Starting phenix.real_space_refine on Tue Apr 9 09:26:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6h_4466/04_2024/6q6h_4466.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6h_4466/04_2024/6q6h_4466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6h_4466/04_2024/6q6h_4466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6h_4466/04_2024/6q6h_4466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6h_4466/04_2024/6q6h_4466.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6h_4466/04_2024/6q6h_4466.pdb" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 414 5.16 5 C 43441 2.51 5 N 11622 2.21 5 O 12467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 17": "OE1" <-> "OE2" Residue "L ASP 43": "OD1" <-> "OD2" Residue "L TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ASP 804": "OD1" <-> "OD2" Residue "A PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 928": "OE1" <-> "OE2" Residue "A TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1022": "OE1" <-> "OE2" Residue "A ARG 1048": "NH1" <-> "NH2" Residue "A GLU 1064": "OE1" <-> "OE2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "A GLU 1242": "OE1" <-> "OE2" Residue "A ASP 1244": "OD1" <-> "OD2" Residue "A GLU 1284": "OE1" <-> "OE2" Residue "A GLU 1323": "OE1" <-> "OE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A ARG 1381": "NH1" <-> "NH2" Residue "A ARG 1540": "NH1" <-> "NH2" Residue "A GLU 1635": "OE1" <-> "OE2" Residue "A TYR 1638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1726": "NH1" <-> "NH2" Residue "A GLU 1766": "OE1" <-> "OE2" Residue "A ASP 1769": "OD1" <-> "OD2" Residue "A PHE 1839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1879": "OE1" <-> "OE2" Residue "N PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 274": "OE1" <-> "OE2" Residue "N GLU 282": "OE1" <-> "OE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 287": "NH1" <-> "NH2" Residue "N PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 323": "NH1" <-> "NH2" Residue "N ARG 325": "NH1" <-> "NH2" Residue "N GLU 342": "OE1" <-> "OE2" Residue "N GLU 343": "OE1" <-> "OE2" Residue "N ASP 353": "OD1" <-> "OD2" Residue "N ARG 367": "NH1" <-> "NH2" Residue "N ARG 385": "NH1" <-> "NH2" Residue "N ASP 395": "OD1" <-> "OD2" Residue "N GLU 422": "OE1" <-> "OE2" Residue "N ASP 445": "OD1" <-> "OD2" Residue "N ASP 451": "OD1" <-> "OD2" Residue "N GLU 478": "OE1" <-> "OE2" Residue "N ASP 525": "OD1" <-> "OD2" Residue "N PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 563": "OD1" <-> "OD2" Residue "N ARG 569": "NH1" <-> "NH2" Residue "N ASP 578": "OD1" <-> "OD2" Residue "N PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 614": "OD1" <-> "OD2" Residue "N ASP 647": "OD1" <-> "OD2" Residue "N ASP 652": "OD1" <-> "OD2" Residue "N GLU 707": "OE1" <-> "OE2" Residue "N GLU 708": "OE1" <-> "OE2" Residue "N GLU 719": "OE1" <-> "OE2" Residue "N ASP 723": "OD1" <-> "OD2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 158": "OE1" <-> "OE2" Residue "I GLU 277": "OE1" <-> "OE2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I GLU 357": "OE1" <-> "OE2" Residue "I ARG 419": "NH1" <-> "NH2" Residue "I GLU 450": "OE1" <-> "OE2" Residue "I TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 563": "OE1" <-> "OE2" Residue "I TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 708": "OE1" <-> "OE2" Residue "I GLU 753": "OE1" <-> "OE2" Residue "O PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 109": "OE1" <-> "OE2" Residue "O ASP 113": "OD1" <-> "OD2" Residue "O ASP 117": "OD1" <-> "OD2" Residue "O GLU 213": "OE1" <-> "OE2" Residue "O ASP 226": "OD1" <-> "OD2" Residue "O ASP 249": "OD1" <-> "OD2" Residue "O GLU 287": "OE1" <-> "OE2" Residue "O ASP 356": "OD1" <-> "OD2" Residue "O GLU 362": "OE1" <-> "OE2" Residue "O ASP 406": "OD1" <-> "OD2" Residue "O GLU 622": "OE1" <-> "OE2" Residue "K ASP 27": "OD1" <-> "OD2" Residue "K ARG 34": "NH1" <-> "NH2" Residue "K ARG 146": "NH1" <-> "NH2" Residue "K ASP 168": "OD1" <-> "OD2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 317": "OE1" <-> "OE2" Residue "K GLU 430": "OE1" <-> "OE2" Residue "K ASP 442": "OD1" <-> "OD2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "W GLU 10": "OE1" <-> "OE2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "J ASP 165": "OD1" <-> "OD2" Residue "J GLU 514": "OE1" <-> "OE2" Residue "J ASP 558": "OD1" <-> "OD2" Residue "J GLU 615": "OE1" <-> "OE2" Residue "J ASP 663": "OD1" <-> "OD2" Residue "J GLU 686": "OE1" <-> "OE2" Residue "J GLU 725": "OE1" <-> "OE2" Residue "J GLU 727": "OE1" <-> "OE2" Residue "J ASP 767": "OD1" <-> "OD2" Residue "P GLU 157": "OE1" <-> "OE2" Residue "P GLU 460": "OE1" <-> "OE2" Residue "P TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 524": "OE1" <-> "OE2" Residue "P ASP 558": "OD1" <-> "OD2" Residue "P GLU 655": "OE1" <-> "OE2" Residue "P GLU 728": "OE1" <-> "OE2" Residue "Q ASP 27": "OD1" <-> "OD2" Residue "Q ARG 34": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ASP 91": "OD1" <-> "OD2" Residue "Q TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 168": "OD1" <-> "OD2" Residue "Q ASP 225": "OD1" <-> "OD2" Residue "Q ARG 240": "NH1" <-> "NH2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q ARG 469": "NH1" <-> "NH2" Residue "Q PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 500": "OD1" <-> "OD2" Residue "Q ASP 511": "OD1" <-> "OD2" Residue "Y ASP 204": "OD1" <-> "OD2" Residue "Y ASP 269": "OD1" <-> "OD2" Residue "Y ASP 301": "OD1" <-> "OD2" Residue "Y GLU 322": "OE1" <-> "OE2" Residue "Y ARG 354": "NH1" <-> "NH2" Residue "Y GLU 493": "OE1" <-> "OE2" Residue "U PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 44": "NH1" <-> "NH2" Residue "U ASP 80": "OD1" <-> "OD2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 101": "NH1" <-> "NH2" Residue "U ASP 131": "OD1" <-> "OD2" Residue "U ASP 132": "OD1" <-> "OD2" Residue "U GLU 149": "OE1" <-> "OE2" Residue "U ARG 165": "NH1" <-> "NH2" Residue "U GLU 231": "OE1" <-> "OE2" Residue "U GLU 245": "OE1" <-> "OE2" Residue "U GLU 246": "OE1" <-> "OE2" Residue "U ARG 296": "NH1" <-> "NH2" Residue "U GLU 298": "OE1" <-> "OE2" Residue "U ASP 327": "OD1" <-> "OD2" Residue "U ARG 330": "NH1" <-> "NH2" Residue "U GLU 348": "OE1" <-> "OE2" Residue "U ARG 363": "NH1" <-> "NH2" Residue "U GLU 393": "OE1" <-> "OE2" Residue "U ARG 397": "NH1" <-> "NH2" Residue "U ASP 398": "OD1" <-> "OD2" Residue "V GLU 45": "OE1" <-> "OE2" Residue "V ARG 101": "NH1" <-> "NH2" Residue "V PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 132": "OD1" <-> "OD2" Residue "V ARG 165": "NH1" <-> "NH2" Residue "V GLU 166": "OE1" <-> "OE2" Residue "V ASP 168": "OD1" <-> "OD2" Residue "V ASP 190": "OD1" <-> "OD2" Residue "V GLU 194": "OE1" <-> "OE2" Residue "V GLU 231": "OE1" <-> "OE2" Residue "V GLU 245": "OE1" <-> "OE2" Residue "V GLU 246": "OE1" <-> "OE2" Residue "V ARG 296": "NH1" <-> "NH2" Residue "V ARG 330": "NH1" <-> "NH2" Residue "V ARG 397": "NH1" <-> "NH2" Residue "V ASP 527": "OD1" <-> "OD2" Residue "V PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 152": "OD1" <-> "OD2" Residue "Z GLU 185": "OE1" <-> "OE2" Residue "Z GLU 194": "OE1" <-> "OE2" Residue "Z GLU 295": "OE1" <-> "OE2" Residue "Z TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 354": "NH1" <-> "NH2" Residue "Z GLU 398": "OE1" <-> "OE2" Residue "Z GLU 493": "OE1" <-> "OE2" Residue "Z ASP 517": "OD1" <-> "OD2" Residue "R ASP 184": "OD1" <-> "OD2" Residue "R TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 223": "OE1" <-> "OE2" Residue "R TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 237": "OE1" <-> "OE2" Residue "R GLU 249": "OE1" <-> "OE2" Residue "R ARG 270": "NH1" <-> "NH2" Residue "R ARG 296": "NH1" <-> "NH2" Residue "R GLU 299": "OE1" <-> "OE2" Residue "R GLU 342": "OE1" <-> "OE2" Residue "R ARG 383": "NH1" <-> "NH2" Residue "R GLU 438": "OE1" <-> "OE2" Residue "R ARG 445": "NH1" <-> "NH2" Residue "R ARG 468": "NH1" <-> "NH2" Residue "S ASP 77": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 67944 Number of models: 1 Model: "" Number of chains: 21 Chain: "L" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1446 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 470 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 56, 462 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} Conformer: "B" Number of residues, atoms: 56, 462 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} bond proxies already assigned to first conformer: 465 Chain: "A" Number of atoms: 12131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1551, 12131 Classifications: {'peptide': 1551} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 87, 'TRANS': 1462} Chain breaks: 17 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 82 Chain: "N" Number of atoms: 5238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5238 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "I" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5752 Classifications: {'peptide': 729} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 705} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "O" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5532 Classifications: {'peptide': 703} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 19, 'TRANS': 683} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "K" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4187 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 501} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 79} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLU%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 226 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "W" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 225 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 499 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 459 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 3964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3964 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "P" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3883 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4055 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 14, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "Y" Number of atoms: 3911 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 499, 3903 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 499, 3903 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 3954 Chain: "U" Number of atoms: 4160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4160 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 12, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "V" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4311 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "Z" Number of atoms: 3807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 486, 3799 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 486, 3799 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 3850 Chain: "R" Number of atoms: 2897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 375, 2883 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 357} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 375, 2883 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 357} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 2941 Chain: "S" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS R 388 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS R 388 " occ=0.50 residue: pdb=" N AMET R 451 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET R 451 " occ=0.50 Time building chain proxies: 29.35, per 1000 atoms: 0.43 Number of scatterers: 67944 At special positions: 0 Unit cell: (233.481, 194.742, 229.293, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 414 16.00 O 12467 8.00 N 11622 7.00 C 43441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.40 Conformation dependent library (CDL) restraints added in 10.8 seconds 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16348 Finding SS restraints... Secondary structure from input PDB file: 411 helices and 35 sheets defined 65.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'L' and resid 12 through 19 Processing helix chain 'L' and resid 41 through 46 Processing helix chain 'L' and resid 101 through 105 removed outlier: 3.847A pdb=" N ASN L 104 " --> pdb=" O ASN L 101 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU L 105 " --> pdb=" O PHE L 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 101 through 105' Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 175 through 180 Processing helix chain 'D' and resid 25 through 46 removed outlier: 4.191A pdb=" N GLU D 29 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS D 37 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 616 through 629 removed outlier: 3.792A pdb=" N PHE A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 628 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 629 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 646 removed outlier: 3.501A pdb=" N GLN A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 removed outlier: 3.588A pdb=" N CYS A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 666 " --> pdb=" O THR A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 774 removed outlier: 3.751A pdb=" N VAL A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 774 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 782 through 795 removed outlier: 4.727A pdb=" N GLU A 788 " --> pdb=" O CYS A 784 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 808 removed outlier: 4.356A pdb=" N VAL A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 804 " --> pdb=" O GLY A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 850 Processing helix chain 'A' and resid 867 through 881 removed outlier: 3.623A pdb=" N LEU A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 938 Processing helix chain 'A' and resid 940 through 945 removed outlier: 3.781A pdb=" N GLU A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 964 Proline residue: A 954 - end of helix Processing helix chain 'A' and resid 974 through 979 Processing helix chain 'A' and resid 980 through 984 removed outlier: 4.206A pdb=" N LEU A 983 " --> pdb=" O ARG A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 removed outlier: 3.500A pdb=" N TRP A1028 " --> pdb=" O MET A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1041 Processing helix chain 'A' and resid 1058 through 1078 removed outlier: 3.636A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.402A pdb=" N GLY A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1145 Processing helix chain 'A' and resid 1154 through 1160 Processing helix chain 'A' and resid 1168 through 1182 Processing helix chain 'A' and resid 1184 through 1188 Processing helix chain 'A' and resid 1189 through 1198 Processing helix chain 'A' and resid 1201 through 1215 removed outlier: 3.559A pdb=" N SER A1205 " --> pdb=" O HIS A1201 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A1213 " --> pdb=" O LEU A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1230 removed outlier: 3.775A pdb=" N ILE A1230 " --> pdb=" O ARG A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1261 removed outlier: 3.609A pdb=" N VAL A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A1255 " --> pdb=" O VAL A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1278 removed outlier: 3.587A pdb=" N ALA A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 removed outlier: 3.779A pdb=" N CYS A1306 " --> pdb=" O LEU A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1331 removed outlier: 3.612A pdb=" N GLY A1331 " --> pdb=" O GLN A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1375 Proline residue: A1365 - end of helix removed outlier: 3.580A pdb=" N TYR A1375 " --> pdb=" O LEU A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1397 removed outlier: 3.899A pdb=" N ASP A1397 " --> pdb=" O MET