0.5409 (mmp-170) REVERT: 9 192 ASP cc_start: 0.7085 (t0) cc_final: 0.6850 (t70) REVERT: 9 209 GLN cc_start: 0.8043 (tt0) cc_final: 0.7827 (tm-30) REVERT: 9 210 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7833 (tm-30) REVERT: M 163 MET cc_start: 0.8144 (ptm) cc_final: 0.7724 (mtp) REVERT: V 492 MET cc_start: 0.8315 (tpt) cc_final: 0.8063 (tpp) REVERT: V 573 GLU cc_start: 0.7756 (mp0) cc_final: 0.7542 (mp0) REVERT: V 619 ASP cc_start: 0.7648 (p0) cc_final: 0.7348 (p0) REVERT: K 110 PRO cc_start: 0.4494 (Cg_endo) cc_final: 0.4250 (Cg_exo) REVERT: K 149 SER cc_start: 0.3168 (t) cc_final: 0.2820 (p) REVERT: K 153 SER cc_start: 0.6599 (t) cc_final: 0.6375 (p) outliers start: 265 outliers final: 118 residues processed: 1456 average time/residue: 1.8052 time to fit residues: 3626.5680 Evaluate side-chains 1356 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1212 time to evaluate : 8.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 858 GLN Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1370 ARG Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1394 GLN Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1655 THR Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 2073 TRP Chi-restraints excluded: chain A residue 2074 ARG Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2223 CYS Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2303 GLU Chi-restraints excluded: chain A residue 2331 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 683 ASN Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain v residue 14 ASN Chi-restraints excluded: chain v residue 50 ARG Chi-restraints excluded: chain 1 residue 118 GLU Chi-restraints excluded: chain 1 residue 166 ARG Chi-restraints excluded: chain 1 residue 172 LEU Chi-restraints excluded: chain 1 residue 547 GLN Chi-restraints excluded: chain 1 residue 688 GLU Chi-restraints excluded: chain 1 residue 690 ILE Chi-restraints excluded: chain 1 residue 733 LYS Chi-restraints excluded: chain 1 residue 883 ASP Chi-restraints excluded: chain 1 residue 936 VAL Chi-restraints excluded: chain 1 residue 1127 THR Chi-restraints excluded: chain 1 residue 1128 VAL Chi-restraints excluded: chain 1 residue 1226 VAL Chi-restraints excluded: chain 1 residue 1239 VAL Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 3 residue 131 MET Chi-restraints excluded: chain 3 residue 171 VAL Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 322 VAL Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 425 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 587 VAL Chi-restraints excluded: chain 3 residue 605 LEU Chi-restraints excluded: chain 3 residue 610 VAL Chi-restraints excluded: chain 3 residue 620 ASP Chi-restraints excluded: chain 3 residue 663 LEU Chi-restraints excluded: chain 3 residue 691 THR Chi-restraints excluded: chain 3 residue 697 ARG Chi-restraints excluded: chain 3 residue 699 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 722 SER Chi-restraints excluded: chain 3 residue 743 SER Chi-restraints excluded: chain 3 residue 849 GLU Chi-restraints excluded: chain 3 residue 943 THR Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1064 ASP Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 5 residue 31 THR Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 74 CYS Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 101 MET Chi-restraints excluded: chain 6 residue 57 ARG Chi-restraints excluded: chain 6 residue 95 LYS Chi-restraints excluded: chain 7 residue 71 LYS Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 245 TRP Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain P residue 218 GLU Chi-restraints excluded: chain R residue 279 HIS Chi-restraints excluded: chain R residue 303 GLU Chi-restraints excluded: chain R residue 418 MET Chi-restraints excluded: chain T residue 216 ASN Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 384 HIS Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain X residue 254 ILE Chi-restraints excluded: chain X residue 257 LYS Chi-restraints excluded: chain X residue 258 ARG Chi-restraints excluded: chain X residue 264 PHE Chi-restraints excluded: chain X residue 333 SER Chi-restraints excluded: chain X residue 337 THR Chi-restraints excluded: chain Y residue 54 CYS Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 80 CYS Chi-restraints excluded: chain Z residue 526 ILE Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 82 LYS Chi-restraints excluded: chain 9 residue 86 ARG Chi-restraints excluded: chain 9 residue 92 ASN Chi-restraints excluded: chain z residue 27 GLU Chi-restraints excluded: chain z residue 86 GLU Chi-restraints excluded: chain z residue 145 SER Chi-restraints excluded: chain z residue 148 ASP Chi-restraints excluded: chain z residue 156 HIS Chi-restraints excluded: chain z residue 172 ASP Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain V residue 466 SER Chi-restraints excluded: chain V residue 536 ILE Chi-restraints excluded: chain V residue 563 SER Chi-restraints excluded: chain V residue 598 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain K residue 35 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1339 random chunks: chunk 435 optimal weight: 2.9990 chunk 1165 optimal weight: 20.0000 chunk 255 optimal weight: 0.0270 chunk 759 optimal weight: 0.6980 chunk 319 optimal weight: 1.9990 chunk 1295 optimal weight: 0.9990 chunk 1075 optimal weight: 0.7980 chunk 599 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 428 optimal weight: 40.0000 chunk 680 optimal weight: 0.7980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 ASN A1282 GLN C 163 GLN C 807 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 12 GLN ** 1 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 518 GLN 2 541 GLN ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 264 GLN 3 631 GLN 3 844 ASN 31192 ASN 5 76 HIS ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 ASN J 250 GLN ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 453 ASN T 344 GLN Z 507 GLN 9 133 GLN 8 19 ASN 8 74 GLN ** 8 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 ASN ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 161 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 102187 Z= 0.144 Angle : 0.497 11.327 140388 Z= 0.260 Chirality : 0.041 0.205 16414 Planarity : 0.004 0.071 17507 Dihedral : 12.755 177.798 18509 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 3.06 % Allowed : 19.59 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.07), residues: 13107 helix: 1.40 (0.07), residues: 5080 sheet: 0.20 (0.11), residues: 2136 loop : -0.33 (0.08), residues: 5891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP J 313 HIS 0.008 0.001 HIS R 279 PHE 0.026 0.001 PHE J 369 TYR 0.024 0.001 TYR I 47 ARG 0.017 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1516 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1275 time to evaluate : 8.610 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: A 61 MET cc_start: 0.8014 (mtp) cc_final: 0.7621 (mtp) REVERT: A 217 ARG cc_start: 0.8290 (tpp80) cc_final: 0.8022 (tpp-160) REVERT: A 1394 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: A 1548 TYR cc_start: 0.6509 (OUTLIER) cc_final: 0.6202 (t80) REVERT: A 2223 CYS cc_start: 0.3731 (OUTLIER) cc_final: 0.3284 (t) REVERT: A 2284 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6478 (ptp) REVERT: A 2303 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6129 (pp20) REVERT: C 329 ASP cc_start: 0.7558 (t0) cc_final: 0.7328 (t0) REVERT: C 673 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6903 (mmtm) REVERT: C 733 TRP cc_start: 0.7803 (m-10) cc_final: 0.7560 (m100) REVERT: C 822 MET cc_start: 0.8052 (mmm) cc_final: 0.7801 (mmm) REVERT: D 102 TYR cc_start: 0.4624 (t80) cc_final: 0.3655 (m-10) REVERT: D 154 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.5395 (ttt-90) REVERT: E 60 MET cc_start: 0.1850 (ptm) cc_final: 0.1541 (mmt) REVERT: E 176 VAL cc_start: 0.6034 (t) cc_final: 0.5566 (p) REVERT: E 272 ARG cc_start: 0.1168 (OUTLIER) cc_final: -0.0018 (mtm-85) REVERT: E 315 THR cc_start: 0.3781 (m) cc_final: 0.3387 (p) REVERT: v 221 GLU cc_start: 0.6332 (tp30) cc_final: 0.5888 (tp30) REVERT: 1 124 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6940 (ttp-110) REVERT: 1 164 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7326 (tm-30) REVERT: 1 165 GLU cc_start: 0.8174 (tt0) cc_final: 0.7939 (tt0) REVERT: 1 457 ASN cc_start: 0.8123 (p0) cc_final: 0.7809 (t0) REVERT: 1 546 ASP cc_start: 0.7473 (p0) cc_final: 0.7211 (p0) REVERT: 1 547 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: 1 675 MET cc_start: 0.8217 (mmm) cc_final: 0.7926 (mtt) REVERT: 1 688 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: 1 1239 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8933 (t) REVERT: 2 484 ASP cc_start: 0.8144 (t70) cc_final: 0.7821 (t70) REVERT: 2 553 MET cc_start: 0.8104 (mmp) cc_final: 0.7850 (mmp) REVERT: 3 131 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.6687 (tmt) REVERT: 3 331 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: 3 363 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6929 (m90) REVERT: 3 620 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7073 (m-30) REVERT: 3 631 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6986 (pt0) REVERT: 5 57 ARG cc_start: 0.7870 (ttt-90) cc_final: 0.7404 (ttt180) REVERT: 5 72 ASN cc_start: 0.8309 (t0) cc_final: 0.8094 (m110) REVERT: 5 80 PHE cc_start: 0.7888 (t80) cc_final: 0.7577 (t80) REVERT: 5 84 ASN cc_start: 0.7695 (t0) cc_final: 0.7488 (t0) REVERT: 5 116 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7960 (ttpt) REVERT: J 226 ARG cc_start: 0.5975 (ptp-170) cc_final: 0.5566 (ptt90) REVERT: J 285 MET cc_start: 0.5814 (tmm) cc_final: 0.5404 (tpt) REVERT: J 291 GLN cc_start: 0.5477 (tp40) cc_final: 0.4798 (tm130) REVERT: J 337 MET cc_start: 0.4452 (tpp) cc_final: 0.3807 (tpp) REVERT: J 386 GLU cc_start: 0.4128 (mm-30) cc_final: 0.3339 (pp20) REVERT: P 218 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: X 258 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6207 (mtt90) REVERT: X 262 TYR cc_start: 0.7927 (m-80) cc_final: 0.7592 (m-80) REVERT: X 308 TYR cc_start: 0.8824 (m-80) cc_final: 0.8290 (m-80) REVERT: Z 526 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8692 (pp) REVERT: 9 86 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5357 (mmp-170) REVERT: 9 192 ASP cc_start: 0.7179 (t0) cc_final: 0.6931 (t70) REVERT: 9 209 GLN cc_start: 0.8033 (tt0) cc_final: 0.7791 (tm-30) REVERT: M 163 MET cc_start: 0.8071 (ptm) cc_final: 0.7652 (mtp) REVERT: V 492 MET cc_start: 0.8269 (tpt) cc_final: 0.8022 (tpp) REVERT: V 619 ASP cc_start: 0.7569 (p0) cc_final: 0.7325 (p0) REVERT: K 51 GLU cc_start: 0.4488 (pm20) cc_final: 0.4187 (pm20) REVERT: K 110 PRO cc_start: 0.4987 (Cg_endo) cc_final: 0.4735 (Cg_exo) REVERT: K 149 SER cc_start: 0.3286 (t) cc_final: 0.3006 (p) REVERT: K 165 GLU cc_start: 0.5813 (tp30) cc_final: 0.5099 (tp30) outliers start: 241 outliers final: 107 residues processed: 1438 average time/residue: 1.8096 time to fit residues: 3621.8592 Evaluate side-chains 1331 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1203 time to evaluate : 8.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1104 ASP Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1394 GLN Chi-restraints excluded: chain A residue 1459 ARG Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1655 THR Chi-restraints excluded: chain A residue 1757 GLU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 2074 ARG Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2223 CYS Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2303 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 272 ARG Chi-restraints excluded: chain v residue 36 MET Chi-restraints excluded: chain 1 residue 124 ARG Chi-restraints excluded: chain 1 residue 166 ARG Chi-restraints excluded: chain 1 residue 479 LEU Chi-restraints excluded: chain 1 residue 547 GLN Chi-restraints excluded: chain 1 residue 688 GLU Chi-restraints excluded: chain 1 residue 690 ILE Chi-restraints excluded: chain 1 residue 726 SER Chi-restraints excluded: chain 1 residue 733 LYS Chi-restraints excluded: chain 1 residue 936 VAL Chi-restraints excluded: chain 1 residue 1127 THR Chi-restraints excluded: chain 1 residue 1128 VAL Chi-restraints excluded: chain 1 residue 1226 VAL Chi-restraints excluded: chain 1 residue 1228 GLN Chi-restraints excluded: chain 1 residue 1239 VAL Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 2 residue 599 THR Chi-restraints excluded: chain 3 residue 131 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 322 VAL Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 363 HIS Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 605 LEU Chi-restraints excluded: chain 3 residue 610 VAL Chi-restraints excluded: chain 3 residue 620 ASP Chi-restraints excluded: chain 3 residue 631 GLN Chi-restraints excluded: chain 3 residue 691 THR Chi-restraints excluded: chain 3 residue 699 VAL Chi-restraints excluded: chain 3 residue 722 SER Chi-restraints excluded: chain 3 residue 743 SER Chi-restraints excluded: chain 3 residue 909 VAL Chi-restraints excluded: chain 3 residue 943 THR Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1064 ASP Chi-restraints excluded: chain 5 residue 31 THR Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 6 residue 95 LYS Chi-restraints excluded: chain 7 residue 71 LYS Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain P residue 218 GLU Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 418 MET Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 384 HIS Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain X residue 254 ILE Chi-restraints excluded: chain X residue 257 LYS Chi-restraints excluded: chain X residue 258 ARG Chi-restraints excluded: chain X residue 264 PHE Chi-restraints excluded: chain Y residue 54 CYS Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 80 CYS Chi-restraints excluded: chain Z residue 526 ILE Chi-restraints excluded: chain Z residue 610 LEU Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 86 ARG Chi-restraints excluded: chain 9 residue 191 GLN Chi-restraints excluded: chain z residue 27 GLU Chi-restraints excluded: chain z