A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1415 removed outlier: 3.741A pdb=" N LEU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1428 Processing helix chain 'A' and resid 1431 through 1437 removed outlier: 3.642A pdb=" N GLU A1436 " --> pdb=" O GLN A1432 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN A1437 " --> pdb=" O ILE A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1476 removed outlier: 3.691A pdb=" N VAL A1462 " --> pdb=" O SER A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1500 removed outlier: 3.694A pdb=" N CYS A1487 " --> pdb=" O SER A1483 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A1500 " --> pdb=" O MET A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1508 Processing helix chain 'A' and resid 1508 through 1527 Processing helix chain 'A' and resid 1532 through 1544 Processing helix chain 'A' and resid 1551 through 1566 removed outlier: 3.605A pdb=" N PHE A1566 " --> pdb=" O LEU A1562 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1570 Processing helix chain 'A' and resid 1577 through 1588 removed outlier: 3.778A pdb=" N ALA A1582 " --> pdb=" O ASN A1578 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS A1586 " --> pdb=" O ALA A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1612 removed outlier: 3.542A pdb=" N ARG A1607 " --> pdb=" O GLN A1604 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A1608 " --> pdb=" O ALA A1605 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR A1610 " --> pdb=" O ARG A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1693 removed outlier: 3.929A pdb=" N LEU A1687 " --> pdb=" O GLY A1683 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A1693 " --> pdb=" O SER A1689 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1732 Processing helix chain 'A' and resid 1736 through 1741 removed outlier: 4.208A pdb=" N SER A1739 " --> pdb=" O GLU A1736 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1754 Processing helix chain 'A' and resid 1764 through 1781 removed outlier: 3.934A pdb=" N LEU A1768 " --> pdb=" O LYS A1764 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A1781 " --> pdb=" O GLU A1777 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1800 removed outlier: 3.527A pdb=" N ILE A1791 " --> pdb=" O LEU A1787 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A1794 " --> pdb=" O TYR A1790 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A1798 " --> pdb=" O ASP A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1808 through 1819 Processing helix chain 'A' and resid 1823 through 1829 Processing helix chain 'A' and resid 1844 through 1863 Processing helix chain 'A' and resid 1864 through 1874 removed outlier: 3.680A pdb=" N HIS A1869 " --> pdb=" O ASP A1865 " (cutoff:3.500A) Processing helix chain 'A' and resid 1881 through 1892 removed outlier: 3.644A pdb=" N CYS A1887 " --> pdb=" O SER A1883 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A1891 " --> pdb=" O CYS A1887 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1920 removed outlier: 3.661A pdb=" N LYS A1917 " --> pdb=" O GLU A1913 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A1920 " --> pdb=" O PHE A1916 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1932 removed outlier: 3.676A pdb=" N LEU A1928 " --> pdb=" O PRO A1924 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG A1930 " --> pdb=" O ARG A1926 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 29 removed outlier: 4.182A pdb=" N VAL N 27 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 65 removed outlier: 3.824A pdb=" N ARG N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA N 57 " --> pdb=" O GLU N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 86 removed outlier: 4.241A pdb=" N GLU N 73 " --> pdb=" O SER N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 101 removed outlier: 4.444A pdb=" N ALA N 94 " --> pdb=" O GLU N 90 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE N 95 " --> pdb=" O PHE N 91 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER N 96 " --> pdb=" O TRP N 92 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 138 Proline residue: N 124 - end of helix removed outlier: 3.794A pdb=" N LEU N 138 " --> pdb=" O LYS N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 162 removed outlier: 3.655A pdb=" N LEU N 161 " --> pdb=" O LEU N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 193 removed outlier: 3.693A pdb=" N MET N 172 " --> pdb=" O THR N 168 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU N 192 " --> pdb=" O LYS N 188 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY N 193 " --> pdb=" O ARG N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 207 through 215 Processing helix chain 'N' and resid 216 through 218 No H-bonds generated for 'chain 'N' and resid 216 through 218' Processing helix chain 'N' and resid 235 through 250 removed outlier: 3.960A pdb=" N HIS N 241 " --> pdb=" O LEU N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 257 removed outlier: 3.673A pdb=" N SER N 257 " --> pdb=" O LEU N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 278 removed outlier: 3.690A pdb=" N THR N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG N 270 " --> pdb=" O HIS N 266 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 285 through 304 removed outlier: 4.189A pdb=" N GLU N 294 " --> pdb=" O HIS N 290 " (cutoff:3.500A) Processing helix chain 'N' and resid 315 through 343 removed outlier: 3.959A pdb=" N SER N 338 " --> pdb=" O ARG N 334 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 349 Processing helix chain 'N' and resid 355 through 366 removed outlier: 4.241A pdb=" N GLU N 366 " --> pdb=" O LYS N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 386 removed outlier: 3.797A pdb=" N THR N 384 " --> pdb=" O ALA N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 392 through 411 removed outlier: 3.578A pdb=" N ILE N 396 " --> pdb=" O ASN N 392 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL N 409 " --> pdb=" O LYS N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 421 removed outlier: 3.613A pdb=" N GLU N 418 " --> pdb=" O MET N 414 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 430 removed outlier: 3.793A pdb=" N ARG N 429 " --> pdb=" O ARG N 425 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR N 430 " --> pdb=" O ARG N 426 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 445 removed outlier: 3.983A pdb=" N LEU N 442 " --> pdb=" O ILE N 438 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR N 443 " --> pdb=" O VAL N 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP N 445 " --> pdb=" O GLY N 441 " (cutoff:3.500A) Processing helix chain 'N' and resid 500 through 507 removed outlier: 3.643A pdb=" N SER N 507 " --> pdb=" O SER N 503 " (cutoff:3.500A) Processing helix chain 'N' and resid 512 through 528 removed outlier: 3.624A pdb=" N ILE N 516 " --> pdb=" O LYS N 512 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER N 521 " --> pdb=" O ASN N 517 " (cutoff:3.500A) Processing helix chain 'N' and resid 537 through 544 removed outlier: 3.622A pdb=" N LEU N 544 " --> pdb=" O ARG N 540 " (cutoff:3.500A) Processing helix chain 'N' and resid 545 through 550 Processing helix chain 'N' and resid 551 through 553 No H-bonds generated for 'chain 'N' and resid 551 through 553' Processing helix chain 'N' and resid 554 through 575 removed outlier: 4.244A pdb=" N VAL N 559 " --> pdb=" O HIS N 555 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N MET N 560 " --> pdb=" O PHE N 556 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU N 561 " --> pdb=" O CYS N 557 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP N 563 " --> pdb=" O VAL N 559 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA N 565 " --> pdb=" O LEU N 561 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN N 571 " --> pdb=" O SER N 567 " (cutoff:3.500A) Processing helix chain 'N' and resid 612 through 630 removed outlier: 3.704A pdb=" N ALA N 617 " --> pdb=" O GLU N 613 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA N 618 " --> pdb=" O ASP N 614 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR N 622 " --> pdb=" O ALA N 618 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN N 628 " --> pdb=" O LYS N 624 " (cutoff:3.500A) Processing helix chain 'N' and resid 660 through 669 removed outlier: 4.524A pdb=" N ILE N 666 " --> pdb=" O VAL N 662 " (cutoff:3.500A) Processing helix chain 'N' and resid 677 through 685 removed outlier: 3.664A pdb=" N LYS N 683 " --> pdb=" O GLU N 679 " (cutoff:3.500A) Processing helix chain 'N' and resid 693 through 701 removed outlier: 3.986A pdb=" N VAL N 698 " --> pdb=" O ARG N 695 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP N 699 " --> pdb=" O MET N 696 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU N 700 " --> pdb=" O SER N 697 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 124 removed outlier: 3.511A pdb=" N SER I 122 " --> pdb=" O THR I 119 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL I 124 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 170 removed outlier: 4.061A pdb=" N ASP I 170 " --> pdb=" O LYS I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 244 Processing helix chain 'I' and resid 244 through 275 removed outlier: 3.794A pdb=" N HIS I 257 " --> pdb=" O ARG I 253 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU I 269 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA I 275 " --> pdb=" O CYS I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 293 removed outlier: 3.644A pdb=" N VAL I 291 " --> pdb=" O LEU I 287 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN I 292 " --> pdb=" O THR I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 311 Processing helix chain 'I' and resid 314 through 323 Processing helix chain 'I' and resid 328 through 350 removed outlier: 4.292A pdb=" N LYS I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE I 349 " --> pdb=" O GLN I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 372 removed outlier: 3.560A pdb=" N GLU I 365 " --> pdb=" O TYR I 361 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP I 372 " --> pdb=" O GLY I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 427 removed outlier: 3.629A pdb=" N ILE I 386 " --> pdb=" O ASP I 382 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR I 391 " --> pdb=" O GLU I 387 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA I 416 " --> pdb=" O LYS I 412 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 456 Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.664A pdb=" N LEU I 479 " --> pdb=" O VAL I 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 503 removed outlier: 3.734A pdb=" N ASN I 503 " --> pdb=" O ASP I 499 " (cutoff:3.500A) Processing helix chain 'I' and resid 521 through 546 removed outlier: 3.701A pdb=" N ILE I 532 " --> pdb=" O ARG I 528 " (cutoff:3.500A) Proline residue: I 540 - end of helix removed outlier: 3.589A pdb=" N GLY I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) Processing helix chain 'I' and resid 560 through 564 removed outlier: 3.948A pdb=" N ASP I 564 " --> pdb=" O ARG I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 671 through 675 Processing helix chain 'I' and resid 676 through 681 Processing helix chain 'O' and resid 31 through 45 removed outlier: 3.609A pdb=" N MET O 44 " --> pdb=" O LEU O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 70 removed outlier: 3.646A pdb=" N ARG O 57 " --> pdb=" O SER O 53 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU O 63 " --> pdb=" O ARG O 59 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU O 65 " --> pdb=" O ASN O 61 " (cutoff:3.500A) Proline residue: O 66 - end of helix removed outlier: 3.644A pdb=" N GLN O 69 " --> pdb=" O LEU O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 removed outlier: 3.935A pdb=" N GLU O 84 " --> pdb=" O LYS O 80 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 103 removed outlier: 3.742A pdb=" N ASN O 91 " --> pdb=" O PRO O 87 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG O 96 " --> pdb=" O SER O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 116 removed outlier: 3.777A pdb=" N MET O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 119 No H-bonds generated for 'chain 'O' and resid 117 through 119' Processing helix chain 'O' and resid 130 through 145 Processing helix chain 'O' and resid 147 through 169 removed outlier: 3.783A pdb=" N LYS O 168 " --> pdb=" O ASN O 164 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR O 169 " --> pdb=" O GLY O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 226 removed outlier: 3.534A pdb=" N GLU O 213 " --> pdb=" O GLN O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 247 removed outlier: 3.781A pdb=" N PHE O 246 " --> pdb=" O ASN O 242 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN O 247 " --> pdb=" O LEU O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 263 removed outlier: 3.681A pdb=" N TYR O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG O 263 " --> pdb=" O LEU O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 281 removed outlier: 3.765A pdb=" N SER O 270 " --> pdb=" O ASP O 266 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU O 275 " --> pdb=" O THR O 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 315 removed outlier: 3.759A pdb=" N ALA O 304 " --> pdb=" O LEU O 300 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU O 305 " --> pdb=" O ARG O 301 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 334 removed outlier: 3.699A pdb=" N GLU O 326 " --> pdb=" O LEU O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 351 removed outlier: 3.609A pdb=" N GLN O 341 " --> pdb=" O HIS O 337 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 370 removed outlier: 3.741A pdb=" N LEU O 360 " --> pdb=" O ASP O 356 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 391 removed outlier: 3.554A pdb=" N ALA O 377 " --> pdb=" O LEU O 373 " (cutoff:3.500A) Processing helix chain 'O' and resid 394 through 413 removed outlier: 3.812A pdb=" N ASP O 404 " --> pdb=" O ASP O 400 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER O 405 " --> pdb=" O ALA O 401 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU O 408 " --> pdb=" O ASP O 404 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP O 410 " --> pdb=" O ASP O 406 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 432 removed outlier: 3.793A pdb=" N ARG O 430 " --> pdb=" O THR O 426 " (cutoff:3.500A) Processing helix chain 'O' and resid 434 through 447 Processing helix chain 'O' and resid 463 through 480 removed outlier: 3.547A pdb=" N ALA O 467 " --> pdb=" O THR O 463 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN O 480 " --> pdb=" O LEU O 476 " (cutoff:3.500A) Processing helix chain 'O' and resid 482 through 497 Processing helix chain 'O' and resid 504 through 523 removed outlier: 3.825A pdb=" N CYS O 510 " --> pdb=" O LEU O 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 524 through 539 removed outlier: 4.090A pdb=" N THR O 533 " --> pdb=" O ASP O 529 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) Processing helix chain 'O' and resid 539 through 554 Processing helix chain 'O' and resid 556 through 575 Processing helix chain 'O' and resid 576 through 592 Processing helix chain 'O' and resid 596 through 599 removed outlier: 3.590A pdb=" N ILE O 599 " --> pdb=" O SER O 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 596 through 599' Processing helix chain 'O' and resid 600 through 614 removed outlier: 3.606A pdb=" N ALA O 609 " --> pdb=" O LEU O 605 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU O 613 " --> pdb=" O ALA O 609 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR O 614 " --> pdb=" O LEU O 610 " (cutoff:3.500A) Processing helix chain 'O' and resid 616 through 634 removed outlier: 3.791A pdb=" N GLU O 622 " --> pdb=" O TYR O 618 " (cutoff:3.500A) Processing helix