residue 86 GLU Chi-restraints excluded: chain z residue 148 ASP Chi-restraints excluded: chain z residue 156 HIS Chi-restraints excluded: chain z residue 172 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain V residue 536 ILE Chi-restraints excluded: chain V residue 563 SER Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1339 random chunks: chunk 1249 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 738 optimal weight: 2.9990 chunk 946 optimal weight: 6.9990 chunk 733 optimal weight: 3.9990 chunk 1090 optimal weight: 1.9990 chunk 723 optimal weight: 0.3980 chunk 1290 optimal weight: 3.9990 chunk 807 optimal weight: 0.0570 chunk 786 optimal weight: 0.0020 chunk 595 optimal weight: 9.9990 overall best weight: 0.8910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 297 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 12 GLN ** 1 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 518 GLN 1 891 GLN 2 541 GLN 2 695 GLN ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 264 GLN 3 844 ASN 31192 ASN 5 76 HIS L 13 ASN L 109 GLN J 250 GLN ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 453 ASN T 344 GLN Z 591 ASN 9 133 GLN M 304 ASN V 600 ASN 8 74 GLN ** 8 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 GLN ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 102187 Z= 0.154 Angle : 0.495 10.128 140388 Z= 0.258 Chirality : 0.041 0.202 16414 Planarity : 0.004 0.055 17507 Dihedral : 12.665 177.656 18496 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.18 % Favored : 97.80 % Rotamer: Outliers : 3.00 % Allowed : 20.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.07), residues: 13107 helix: 1.51 (0.07), residues: 5101 sheet: 0.29 (0.11), residues: 2164 loop : -0.28 (0.08), residues: 5842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 313 HIS 0.006 0.001 HIS K 124 PHE 0.030 0.001 PHE J 369 TYR 0.024 0.001 TYR A 351 ARG 0.012 0.000 ARG 1 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1251 time to evaluate : 8.687 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: A 61 MET cc_start: 0.8005 (mtp) cc_final: 0.7646 (mtp) REVERT: A 71 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7924 (tpp-160) REVERT: A 465 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7565 (mttt) REVERT: A 2223 CYS cc_start: 0.3747 (OUTLIER) cc_final: 0.3318 (t) REVERT: A 2284 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6482 (ptp) REVERT: A 2303 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6206 (pp20) REVERT: C 204 ASP cc_start: 0.7459 (t0) cc_final: 0.7210 (t0) REVERT: C 329 ASP cc_start: 0.7520 (t0) cc_final: 0.7309 (t0) REVERT: C 394 ARG cc_start: 0.7463 (ttp80) cc_final: 0.7150 (ttp80) REVERT: C 733 TRP cc_start: 0.7781 (m-10) cc_final: 0.7530 (m100) REVERT: C 822 MET cc_start: 0.8019 (mmm) cc_final: 0.7756 (mmm) REVERT: D 102 TYR cc_start: 0.4560 (t80) cc_final: 0.3627 (m-10) REVERT: D 154 ARG cc_start: 0.6436 (OUTLIER) cc_final: 0.5420 (ttt-90) REVERT: E 60 MET cc_start: 0.2065 (ptm) cc_final: 0.1568 (mmt) REVERT: E 176 VAL cc_start: 0.5959 (t) cc_final: 0.5488 (p) REVERT: E 231 MET cc_start: 0.2937 (tmm) cc_final: 0.2374 (tmm) REVERT: E 315 THR cc_start: 0.3765 (m) cc_final: 0.3375 (p) REVERT: v 221 GLU cc_start: 0.6596 (tp30) cc_final: 0.6289 (tp30) REVERT: 1 124 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6944 (ttp-110) REVERT: 1 126 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7765 (mtm) REVERT: 1 164 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7277 (tm-30) REVERT: 1 165 GLU cc_start: 0.8214 (tt0) cc_final: 0.7924 (tt0) REVERT: 1 457 ASN cc_start: 0.8131 (p0) cc_final: 0.7813 (t0) REVERT: 1 547 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: 1 675 MET cc_start: 0.8145 (mmm) cc_final: 0.7864 (mtt) REVERT: 1 688 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: 1 1239 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8932 (t) REVERT: 2 484 ASP cc_start: 0.8180 (t70) cc_final: 0.7852 (t70) REVERT: 2 541 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8135 (tp40) REVERT: 2 695 GLN cc_start: 0.8651 (tt0) cc_final: 0.8354 (tt0) REVERT: 3 131 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.6714 (tmt) REVERT: 3 363 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.6994 (m90) REVERT: 5 57 ARG cc_start: 0.7845 (ttt-90) cc_final: 0.7490 (ttt180) REVERT: 5 72 ASN cc_start: 0.8293 (t0) cc_final: 0.8090 (m110) REVERT: 5 80 PHE cc_start: 0.7883 (t80) cc_final: 0.7564 (t80) REVERT: 5 84 ASN cc_start: 0.7747 (t0) cc_final: 0.7524 (t0) REVERT: 5 116 LYS cc_start: 0.8259 (ttmm) cc_final: 0.7937 (tttt) REVERT: 7 69 MET cc_start: 0.8486 (mmm) cc_final: 0.8266 (mmm) REVERT: L 54 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9141 (mt) REVERT: J 226 ARG cc_start: 0.5904 (ptp-170) cc_final: 0.5521 (ptt90) REVERT: J 285 MET cc_start: 0.5793 (tmm) cc_final: 0.5412 (tpt) REVERT: J 291 GLN cc_start: 0.5313 (tp40) cc_final: 0.4581 (tm130) REVERT: J 363 ARG cc_start: 0.5261 (tpp80) cc_final: 0.4933 (mmm-85) REVERT: J 386 GLU cc_start: 0.4264 (mm-30) cc_final: 0.3539 (pp20) REVERT: R 402 SER cc_start: 0.6505 (t) cc_final: 0.6205 (t) REVERT: X 258 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6223 (mtt90) REVERT: X 262 TYR cc_start: 0.7897 (m-80) cc_final: 0.7596 (m-80) REVERT: X 366 GLU cc_start: 0.6122 (mm-30) cc_final: 0.5795 (mp0) REVERT: Y 46 GLU cc_start: 0.8239 (pm20) cc_final: 0.8019 (pm20) REVERT: Z 517 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: Z 526 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8730 (pp) REVERT: 9 86 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.5348 (mmp-170) REVERT: 9 192 ASP cc_start: 0.7104 (t0) cc_final: 0.6889 (t70) REVERT: 9 209 GLN cc_start: 0.8024 (tt0) cc_final: 0.7789 (tm-30) REVERT: 9 214 GLU cc_start: 0.7124 (tt0) cc_final: 0.6867 (tt0) REVERT: x 1031 LYS cc_start: 0.6915 (mtpt) cc_final: 0.6587 (ttpt) REVERT: M 163 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7683 (mtp) REVERT: V 492 MET cc_start: 0.8261 (tpt) cc_final: 0.8002 (tpp) REVERT: V 619 ASP cc_start: 0.7578 (p0) cc_final: 0.7336 (p0) REVERT: 0 14 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9094 (tp) REVERT: I 130 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.4098 (mp0) REVERT: K 51 GLU cc_start: 0.4518 (pm20) cc_final: 0.4118 (pm20) REVERT: K 110 PRO cc_start: 0.5037 (Cg_endo) cc_final: 0.4766 (Cg_exo) REVERT: K 149 SER cc_start: 0.3212 (t) cc_final: 0.2946 (p) outliers start: 236 outliers final: 123 residues processed: 1400 average time/residue: 1.8073 time to fit residues: 3526.4750 Evaluate side-chains 1359 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1215 time to evaluate : 8.