chain 'O' and resid 636 through 647 removed outlier: 4.107A pdb=" N MET O 646 " --> pdb=" O SER O 642 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA O 647 " --> pdb=" O LEU O 643 " (cutoff:3.500A) Processing helix chain 'O' and resid 648 through 654 Processing helix chain 'O' and resid 656 through 674 removed outlier: 3.573A pdb=" N MET O 664 " --> pdb=" O LYS O 660 " (cutoff:3.500A) Processing helix chain 'O' and resid 679 through 705 removed outlier: 3.718A pdb=" N ALA O 690 " --> pdb=" O ALA O 686 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE O 691 " --> pdb=" O LEU O 687 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU O 692 " --> pdb=" O GLU O 688 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN O 693 " --> pdb=" O ALA O 689 " (cutoff:3.500A) Processing helix chain 'O' and resid 706 through 725 removed outlier: 4.127A pdb=" N ASP O 712 " --> pdb=" O GLU O 708 " (cutoff:3.500A) Processing helix chain 'O' and resid 726 through 742 removed outlier: 4.366A pdb=" N ARG O 732 " --> pdb=" O GLN O 728 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN O 742 " --> pdb=" O ARG O 738 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'K' and resid 18 through 33 Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 62 removed outlier: 3.749A pdb=" N LEU K 60 " --> pdb=" O ALA K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 85 through 94 removed outlier: 3.571A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP K 94 " --> pdb=" O LEU K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 143 Processing helix chain 'K' and resid 145 through 160 Processing helix chain 'K' and resid 163 through 171 Processing helix chain 'K' and resid 177 through 188 removed outlier: 3.781A pdb=" N LEU K 185 " --> pdb=" O GLU K 181 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU K 186 " --> pdb=" O LYS K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 210 removed outlier: 3.691A pdb=" N LEU K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 230 removed outlier: 3.557A pdb=" N GLN K 228 " --> pdb=" O ASP K 225 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU K 229 " --> pdb=" O GLY K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 246 through 261 removed outlier: 3.829A pdb=" N VAL K 256 " --> pdb=" O LYS K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 276 removed outlier: 4.717A pdb=" N VAL K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 298 through 313 removed outlier: 4.103A pdb=" N TRP K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY K 313 " --> pdb=" O TYR K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 removed outlier: 3.764A pdb=" N ARG K 321 " --> pdb=" O GLU K 317 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR K 322 " --> pdb=" O HIS K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 346 removed outlier: 4.079A pdb=" N TRP K 337 " --> pdb=" O TYR K 333 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE K 338 " --> pdb=" O GLY K 334 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE K 344 " --> pdb=" O TYR K 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 364 removed outlier: 3.767A pdb=" N LEU K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 380 removed outlier: 3.601A pdb=" N ILE K 374 " --> pdb=" O PRO K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 398 removed outlier: 4.213A pdb=" N PHE K 390 " --> pdb=" O LEU K 386 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN K 393 " --> pdb=" O ARG K 389 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 414 Processing helix chain 'K' and resid 417 through 436 removed outlier: 3.771A pdb=" N LYS K 423 " --> pdb=" O LYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 444 through 458 removed outlier: 3.584A pdb=" N LEU K 448 " --> pdb=" O TRP K 444 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS K 455 " --> pdb=" O LEU K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 475 removed outlier: 3.717A pdb=" N VAL K 473 " --> pdb=" O ARG K 469 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU K 474 " --> pdb=" O GLN K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 492 Processing helix chain 'K' and resid 494 through 509 Processing helix chain 'K' and resid 512 through 528 removed outlier: 3.821A pdb=" N GLU K 524 " --> pdb=" O GLY K 520 " (cutoff:3.500A) Processing helix chain 'K' and resid 554 through 560 Processing helix chain 'C' and resid 34 through 38 removed outlier: 3.731A pdb=" N LYS C 38 " --> pdb=" O PRO C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.746A pdb=" N LEU C 61 " --> pdb=" O MET C 57 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS C 62 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP C 63 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 14 No H-bonds generated for 'chain 'G' and resid 12 through 14' Processing helix chain 'G' and resid 15 through 27 removed outlier: 3.822A pdb=" N PHE G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 14 No H-bonds generated for 'chain 'W' and resid 12 through 14' Processing helix chain 'W' and resid 15 through 25 removed outlier: 4.268A pdb=" N ILE W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 15 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 51 through 56 removed outlier: 3.632A pdb=" N LYS M 56 " --> pdb=" O GLN M 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 92 removed outlier: 3.758A pdb=" N GLN H 75 " --> pdb=" O LYS H 71 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU H 88 " --> pdb=" O GLY H 84 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU H 90 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 Processing helix chain 'H' and resid 98 through 103 Processing helix chain 'J' and resid 6 through 18 Processing helix chain 'J' and resid 20 through 35 Processing helix chain 'J' and resid 37 through 51 Processing helix chain 'J' and resid 53 through 63 removed outlier: 3.829A pdb=" N ALA J 57 " --> pdb=" O LYS J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 82 Processing helix chain 'J' and resid 84 through 93 removed outlier: 3.531A pdb=" N LEU J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 111 Processing helix chain 'J' and resid 113 through 128 Processing helix chain 'J' and resid 130 through 145 Processing helix chain 'J' and resid 148 through 158 removed outlier: 4.266A pdb=" N PHE J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 168 Processing helix chain 'J' and resid 452 through 478 removed outlier: 4.036A pdb=" N ALA J 458 " --> pdb=" O LEU J 454 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU J 462 " --> pdb=" O ALA J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 490 removed outlier: 3.522A pdb=" N HIS J 490 " --> pdb=" O ASN J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 497 Processing helix chain 'J' and resid 498 through 512 Processing helix chain 'J' and resid 514 through 529 Processing helix chain 'J' and resid 535 through 547 removed outlier: 3.841A pdb=" N TYR J 539 " --> pdb=" O GLY J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 563 removed outlier: 3.602A pdb=" N ASP J 561 " --> pdb=" O LYS J 557 " (cutoff:3.500A) Processing helix chain 'J' and resid 566 through 580 removed outlier: 3.706A pdb=" N TRP J 570 " --> pdb=" O SER J 566 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN J 580 " --> pdb=" O CYS J 576 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 597 Processing helix chain 'J' and resid 600 through 614 removed outlier: 3.864A pdb=" N TYR J 604 " --> pdb=" O TYR J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 616 through 631 Processing helix chain 'J' and resid 634 through 648 removed outlier: 3.680A pdb=" N TRP J 638 " --> pdb=" O HIS J 634 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 665 Processing helix chain 'J' and resid 668 through 682 Processing helix chain 'J' and resid 684 through 699 removed outlier: 3.656A pdb=" N ASP J 690 " --> pdb=" O GLU J 686 " (cutoff:3.500A) Processing