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1459 ARG Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1655 THR Chi-restraints excluded: chain A residue 1757 GLU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1897 LEU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2223 CYS Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2303 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 144 LYS Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain v residue 8 ASP Chi-restraints excluded: chain v residue 36 MET Chi-restraints excluded: chain 1 residue 124 ARG Chi-restraints excluded: chain 1 residue 126 MET Chi-restraints excluded: chain 1 residue 166 ARG Chi-restraints excluded: chain 1 residue 547 GLN Chi-restraints excluded: chain 1 residue 655 LYS Chi-restraints excluded: chain 1 residue 688 GLU Chi-restraints excluded: chain 1 residue 690 ILE Chi-restraints excluded: chain 1 residue 726 SER Chi-restraints excluded: chain 1 residue 733 LYS Chi-restraints excluded: chain 1 residue 936 VAL Chi-restraints excluded: chain 1 residue 942 ASN Chi-restraints excluded: chain 1 residue 1127 THR Chi-restraints excluded: chain 1 residue 1128 VAL Chi-restraints excluded: chain 1 residue 1226 VAL Chi-restraints excluded: chain 1 residue 1228 GLN Chi-restraints excluded: chain 1 residue 1239 VAL Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 2 residue 599 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 3 residue 131 MET Chi-restraints excluded: chain 3 residue 171 VAL Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 320 ASP Chi-restraints excluded: chain 3 residue 322 VAL Chi-restraints excluded: chain 3 residue 363 HIS Chi-restraints excluded: chain 3 residue 466 ILE Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 605 LEU Chi-restraints excluded: chain 3 residue 610 VAL Chi-restraints excluded: chain 3 residue 691 THR Chi-restraints excluded: chain 3 residue 699 VAL Chi-restraints excluded: chain 3 residue 722 SER Chi-restraints excluded: chain 3 residue 743 SER Chi-restraints excluded: chain 3 residue 849 GLU Chi-restraints excluded: chain 3 residue 943 THR Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1064 ASP Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 74 CYS Chi-restraints excluded: chain 5 residue 101 MET Chi-restraints excluded: chain 6 residue 95 LYS Chi-restraints excluded: chain 7 residue 44 MET Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 304 THR Chi-restraints excluded: chain R residue 418 MET Chi-restraints excluded: chain R residue 434 ASP Chi-restraints excluded: chain T residue 216 ASN Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 384 HIS Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain T residue 481 GLU Chi-restraints excluded: chain X residue 254 ILE Chi-restraints excluded: chain X residue 257 LYS Chi-restraints excluded: chain X residue 258 ARG Chi-restraints excluded: chain X residue 264 PHE Chi-restraints excluded: chain X residue 294 ILE Chi-restraints excluded: chain Y residue 54 CYS Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 80 CYS Chi-restraints excluded: chain Z residue 517 GLU Chi-restraints excluded: chain Z residue 526 ILE Chi-restraints excluded: chain Z residue 610 LEU Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 86 ARG Chi-restraints excluded: chain 9 residue 191 GLN Chi-restraints excluded: chain z residue 27 GLU Chi-restraints excluded: chain z residue 86 GLU Chi-restraints excluded: chain z residue 148 ASP Chi-restraints excluded: chain z residue 156 HIS Chi-restraints excluded: chain z residue 172 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain V residue 536 ILE Chi-restraints excluded: chain V residue 563 SER Chi-restraints excluded: chain V residue 598 LYS Chi-restraints excluded: chain 8 residue 82 SER Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1339 random chunks: chunk 798 optimal weight: 0.5980 chunk 515 optimal weight: 0.8980 chunk 770 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 820 optimal weight: 0.0020 chunk 879 optimal weight: 3.9990 chunk 638 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 1014 optimal weight: 2.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS v 12 GLN ** 1 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 518 GLN 1 738 HIS ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 264 GLN 3 844 ASN 5 76 HIS L 13 ASN J 250 GLN ** J 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 453 ASN T 344 GLN Z 591 ASN 9 133 GLN M 308 ASN V 600 ASN 8 74 GLN ** 8 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 GLN ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 102187 Z= 0.171 Angle : 0.501 11.606 140388 Z= 0.261 Chirality : 0.041 0.206 16414 Planarity : 0.004 0.054 17507 Dihedral : 12.614 177.740 18489 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.27 % Favored : 97.70 % Rotamer: Outliers : 2.71 % Allowed : 20.60 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.07), residues: 13107 helix: 1.59 (0.07), residues: 5090 sheet: 0.32 (0.11), residues: 2170 loop : -0.25 (0.08), residues: 5847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP E 262 HIS 0.005 0.001 HIS K 124 PHE 0.027 0.001 PHE 3 842 TYR 0.023 0.001 TYR A 351 ARG 0.013 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1456 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1243 time to evaluate : 8.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8002 (mtp) cc_final: 0.7640 (mtp) REVERT: A 71 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7832 (tpp-160) REVERT: A 465 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7565 (mttt) REVERT: A 976 MET cc_start: 0.8745 (tpt) cc_final: 0.8386 (tpt) REVERT: A 1410 ASP cc_start: 0.7550 (t70) cc_final: 0.7339 (t70) REVERT: A 2124 ILE cc_start: 0.8471 (pt) cc_final: 0.8216 (mp) REVERT: A 2223 CYS cc_start: 0.3784 (OUTLIER) cc_final: 0.3343 (m) REVERT: A 2284 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6542 (ptt) REVERT: A 2303 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6222 (pp20) REVERT: C 733 TRP cc_start: 0.7810 (m-10) cc_final: 0.7523 (m100) REVERT: C 822 MET cc_start: 0.8016 (mmm) cc_final: 0.7747 (mmm) REVERT: D 102 TYR cc_start: 0.4523 (t80) cc_final: 0.3557 (m-10) REVERT: E 60 MET cc_start: 0.2144 (ptm) cc_final: 0.1503 (mmt) REVERT: E 176 VAL cc_start: 0.5551 (t) cc_final: 0.5266 (p) REVERT: E 289 LEU cc_start: 0.4938 (OUTLIER) cc_final: 0.4735 (mm) REVERT: E 315 THR cc_start: 0.3760 (m) cc_final: 0.3373 (p) REVERT: E 353 MET cc_start: 0.3329 (OUTLIER) cc_final: 0.1673 (pmm) REVERT: v 221 GLU cc_start: 0.6681 (tp30) cc_final: 0.6298 (tp30) REVERT: 1 124 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6942 (ttp-110) REVERT: 1 126 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8000 (mtm) REVERT: 1 164 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7249 (tm-30) REVERT: 1 457 ASN cc_start: 0.8140 (p0) cc_final: 0.7901 (t0) REVERT: 1 547 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: 1 675 MET cc_start: 0.8116 (mmm) cc_final: 0.7854 (mtt) REVERT: 1 688 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: 1 737 GLN cc_start: 0.8063 (tm130) cc_final: 0.7673 (tm-30) REVERT: 1 1053 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8151 (mtt180) REVERT: 1 1239 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8946 (t) REVERT: 2 484 ASP cc_start: 0.8187 (t70) cc_final: 0.7843 (t70) REVERT: 2 541 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8178 (tp40) REVERT: 3 131 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.6712 (tmt) REVERT: 3 709 