helix chain 'J' and resid 702 through 716 Processing helix chain 'J' and resid 718 through 731 Processing helix chain 'J' and resid 736 through 750 removed outlier: 4.026A pdb=" N TYR J 740 " --> pdb=" O GLU J 736 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS J 749 " --> pdb=" O LYS J 745 " (cutoff:3.500A) Processing helix chain 'J' and resid 752 through 766 removed outlier: 3.598A pdb=" N TRP J 762 " --> pdb=" O MET J 758 " (cutoff:3.500A) Processing helix chain 'J' and resid 771 through 780 removed outlier: 3.831A pdb=" N ILE J 775 " --> pdb=" O ALA J 771 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS J 776 " --> pdb=" O ASN J 772 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 18 Processing helix chain 'P' and resid 20 through 35 removed outlier: 3.871A pdb=" N PHE P 26 " --> pdb=" O ARG P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 51 removed outlier: 3.532A pdb=" N SER P 51 " --> pdb=" O CYS P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 removed outlier: 3.929A pdb=" N GLY P 63 " --> pdb=" O ARG P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'P' and resid 84 through 93 Processing helix chain 'P' and resid 102 through 111 Processing helix chain 'P' and resid 113 through 128 Processing helix chain 'P' and resid 130 through 145 removed outlier: 3.606A pdb=" N GLU P 136 " --> pdb=" O ALA P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 159 Processing helix chain 'P' and resid 163 through 168 removed outlier: 3.528A pdb=" N PHE P 168 " --> pdb=" O PRO P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 478 removed outlier: 5.001A pdb=" N GLY P 461 " --> pdb=" O ALA P 457 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU P 462 " --> pdb=" O ALA P 458 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY P 472 " --> pdb=" O GLU P 468 " (cutoff:3.500A) Processing helix chain 'P' and resid 480 through 489 Processing helix chain 'P' and resid 492 through 497 Processing helix chain 'P' and resid 498 through 512 Processing helix chain 'P' and resid 514 through 529 Processing helix chain 'P' and resid 535 through 546 removed outlier: 3.645A pdb=" N TYR P 539 " --> pdb=" O GLY P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 548 through 561 Processing helix chain 'P' and resid 566 through 580 removed outlier: 3.947A pdb=" N TRP P 570 " --> pdb=" O SER P 566 " (cutoff:3.500A) Processing helix chain 'P' and resid 582 through 597 Processing helix chain 'P' and resid 600 through 614 removed outlier: 4.122A pdb=" N TYR P 604 " --> pdb=" O TYR P 600 " (cutoff:3.500A) Processing helix chain 'P' and resid 616 through 631 removed outlier: 3.843A pdb=" N ALA P 622 " --> pdb=" O ASP P 618 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS P 623 " --> pdb=" O LYS P 619 " (cutoff:3.500A) Processing helix chain 'P' and resid 634 through 648 removed outlier: 3.728A pdb=" N TRP P 638 " --> pdb=" O HIS P 634 " (cutoff:3.500A) Processing helix chain 'P' and resid 650 through 665 removed outlier: 3.793A pdb=" N ILE P 664 " --> pdb=" O LYS P 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 668 through 682 Processing helix chain 'P' and resid 684 through 699 removed outlier: 4.048A pdb=" N ASP P 690 " --> pdb=" O GLU P 686 " (cutoff:3.500A) Processing helix chain 'P' and resid 702 through 716 removed outlier: 4.269A pdb=" N LYS P 706 " --> pdb=" O ASN P 702 " (cutoff:3.500A) Processing helix chain 'P' and resid 718 through 731 removed outlier: 3.640A pdb=" N GLN P 731 " --> pdb=" O GLU P 727 " (cutoff:3.500A) Processing helix chain 'P' and resid 737 through 750 Processing helix chain 'P' and resid 752 through 767 removed outlier: 3.526A pdb=" N ASN P 759 " --> pdb=" O LEU P 755 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP P 762 " --> pdb=" O MET P 758 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 16 Processing helix chain 'Q' and resid 18 through 33 removed outlier: 3.533A pdb=" N PHE Q 24 " --> pdb=" O GLN Q 20 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP Q 25 " --> pdb=" O SER Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 62 Processing helix chain 'Q' and resid 64 through 69 removed outlier: 3.982A pdb=" N LEU Q 68 " --> pdb=" O LYS Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 83 Processing helix chain 'Q' and resid 85 through 94 Processing helix chain 'Q' and resid 125 through 143 removed outlier: 4.243A pdb=" N LYS Q 129 " --> pdb=" O GLN Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 160 removed outlier: 4.203A pdb=" N TYR Q 151 " --> pdb=" O THR Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 172 removed outlier: 3.868A pdb=" N PHE Q 167 " --> pdb=" O CYS Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 188 Processing helix chain 'Q' and resid 195 through 207 Processing helix chain 'Q' and resid 230 through 244 Processing helix chain 'Q' and resid 246 through 252 Processing helix chain 'Q' and resid 256 through 261 Processing helix chain 'Q' and resid 266 through 278 removed outlier: 4.501A pdb=" N VAL Q 270 " --> pdb=" O SER Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 295 Processing helix chain 'Q' and resid 298 through 313 removed outlier: 3.964A pdb=" N TRP Q 302 " --> pdb=" O ASN Q 298 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY Q 313 " --> pdb=" O TYR Q 309 " (cutoff:3.500A) Processing helix chain 'Q' and resid 315 through 330 removed outlier: 3.529A pdb=" N GLU Q 330 " --> pdb=" O ALA Q 326 " (cutoff:3.500A) Processing helix chain 'Q' and resid 333 through 346 removed outlier: 4.204A pdb=" N TRP Q 337 " --> pdb=" O TYR Q 333 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE Q 338 " --> pdb=" O GLY Q 334 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE Q 344 " --> pdb=" O TYR Q 340 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 364 removed outlier: 3.527A pdb=" N ALA Q 356 " --> pdb=" O GLN Q 352 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 381 Processing helix chain 'Q' and resid 383 through 398 Processing helix chain 'Q' and resid 401 through 416 removed outlier: 3.633A pdb=" N GLU Q 407 " --> pdb=" O PHE Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 417 through 433 Processing helix chain 'Q' and resid 444 through 458 removed outlier: 3.710A pdb=" N CYS Q 455 " --> pdb=" O LEU Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 475 removed outlier: 3.706A pdb=" N ASP Q 466 " --> pdb=" O ALA Q 462 " (cutoff:3.500A) Processing helix chain 'Q' and resid 478 through 493 Processing helix chain 'Q' and resid 494 through 510 removed outlier: 3.640A pdb=" N THR Q 504 " --> pdb=" O ASP Q 500 " (cutoff:3.500A) Processing helix chain 'Q' and resid 513 through 528 removed outlier: 3.872A pdb=" N THR Q 517 " --> pdb=" O THR Q 513 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU Q 519 " --> pdb=" O SER Q 515 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE Q 527 " --> pdb=" O ILE Q 523 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 48 Processing helix chain 'Y' and resid 51 through 67 removed outlier: 4.365A pdb=" N LEU Y 55 " --> pdb=" O SER Y 51 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR Y 62 " --> pdb=" O SER Y 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 72 through 89 Processing helix chain 'Y' and resid 92 through 109 Processing helix chain 'Y' and resid 134 through 149 Processing helix chain 'Y' and resid 151 through 162 removed outlier: 3.537A pdb=" N ALA Y 155 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE Y 162 " --> pdb=" O ILE Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 163 through 167 removed outlier: 3.997A pdb=" N ARG Y 167 " --> pdb=" O SER Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 168 through 182 removed outlier: 3.594A pdb=" N ASN Y 172 " --> pdb=" O THR Y 168 " (cutoff:3.500A) Processing helix chain 'Y' and resid 184 through 199 removed outlier: 3.769A pdb=" N THR Y 190 " --> pdb=" O ARG Y 186 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER Y 191 " --> pdb=" O PRO Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 212 Processing helix chain 'Y' and resid 215 through 223 removed outlier: 3.921A pdb=" N VAL Y 219 " --> pdb=" O LYS Y 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 228 removed outlier: 3.789A pdb=" N ILE Y 227 " --> pdb=" O THR Y 223 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Y 228 " --> pdb=" O MET Y 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 223 through 228' Processing helix chain 'Y' and resid 235 through 247 removed outlier: 3.556A pdb=" N PHE Y 245 " --> pdb=" O LYS Y 241 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS Y 247 " --> pdb=" O TYR Y 243 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 265 Processing helix chain 'Y' and resid 270 through 285 Processing helix chain 'Y' and resid 290 through 301 removed outlier: 3.747A pdb=" N GLN Y 296 " --> pdb=" O LEU Y 292 " (cutoff:3.500A) Processing helix chain 'Y' and resid 307 through 318 removed outlier: 3.534A pdb=" N TYR Y 313 " --> pdb=" O ASP Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 320 through 333 Processing helix chain 'Y' and resid 339 through 352 Processing helix chain 'Y' and resid 354 through 369 removed outlier: 3.551A pdb=" N TYR Y 360 " --> pdb=" O SER Y 356 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA Y 365 " --> pdb=" O LEU Y 361 " (cutoff:3.500A) Processing helix chain 'Y' and resid 372 through 387 removed outlier: 3.651A pdb=" N LEU Y 376 " --> pdb=" O SER Y 372 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 403 removed outlier: 3.752A pdb=" N ILE Y 394 " --> pdb=" O GLN Y 390 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS Y 395 " --> pdb=" O GLU Y 391 " (cutoff:3.500A) Processing helix chain 'Y' and resid 406 through 420 removed outlier: 3.835A pdb=" N TYR Y 410 " --> pdb=" O ARG Y 406 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU Y 413 " --> pdb=" O CYS Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 437 Processing helix chain 'Y' and resid 440 through 450 removed outlier: 3.531A pdb=" N VAL Y 450 " --> pdb=" O LEU Y 446 " (cutoff:3.500A) Processing helix chain 'Y' and resid 451 through 453 No H-bonds generated for 'chain 'Y' and resid 451 through 453' Processing helix chain 'Y' and resid 454 through 456 No H-bonds generated for 'chain 'Y' and resid 454 through 456' Processing helix chain 'Y' and resid 457 through 472 removed outlier: 3.739A pdb=" N THR Y 463 " --> pdb=" O GLU Y 459 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU Y 465 " --> pdb=" O ALA Y 461 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU Y 469 " --> pdb=" O LEU Y 465 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN Y 471 " --> pdb=" O LYS Y 467 " (cutoff:3.500A) Processing helix chain 'Y' and resid 475 through 490 Processing helix chain 'Y' and resid 491 through 504 Processing helix chain 'Y' and resid 508 through 523 removed outlier: 3.585A pdb=" N HIS Y 512 " --> pdb=" O ASP Y 508 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA Y 521 " --> pdb=" O ASP Y 517 " (cutoff:3.500A) Processing helix chain 'Y' and resid 524 through 539 Processing helix chain 'Y' and resid 542 through 554 removed outlier: 3.704A pdb=" N MET Y 552 " --> pdb=" O GLY Y 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 46 removed outlier: 3.550A pdb=" N ARG U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 62 removed outlier: 3.589A pdb=" N SER U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 82 Processing helix chain 'U' and resid 83 through 96 removed outlier: 3.829A pdb=" N VAL U 96 " --> pdb=" O ALA U 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 98 through 106 Processing helix chain 'U' and resid 111 through 134 removed outlier: 3.548A pdb=" N THR U 134 " --> pdb=" O LYS U 130 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 164 removed outlier: 3.753A pdb=" N LEU U 154 " --> pdb=" O ALA U 150 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA U 164 " --> pdb=" O LYS U 160 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 182 Processing helix chain 'U' and resid 184 through 199 removed outlier: 3.932A pdb=" N ASP U 190 " --> pdb=" O LYS U 186 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL U 191 " --> pdb=" O GLU U 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 211 removed outlier: 4.074A pdb=" N TRP U 206 " --> pdb=" O HIS U 202 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN U 211 " --> pdb=" O LEU U 207 " (cutoff:3.500A) Processing helix chain 'U' and resid 215 through 222 removed outlier: 3.525A pdb=" N LEU U 222 " --> pdb=" O MET U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 241 removed outlier: 3.939A pdb=" N PHE U 232 " --> pdb=" O TRP U 228 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR U 239 " --> pdb=" O ALA U 235 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU U 240 " --> pdb=" O HIS U 236 " (cutoff:3.500A) Processing helix chain 'U' and resid 243 through 258 removed outlier: 3.705A pdb=" N ALA U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY U 258 " --> pdb=" O LEU U 254 " (cutoff:3.500A) Processing helix chain 'U' and resid 262 through 276 removed outlier: 3.544A pdb=" N VAL U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 293 removed outlier: 3.695A pdb=" N SER U 284 " --> pdb=" O ASP U 280 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE U 285 " --> pdb=" O LYS U 281 " (cutoff:3.500A) Processing helix chain 'U' and resid 299 through 309 removed outlier: 3.565A pdb=" N PHE U 303 " --> pdb=" O ASN U 299 " (cutoff:3.500A) Processing helix chain 'U' and resid 312 through 327 removed outlier: 3.838A pdb=" N TYR U 318 " --> pdb=" O SER U 314 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE U 326 " --> pdb=" O ASN U 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 330 through 344 Processing helix chain 'U' and resid 346 through 361 Processing helix chain 'U' and resid 367 through 378 Processing helix chain 'U' and resid 380 through 395 Processing helix chain 'U' and resid 398 through 412 Processing helix chain 'U' and resid 414 through 429 removed outlier: 3.886A pdb=" N LEU U 428 " --> pdb=" O ARG U 424 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 446 removed outlier: 4.061A pdb=" N LEU U 436 " --> pdb=" O ASP U 432 " (cutoff:3.500A) Processing helix chain 'U' and resid 448 through 462 removed outlier: 3.541A pdb=" N ALA U 452 " --> pdb=" O GLN U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 468 through 480 removed outlier: 3.716A pdb=" N HIS U 477 " --> pdb=" O LEU U 473 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU U 478 " --> pdb=" O ALA U 474 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN U 479 " --> pdb=" O LYS U 475 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU U 480 " --> pdb=" O LEU U 476 " (cutoff:3.500A) Processing helix chain 'U' and resid 483 through 500 removed outlier: 3.557A pdb=" N LYS U 492 " --> pdb=" O GLN U 488 " (cutoff:3.500A) Processing helix chain 'U' and resid 510 through 517 removed outlier: 3.683A pdb=" N ARG U 514 " --> pdb=" O SER U 510 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR U 515 " --> pdb=" O THR U 511 " (cutoff:3.500A) Processing helix chain 'U' and resid 518 through 523 Processing helix chain 'U' and resid 526 through 536 removed outlier: 3.575A pdb=" N THR U 531 " --> pdb=" O ASP U 527 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN U 534 " --> pdb=" O SER U 530 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS U 535 " --> pdb=" O THR U 531 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS U 536 " --> pdb=" O CYS U 532 " (cutoff:3.500A) Processing helix chain 'U' and resid 542 through 553 removed outlier: 3.538A pdb=" N GLY U 546 " --> pdb=" O THR U 542 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 46 removed outlier: 3.621A pdb=" N LYS V 34 " --> pdb=" O ARG V 30 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG V 44 " --> pdb=" O ALA