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7743 (mp10) REVERT: 5 57 ARG cc_start: 0.7852 (ttt-90) cc_final: 0.7472 (ttt180) REVERT: 5 80 PHE cc_start: 0.7862 (t80) cc_final: 0.7555 (t80) REVERT: 5 84 ASN cc_start: 0.7768 (t0) cc_final: 0.7526 (t0) REVERT: 5 116 LYS cc_start: 0.8265 (ttmm) cc_final: 0.7963 (tttt) REVERT: 7 69 MET cc_start: 0.8471 (mmm) cc_final: 0.8251 (mmm) REVERT: L 54 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9168 (mt) REVERT: J 226 ARG cc_start: 0.5905 (ptp-170) cc_final: 0.5442 (ptt90) REVERT: J 285 MET cc_start: 0.5691 (tmm) cc_final: 0.5332 (tpt) REVERT: J 291 GLN cc_start: 0.5333 (tp40) cc_final: 0.4670 (tm130) REVERT: J 337 MET cc_start: 0.4277 (tpp) cc_final: 0.3689 (tpp) REVERT: J 363 ARG cc_start: 0.5288 (tpp80) cc_final: 0.4890 (mmm-85) REVERT: J 386 GLU cc_start: 0.4168 (mm-30) cc_final: 0.3528 (pp20) REVERT: T 365 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.7185 (tpp80) REVERT: X 258 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6121 (mtt90) REVERT: X 262 TYR cc_start: 0.7982 (m-80) cc_final: 0.7648 (m-80) REVERT: Y 52 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8861 (mt) REVERT: Z 517 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: 9 86 ARG cc_start: 0.5955 (OUTLIER) cc_final: 0.5323 (mmp-170) REVERT: 9 192 ASP cc_start: 0.7111 (t0) cc_final: 0.6904 (t70) REVERT: 9 209 GLN cc_start: 0.8016 (tt0) cc_final: 0.7799 (tm-30) REVERT: 9 214 GLU cc_start: 0.7191 (tt0) cc_final: 0.6914 (tt0) REVERT: z 76 GLU cc_start: 0.7169 (tp30) cc_final: 0.6968 (tp30) REVERT: x 1031 LYS cc_start: 0.6930 (mtpt) cc_final: 0.6590 (ttpt) REVERT: M 163 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7479 (mtm) REVERT: V 492 MET cc_start: 0.8302 (tpt) cc_final: 0.8039 (tpp) REVERT: V 619 ASP cc_start: 0.7571 (p0) cc_final: 0.7331 (p0) REVERT: 0 14 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9119 (tp) REVERT: I 124 GLU cc_start: 0.5602 (OUTLIER) cc_final: 0.5325 (mt-10) REVERT: K 110 PRO cc_start: 0.4836 (Cg_endo) cc_final: 0.4586 (Cg_exo) REVERT: K 135 GLU cc_start: 0.3106 (pt0) cc_final: 0.2323 (tm-30) REVERT: K 149 SER cc_start: 0.3182 (t) cc_final: 0.2969 (p) outliers start: 213 outliers final: 127 residues processed: 1386 average time/residue: 1.8141 time to fit residues: 3489.2957 Evaluate side-chains 1355 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1206 time to evaluate : 8.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1655 THR Chi-restraints excluded: chain A residue 1757 GLU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1897 LEU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2223 CYS Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2292 MET Chi-restraints excluded: chain A residue 2303 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain v residue 36 MET Chi-restraints excluded: chain 1 residue 124 ARG Chi-restraints excluded: chain 1 residue 126 MET Chi-restraints excluded: chain 1 residue 166 ARG Chi-restraints excluded: chain 1 residue 479 LEU Chi-restraints excluded: chain 1 residue 546 ASP Chi-restraints excluded: chain 1 residue 547 GLN Chi-restraints excluded: chain 1 residue 655 LYS Chi-restraints excluded: chain 1 residue 688 GLU Chi-restraints excluded: chain 1 residue 690 ILE Chi-restraints excluded: chain 1 residue 726 SER Chi-restraints excluded: chain 1 residue 733 LYS Chi-restraints excluded: chain 1 residue 936 VAL Chi-restraints excluded: chain 1 residue 942 ASN Chi-restraints excluded: chain 1 residue 1053 ARG Chi-restraints excluded: chain 1 residue 1127 THR Chi-restraints excluded: chain 1 residue 1128 VAL Chi-restraints excluded: chain 1 residue 1226 VAL Chi-restraints excluded: chain 1 residue 1228 GLN Chi-restraints excluded: chain 1 residue 1239 VAL Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 2 residue 599 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 131 MET Chi-restraints excluded: chain 3 residue 171 VAL Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 320 ASP Chi-restraints excluded: chain 3 residue 322 VAL Chi-restraints excluded: chain 3 residue 466 ILE Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 605 LEU Chi-restraints excluded: chain 3 residue 610 VAL Chi-restraints excluded: chain 3 residue 691 THR Chi-restraints excluded: chain 3 residue 699 VAL Chi-restraints excluded: chain 3 residue 722 SER Chi-restraints excluded: chain 3 residue 743 SER Chi-restraints excluded: chain 3 residue 759 THR Chi-restraints excluded: chain 3 residue 909 VAL Chi-restraints excluded: chain 3 residue 943 THR Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1064 ASP Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 63 VAL Chi-restraints excluded: chain 5 residue 74 CYS Chi-restraints excluded: chain 6 residue 95 LYS Chi-restraints excluded: chain 7 residue 44 MET Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain R residue 304 MET Chi-restraints excluded: chain R residue 418 MET Chi-restraints excluded: chain R residue 434 ASP Chi-restraints excluded: chain T residue 216 ASN Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 288 LEU Chi-restraints excluded: chain T residue 384 HIS Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain X residue 257 LYS Chi-restraints excluded: chain X residue 258 ARG Chi-restraints excluded: chain X residue 264 PHE Chi-restraints excluded: chain X residue 337 THR Chi-restraints excluded: chain Y residue 52 ILE Chi-restraints excluded: chain Y residue 54 CYS Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 80 CYS Chi-restraints excluded: chain Z residue 517 GLU Chi-restraints excluded: chain Z residue 610 LEU Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 86 ARG Chi-restraints excluded: chain 9 residue 191 GLN Chi-restraints excluded: chain z residue 27 GLU Chi-restraints excluded: chain z residue 86 GLU Chi-restraints excluded: chain z residue 148 ASP Chi-restraints excluded: chain z residue 156 HIS Chi-restraints excluded: chain z residue 172 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain V residue 536 ILE Chi-restraints excluded: chain V residue 563 SER Chi-restraints excluded: chain V residue 598 LYS Chi-restraints excluded: chain 8 residue 82 SER Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain I residue 79 ASP Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain K residue 35 GLN Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1339 random chunks: chunk 1173 optimal weight: 50.0000 chunk 1236 optimal weight: 30.0000 chunk 1128 optimal weight: 40.0000 chunk 1202 optimal weight: 30.0000 chunk 723 optimal weight: 1.9990 chunk 523 optimal weight: 9.9990 chunk 944 optimal weight: 1.9990 chunk 369 optimal weight: 0.9980 chunk 1086 optimal weight: 1.9990 chunk 1137 optimal weight: 0.8980 chunk 1198 optimal weight: 30.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN C 163 GLN E 101 ASN v 12 GLN 1 518 GLN 1 738 HIS 2 695 GLN ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 264 GLN 3 844 ASN 31192 ASN 5 76 HIS 5 93 ASN L 13 ASN L 109 GLN J 250 GLN R 453 ASN ** T 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 133 GLN V 600 ASN 8 74 GLN ** 8 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 37 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 102187 Z= 0.214 Angle : 0.524 12.868 140388 Z= 0.273 Chirality : 0.042 0.215 16414 Planarity : 0.004 0.057 17507 Dihedral : 12.616 178.134 18489 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 2.74 % Allowed : 20.86 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.07), residues: 13107 helix: 1.59 (0.07), residues: 5101 sheet: 0.36 (0.11), residues: 2175 loop : -0.26 (0.08), residues: 5831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J 313 HIS 0.006 0.001 HIS A 884 PHE 0.040 0.001 PHE J 369 TYR 0.024 0.001 TYR I 47 ARG 0.015 0.001 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1442 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1226 time to evaluate : 8.859 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: A 61 MET cc_start: 0.8030 (mtp) cc_final: 0.7677 (mtp) REVERT: A 71 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7838 (tpp-160) REVERT: A 465 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7573 (mttt) REVERT: A 1533 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8096 (ttp-170) REVERT: A 2124 ILE cc_start: 0.8526 (pt) cc_final: 0.8246 (mp) REVERT: A 2200 MET cc_start: 0.3551 (tpt) cc_final: 0.2965 (tmm) REVERT: A 2223 CYS cc_start: 0.3929 (OUTLIER) cc_final: 0.3366 (t) REVERT: A 2284 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6513 (ptp) REVERT: A 2303 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6411 (pp20) REVERT: C 733 TRP cc_start: 0.7812 (m-10) cc_final: 0.7525 (m100) REVERT: C 822 MET cc_start: 0.7995 (mmm) cc_final: 0.7706 (mmm) REVERT: D 154 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5373 (ttt-90) REVERT: E 60 MET cc_start: 0.2277 (ptm) cc_final: 0.1554 (mmt) REVERT: E 176 VAL cc_start: 0.5476 (t) cc_final: 0.5245 (p) REVERT: E 289 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.4718 (mm) REVERT: E 315 THR cc_start: 0.3771 (m) cc_final: 0.3382 (p) REVERT: E 353 MET cc_start: 0.3100 (OUTLIER) cc_final: 0.1803 (pmm) REVERT: v 221 GLU cc_start: 0.6709 (tp30) cc_final: 0.6282 (tp30) REVERT: 1 124 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6945 (ttp-110) REVERT: 1 126 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8015 (mtm) REVERT: 1 164 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7310 (tm-30) REVERT: 1 457 ASN cc_start: 0.8168 (p0) cc_final: 0.7807 (t0) REVERT: 1 547 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: 1 675 MET cc_start: 0.8115 (mmm) cc_final: 0.7913 (mtt) REVERT: 1 688 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: 1 737 GLN cc_start: 0.8102 (tm130) cc_final: 0.7766 (tm-30) REVERT: 1 1053 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8159 (mtt180) REVERT: 1 1239 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8923 (t) REVERT: 2 541 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8161 (tp40) REVERT: 2 695 GLN cc_start: 0.8683 (tt0) cc_final: 0.8395 (tt0) REVERT: 3 1 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7609 (ttt) REVERT: 3 131 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.6674 (tmt) REVERT: 3 709 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7808 (mp10) REVERT: 5 57 ARG cc_start: 0.7893 (ttt-90) cc_final: 0.7659 (ttt180) REVERT: 5 80 PHE cc_start: 0.7870 (t80) cc_final: 0.7568 (t80) REVERT: 5 84 ASN cc_start: 0.7812 (t0) cc_final: 0.7518 (t0) REVERT: 5 111 LYS cc_start: 0.8325 (tppt) cc_final: 0.8104 (ttmt) REVERT: 5 116 LYS cc_start: 0.8314 (ttmm) cc_final: 0.7981 (tttt) REVERT: 7 69 MET cc_start: 0.8484 (mmm) cc_final: 0.8252 (mmm) REVERT: L 54 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9176 (mt) REVERT: J 226 ARG cc_start: 0.5831 (ptp-170) cc_final: 0.5606 (ptt90) REVERT: J 285 MET cc_start: 0.5771 (tmm) cc_final: 0.5406 (tpt) REVERT: J 291 GLN cc_start: 0.5250 (tp40) cc_final: 0.4583 (tm130) REVERT: J 319 MET cc_start: 0.3940 (tmm) cc_final: 0.3623 (ttp) REVERT: J 337 MET cc_start: 0.4189 (tpp) cc_final: 0.3613 (tpp) REVERT: J 363 ARG cc_start: 0.5314 (tpp80) cc_final: 0.4903 (mmm-85) REVERT: J 379 TRP cc_start: 0.5718 (m100) cc_final: 0.5413 (m100) REVERT: J 386 GLU cc_start: 0.4071 (mm-30) cc_final: 0.3495 (pp20) REVERT: T 344 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: X 258 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6128 (mtt90) REVERT: X 262 TYR cc_start: 0.7982 (m-80) cc_final: 0.7647 (m-80) REVERT: X 366 GLU cc_start: 0.6059 (mm-30) cc_final: 0.5733 (mp0) REVERT: Y 52 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8883 (mt) REVERT: Z 517 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: Z 519 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: 9 86 ARG cc_start: 0.5926 (OUTLIER) cc_final: 0.5291 (mmp-170) REVERT: 9 192 ASP cc_start: 0.7126 (t0) cc_final: 0.6911 (t70) REVERT: 9 209 GLN cc_start: 0.8027 (tt0) cc_final: 0.7785 (tm-30) REVERT: 9 214 GLU cc_start: 0.7223 (tt0) cc_final: 0.6951 (tt0) REVERT: z 76 GLU cc_start: 0.7167 (tp30) cc_final: 0.6962 (tp30) REVERT: M 163 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7609 (mtp) REVERT: V 492 MET cc_start: 0.8292 (tpt) cc_final: 0.8037 (tpp) REVERT: V 619 ASP cc_start: 0.7601 (p0) cc_final: 0.7345 (p0) REVERT: 0 14 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9127 (tp) REVERT: K 110 PRO cc_start: 0.4999 (Cg_endo) cc_final: 0.4744 (Cg_exo) REVERT: K 135 GLU cc_start: 0.2928 (pt0) cc_final: 0.2187 (tm-30) REVERT: K 149 SER cc_start: 0.3665 (t) cc_final: 0.3449 (p) outliers start: 216 outliers final: 137 residues processed: 1361 average time/residue: 1.8064 time to fit residues: 3433.8962 Evaluate side-chains 1355 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1192 time to evaluate : 8.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1533 ARG Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1655 THR Chi-restraints excluded: chain A residue 1757 GLU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1897 LEU Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2223 CYS Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2292 MET Chi-restraints excluded: chain A residue 2303 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain v residue 36 MET Chi-restraints excluded: chain 1 residue 124 ARG Chi-restraints excluded: chain 1 residue 126 MET Chi-restraints excluded: chain 1 residue 166 ARG Chi-restraints excluded: chain 1 residue 543 THR Chi-restraints excluded: chain 1 residue 546 ASP Chi-restraints excluded: chain 1 residue 547 GLN Chi-restraints excluded: chain 1 residue 655 LYS Chi-restraints excluded: chain 1 residue 688 GLU Chi-restraints excluded: chain 1 residue 690 ILE Chi-restraints excluded: chain 1 residue 726 SER Chi-restraints excluded: chain 1 residue 733 LYS Chi-restraints excluded: chain 1 residue 936 VAL Chi-restraints excluded: chain 1 residue 942 ASN Chi-restraints excluded: chain 1 residue 1053 ARG Chi-restraints excluded: chain 1 residue 1127 THR Chi-restraints excluded: chain 1 residue 1128 VAL Chi-restraints excluded: chain 1 residue 1226 VAL Chi-restraints excluded: chain 1 residue 1228 GLN Chi-restraints excluded: chain 1 residue 1239 VAL Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 3 residue 131 MET Chi-restraints excluded: chain 3 residue 171 VAL Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 320 ASP Chi-restraints excluded: chain 3 residue 322 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 605 LEU Chi-restraints excluded: chain 3 residue 610 VAL Chi-restraints excluded: chain 3 residue 691 THR Chi-restraints excluded: chain 3 residue 699 VAL Chi-restraints excluded: chain 3 residue 722 SER Chi-restraints excluded: chain 3 residue 743 SER Chi-restraints excluded: chain 3 residue 759 THR Chi-restraints excluded: chain 3 residue 909 VAL Chi-restraints excluded: chain 3 residue 943 THR Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1064 ASP Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 5 residue 38 ILE Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 74 CYS Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 93 ASN Chi-restraints excluded: chain 5 residue 112 LEU Chi-restraints excluded: chain 7 residue 44 MET Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain R residue 418 MET Chi-restraints excluded: chain R residue 434 ASP Chi-restraints excluded: chain T residue 216 ASN Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 288 LEU Chi-restraints excluded: chain T residue 344 GLN Chi-restraints excluded: chain T residue 384 HIS Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain T residue 418 THR Chi-restraints excluded: chain X residue 254 ILE Chi-restraints excluded: chain X residue 257 LYS Chi-restraints excluded: chain X residue 258 ARG Chi-restraints excluded: chain X residue 264 PHE Chi-restraints excluded: chain X residue 337 THR Chi-restraints excluded: chain Y residue 52 ILE Chi-restraints excluded: chain Y residue 54 CYS Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 80 CYS Chi-restraints excluded: chain Y residue 113 SER Chi-restraints excluded: chain Z residue 517 GLU Chi-restraints excluded: chain Z residue 519 GLN Chi-restraints excluded: chain Z residue 610 LEU Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 82 LYS Chi-restraints excluded: chain 9 residue 86 ARG Chi-restraints excluded: chain 9 residue 191 GLN Chi-restraints excluded: chain z residue 27 GLU Chi-restraints excluded: chain z residue 86 GLU Chi-restraints excluded: chain z residue 148 ASP Chi-restraints excluded: chain z residue 156 HIS Chi-restraints excluded: chain z residue 172 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain V residue 536 ILE Chi-restraints excluded: chain V residue 563 SER Chi-restraints excluded: chain V residue 574 THR Chi-restraints excluded: chain V residue 598 LYS Chi-restraints excluded: chain 8 residue 82 SER Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1339 random chunks: chunk 789 optimal weight: 0.7980 chunk 1271 optimal weight: 1.9990 chunk 776 optimal weight: 4.9990 chunk 603 optimal weight: 40.0000 chunk 884 optimal weight: 0.5980 chunk 1333 optimal weight: 0.1980 chunk 1227 optimal weight: 0.9980 chunk 1062 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 820 optimal weight: 0.1980 chunk 651 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN A1042 GLN C 706 GLN v 12 GLN 1 518 GLN 1 738 HIS 11228 GLN ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 264 GLN 3 844 ASN 5 76 HIS 5 93 ASN L 13 ASN L 81 GLN J 250 GLN J 275 ASN ** J 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 453 ASN ** T 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 133 GLN 9 261 HIS V 600 ASN 8 74 GLN ** 8 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 37 ASN ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 161 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 102187 Z= 0.139 Angle : 0.506 14.004 140388 Z= 0.263 Chirality : 0.041 0.198 16414 Planarity : 0.004 0.065 17507 Dihedral : 12.564 177.087 18489 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.06 % Favored : 97.91 % Rotamer: Outliers : 2.06 % Allowed : 21.77 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.07), residues: 13107 helix: 1.70 (0.08), residues: 5083 sheet: 0.39 (0.11), residues: 2208 loop : -0.22 (0.08), residues: 5816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP J 313 HIS 0.006 0.001 HIS K 124 PHE 0.041 0.001 PHE J 369 TYR 0.025 0.001 TYR A 351 ARG 0.015 0.000 ARG 1 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26214 Ramachandran restraints generated. 13107 Oldfield, 0 Emsley, 13107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1249 time to evaluate : 8.577 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: A 61 MET cc_start: 0.7956 (mtp) cc_final: 0.7609 (mtp) REVERT: A 71 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7811 (tpp-160) REVERT: A 465 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7547 (mttt) REVERT: A 976 MET cc_start: 0.8769 (tpt) cc_final: 0.8363 (tpt) REVERT: A 2124 ILE cc_start: 0.8548 (pt) cc_final: 0.8261 (mp) REVERT: A 2200 MET cc_start: 0.3408 (tpt) cc_final: 0.2862 (tmm) REVERT: A 2223 CYS cc_start: 0.4005 (OUTLIER) cc_final: 0.3440 (t) REVERT: A 2261 MET cc_start: 0.4590 (mtm) cc_final: 0.4322 (mtm) REVERT: A 2284 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6522 (ptp) REVERT: C 394 ARG cc_start: 0.7628 (tmm-80) cc_final: 0.7171 (ttp80) REVERT: C 733 TRP cc_start: 0.7753 (m-10) cc_final: 0.7494 (m100) REVERT: C 822 MET cc_start: 0.8042 (mmm) cc_final: 0.7787 (mmm) REVERT: D 121 GLN cc_start: 0.7277 (tm-30) cc_final: 0.6932 (tt0) REVERT: E 60 MET cc_start: 0.2073 (ptm) cc_final: 0.1578 (mmt) REVERT: E 289 LEU cc_start: 0.4900 (OUTLIER) cc_final: 0.4665 (mm) REVERT: E 315 THR cc_start: 0.3755 (m) cc_final: 0.3370 (p) REVERT: E 353 MET cc_start: 0.2974 (OUTLIER) cc_final: 0.2735 (ptp) REVERT: v 221 GLU cc_start: 0.6695 (tp30) cc_final: 0.6377 (tp30) REVERT: 1 124 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6773 (ttp-110) REVERT: 1 126 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7987 (mtm) REVERT: 1 164 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7237 (tm-30) REVERT: 1 457 ASN cc_start: 0.8140 (p0) cc_final: 0.7895 (t0) REVERT: 1 613 MET cc_start: 0.7813 (mtp) cc_final: 0.7612 (mtp) REVERT: 1 675 MET cc_start: 0.8044 (mmm) cc_final: 0.7765 (mtt) REVERT: 1 737 GLN cc_start: 0.8072 (tm130) cc_final: 0.7861 (tt0) REVERT: 1 1239 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8934 (t) REVERT: 2 538 GLU cc_start: 0.7664 (tt0) cc_final: 0.7441 (mt-10) REVERT: 2 541 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8185 (tp40) REVERT: 3 131 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.6694 (tmt) REVERT: 3 620 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.6988 (m-30) REVERT: 3 709 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7812 (mp10) REVERT: 5 57 ARG cc_start: 0.7862 (ttt-90) cc_final: 0.7613 (ttt180) REVERT: 5 80 PHE cc_start: 0.7829 (t80) cc_final: 0.7518 (t80) REVERT: 5 84 ASN cc_start: 0.7829 (t0) cc_final: 0.7522 (t0) REVERT: 5 111 LYS cc_start: 0.8333 (tppt) cc_final: 0.8085 (ttmt) REVERT: 5 116 LYS cc_start: 0.8332 (ttmm) cc_final: 0.7971 (tttt) REVERT: 7 69 MET cc_start: 0.8481 (mmm) cc_final: 0.8251 (mmm) REVERT: L 76 LYS cc_start: 0.8752 (tppp) cc_final: 0.8536 (tppt) REVERT: J 226 ARG cc_start: 0.5870 (ptp-170) cc_final: 0.5439 (ptt90) REVERT: J 285 MET cc_start: 0.5686 (tmm) cc_final: 0.5375 (tpt) REVERT: J 291 GLN cc_start: 0.5239 (tp40) cc_final: 0.4591 (tm130) REVERT: J 319 MET cc_start: 0.3850 (tmm) cc_final: 0.3537 (ttp) REVERT: J 337 MET cc_start: 0.4011 (tpp) cc_final: 0.3432 (tpp) REVERT: J 363 ARG cc_start: 0.5236 (tpp80) cc_final: 0.4697 (mmm-85) REVERT: J 379 TRP cc_start: 0.5692 (m100) cc_final: 0.5398 (m100) REVERT: J 386 GLU cc_start: 0.3977 (mm-30) cc_final: 0.3522 (pp20) REVERT: X 258 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6049 (mtt90) REVERT: X 262 TYR cc_start: 0.7969 (m-80) cc_final: 0.7616 (m-80) REVERT: X 366 GLU cc_start: 0.6103 (mm-30) cc_final: 0.5764 (mp0) REVERT: Z 517 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: Z 526 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8592 (pp) REVERT: 9 192 ASP cc_start: 0.7149 (t0) cc_final: 0.6939 (t70) REVERT: 9 209 GLN cc_start: 0.7982 (tt0) cc_final: 0.7772 (tm-30) REVERT: 9 214 GLU cc_start: 0.7201 (tt0) cc_final: 0.6929 (tt0) REVERT: x 1031 LYS cc_start: 0.6841 (mtpt) cc_final: 0.6500 (ttpt) REVERT: M 163 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7440 (mtm) REVERT: V 492 MET cc_start: 0.8268 (tpt) cc_final: 0.8009 (tpp) REVERT: V 619 ASP cc_start: 0.7549 (p0) cc_final: 0.7337 (p0) REVERT: I 135 LEU cc_start: 0.6477 (mm) cc_final: 0.6254 (mm) REVERT: K 110 PRO cc_start: 0.5006 (Cg_endo) cc_final: 0.4726 (Cg_exo) REVERT: K 123 MET cc_start: 0.4989 (tmm) cc_final: 0.4611 (mtp) REVERT: K 135 GLU cc_start: 0.2835 (pt0) cc_final: 0.2150 (tm-30) outliers start: 162 outliers final: 106 residues processed: 1362 average time/residue: 1.8935 time to fit residues: 3628.1565 Evaluate side-chains 1334 residues out of total 11809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1213 time to evaluate : 8.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 955 TRP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1610 GLN Chi-restraints excluded: chain A residue 1655 THR Chi-restraints excluded: chain A residue 1757 GLU Chi-restraints excluded: chain A residue 1878 ASP Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2223 CYS Chi-restraints excluded: chain A residue 2259 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 841 ASP Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain 1 residue 124 ARG Chi-restraints excluded: chain 1 residue 126 MET Chi-restraints excluded: chain 1 residue 166 ARG Chi-restraints excluded: chain 1 residue 543 THR Chi-restraints excluded: chain 1 residue 655 LYS Chi-restraints excluded: chain 1 residue 690 ILE Chi-restraints excluded: chain 1 residue 936 VAL Chi-restraints excluded: chain 1 residue 1127 THR Chi-restraints excluded: chain 1 residue 1128 VAL Chi-restraints excluded: chain 1 residue 1226 VAL Chi-restraints excluded: chain 1 residue 1239 VAL Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 3 residue 131 MET Chi-restraints excluded: chain 3 residue 171 VAL Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 322 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 605 LEU Chi-restraints excluded: chain 3 residue 610 VAL Chi-restraints excluded: chain 3 residue 620 ASP Chi-restraints excluded: chain 3 residue 691 THR Chi-restraints excluded: chain 3 residue 699 VAL Chi-restraints excluded: chain 3 residue 722 SER Chi-restraints excluded: chain 3 residue 759 THR Chi-restraints excluded: chain 3 residue 909 VAL Chi-restraints excluded: chain 3 residue 943 THR Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1064 ASP Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 5 residue 53 THR Chi-restraints excluded: chain 5 residue 63 VAL Chi-restraints excluded: chain 5 residue 74 CYS Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain R residue 418 MET Chi-restraints excluded: chain R residue 434 ASP Chi-restraints excluded: chain T residue 216 ASN Chi-restraints excluded: chain T residue 267 ASP Chi-restraints excluded: chain T residue 384 HIS Chi-restraints excluded: chain T residue 393 ASP Chi-restraints excluded: chain X residue 254 ILE Chi-restraints excluded: chain X residue 257 LYS Chi-restraints excluded: chain X residue 258 ARG Chi-restraints excluded: chain X residue 264 PHE Chi-restraints excluded: chain X residue 289 ILE Chi-restraints excluded: chain X residue 337 THR Chi-restraints excluded: chain Y residue 54 CYS Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 80 CYS Chi-restraints excluded: chain Z residue 517 GLU Chi-restraints excluded: chain Z residue 526 ILE Chi-restraints excluded: chain 9 residue 60 VAL Chi-restraints excluded: chain 9 residue 191 GLN Chi-restraints excluded: chain z residue 27 GLU Chi-restraints excluded: chain z residue 86 GLU Chi-restraints excluded: chain z residue 148 ASP Chi-restraints excluded: chain z residue 156 HIS Chi-restraints excluded: chain z residue 172 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 152 ILE Chi-restraints excluded: chain M residue 157 ASN Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain V residue 536 ILE Chi-restraints excluded: chain V residue 598 LYS Chi-restraints excluded: chain 8 residue 82 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1339 random chunks: chunk 843 optimal weight: 8.9990 chunk 1131 optimal weight: 10.0000 chunk 325 optimal weight: 0.7980 chunk 979 optimal weight: 0.0020 chunk 156 optimal weight: 0.0870 chunk 295 optimal weight: 9.9990 chunk 1063 optimal weight: 1.9990 chunk 445 optimal weight: 50.0000 chunk 1092 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 overall best weight: 0.7368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN A1737 ASN C 163 GLN v 12 GLN 1 518 GLN 1 738 HIS 11194 HIS 2 695 GLN ** 3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 264 GLN 3 844 ASN 31152 HIS 31192 ASN 5 76 HIS 5 93 ASN L 13 ASN L 109 GLN J 250 GLN J 275 ASN ** J 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 453 ASN ** T 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 509 GLN Z 591 ASN V 600 ASN 8 74 GLN ** 8 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 161 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.184364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125999 restraints weight = 145970.788| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.57 r_work: 0.3160 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 102187 Z= 0.148 Angle : 0.505 13.462 140388 Z= 0.261 Chirality : 0.041 0.202 16414 Planarity : 0.004 0.061 17507 Dihedral : 12.507 177.356 18488 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % Rotamer: Outliers : 1.91 % Allowed : 22.13 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.07), residues: 13107 helix: 1.74 (0.08), residues: 5093 sheet: 0.42 (0.11), residues: 2200 loop : -0.17 (0.08), residues: 5814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP J 313 HIS 0.008 0.001 HIS 3 465 PHE 0.039 0.001 PHE 3 842 TYR 0.023 0.001 TYR A 351 ARG 0.016 0.000 ARG 1 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51629.63 seconds wall clock time: 894 minutes 47.46 seconds (53687.46 seconds total)