V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 62 removed outlier: 3.728A pdb=" N SER V 61 " --> pdb=" O GLU V 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU V 62 " --> pdb=" O LEU V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 83 Processing helix chain 'V' and resid 83 through 96 removed outlier: 3.701A pdb=" N VAL V 96 " --> pdb=" O ALA V 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 105 removed outlier: 3.637A pdb=" N ALA V 102 " --> pdb=" O GLU V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 135 removed outlier: 3.626A pdb=" N PHE V 116 " --> pdb=" O LYS V 112 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY V 126 " --> pdb=" O ARG V 122 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL V 135 " --> pdb=" O ASP V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 151 through 164 Processing helix chain 'V' and resid 168 through 182 Processing helix chain 'V' and resid 184 through 199 removed outlier: 3.508A pdb=" N ALA V 188 " --> pdb=" O LEU V 184 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP V 190 " --> pdb=" O LYS V 186 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 210 removed outlier: 4.174A pdb=" N TRP V 206 " --> pdb=" O HIS V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 215 through 222 removed outlier: 4.086A pdb=" N LEU V 219 " --> pdb=" O ASP V 215 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS V 220 " --> pdb=" O LYS V 216 " (cutoff:3.500A) Processing helix chain 'V' and resid 228 through 239 removed outlier: 3.655A pdb=" N PHE V 232 " --> pdb=" O TRP V 228 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA V 235 " --> pdb=" O GLU V 231 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR V 239 " --> pdb=" O ALA V 235 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 257 removed outlier: 3.573A pdb=" N VAL V 257 " --> pdb=" O ASN V 253 " (cutoff:3.500A) Processing helix chain 'V' and resid 262 through 276 Processing helix chain 'V' and resid 278 through 293 removed outlier: 3.610A pdb=" N ASN V 287 " --> pdb=" O LEU V 283 " (cutoff:3.500A) Processing helix chain 'V' and resid 299 through 311 removed outlier: 3.579A pdb=" N PHE V 303 " --> pdb=" O ASN V 299 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG V 310 " --> pdb=" O LEU V 306 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 325 removed outlier: 3.596A pdb=" N GLU V 325 " --> pdb=" O HIS V 321 " (cutoff:3.500A) Processing helix chain 'V' and resid 330 through 344 Processing helix chain 'V' and resid 346 through 361 Processing helix chain 'V' and resid 365 through 378 removed outlier: 4.091A pdb=" N THR V 369 " --> pdb=" O LEU V 365 " (cutoff:3.500A) Processing helix chain 'V' and resid 380 through 395 removed outlier: 3.771A pdb=" N VAL V 394 " --> pdb=" O HIS V 390 " (cutoff:3.500A) Processing helix chain 'V' and resid 398 through 412 removed outlier: 3.777A pdb=" N TYR V 409 " --> pdb=" O LEU V 405 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 429 Processing helix chain 'V' and resid 432 through 445 removed outlier: 4.023A pdb=" N LEU V 436 " --> pdb=" O ASP V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 462 removed outlier: 3.611A pdb=" N LYS V 454 " --> pdb=" O VAL V 450 " (cutoff:3.500A) Processing helix chain 'V' and resid 468 through 480 Processing helix chain 'V' and resid 482 through 500 removed outlier: 3.869A pdb=" N GLN V 488 " --> pdb=" O GLU V 484 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS V 500 " --> pdb=" O ASP V 496 " (cutoff:3.500A) Processing helix chain 'V' and resid 508 through 523 Processing helix chain 'V' and resid 525 through 534 removed outlier: 3.506A pdb=" N THR V 531 " --> pdb=" O ASP V 527 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS V 532 " --> pdb=" O GLU V 528 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN V 534 " --> pdb=" O SER V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 535 through 539 removed outlier: 3.797A pdb=" N PHE V 539 " --> pdb=" O CYS V 536 " (cutoff:3.500A) Processing helix chain 'V' and resid 542 through 556 removed outlier: 3.641A pdb=" N ARG V 551 " --> pdb=" O LYS V 547 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 37 through 47 Processing helix chain 'Z' and resid 50 through 67 Processing helix chain 'Z' and resid 72 through 90 removed outlier: 3.504A pdb=" N SER Z 86 " --> pdb=" O TYR Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 111 removed outlier: 3.776A pdb=" N SER Z 111 " --> pdb=" O LYS Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 149 Processing helix chain 'Z' and resid 151 through 160 removed outlier: 3.559A pdb=" N LEU Z 159 " --> pdb=" O ALA Z 155 " (cutoff:3.500A) Processing helix chain 'Z' and resid 168 through 183 Processing helix chain 'Z' and resid 184 through 199 removed outlier: 3.682A pdb=" N SER Z 191 " --> pdb=" O PRO Z 187 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU Z 194 " --> pdb=" O THR Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 202 through 212 Processing helix chain 'Z' and resid 215 through 223 Processing helix chain 'Z' and resid 225 through 229 removed outlier: 3.776A pdb=" N GLN Z 228 " --> pdb=" O ASN Z 225 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR Z 229 " --> pdb=" O VAL Z 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 225 through 229' Processing helix chain 'Z' and resid 235 through 249 removed outlier: 3.543A pdb=" N PHE Z 245 " --> pdb=" O LYS Z 241 " (cutoff:3.500A) Processing helix chain 'Z' and resid 250 through 263 removed outlier: 4.067A pdb=" N SER Z 256 " --> pdb=" O SER Z 252 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS Z 259 " --> pdb=" O ILE Z 255 " (cutoff:3.500A) Processing helix chain 'Z' and resid 270 through 284 Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.608A pdb=" N VAL Z 291 " --> pdb=" O ASN Z 287 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU Z 292 " --> pdb=" O LYS Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 307 through 319 removed outlier: 3.731A pdb=" N GLY Z 312 " --> pdb=" O MET Z 308 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA Z 316 " --> pdb=" O GLY Z 312 " (cutoff:3.500A) Processing helix chain 'Z' and resid 320 through 334 removed outlier: 4.285A pdb=" N ARG Z 330 " --> pdb=" O ASN Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 338 through 351 removed outlier: 4.459A pdb=" N TRP Z 342 " --> pdb=" O HIS Z 338 " (cutoff:3.500A) Processing helix chain 'Z' and resid 354 through 369 removed outlier: 3.913A pdb=" N ALA Z 365 " --> pdb=" O LEU Z 361 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN Z 367 " --> pdb=" O ALA Z 363 " (cutoff:3.500A) Processing helix chain 'Z' and resid 372 through 386 Processing helix chain 'Z' and resid 392 through 403 removed outlier: 4.000A pdb=" N ARG Z 401 " --> pdb=" O ARG Z 397 " (cutoff:3.500A) Processing helix chain 'Z' and resid 406 through 420 removed outlier: 3.595A pdb=" N TYR Z 410 " --> pdb=" O ARG Z 406 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU Z 413 " --> pdb=" O CYS Z 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 423 through 438 Processing helix chain 'Z' and resid 440 through 453 removed outlier: 4.428A pdb=" N GLU Z 453 " --> pdb=" O THR Z 449 " (cutoff:3.500A) Processing helix chain 'Z' and resid 454 through 458 removed outlier: 3.610A pdb=" N GLN Z 458 " --> pdb=" O PRO Z 455 " (cutoff:3.500A) Processing helix chain 'Z' and resid 459 through 472 removed outlier: 3.681A pdb=" N THR Z 463 " --> pdb=" O GLU Z 459 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU Z 464 " --> pdb=" O LYS Z 460 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP Z 466 " --> pdb=" O LYS Z 462 " (cutoff:3.500A) Processing helix chain 'Z' and resid 475 through 489 removed outlier: 3.640A pdb=" N VAL Z 479 " --> pdb=" O TYR Z 475 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 507 removed outlier: 4.027A pdb=" N ALA Z 497 " --> pdb=" O GLU Z 493 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA Z 504 " --> pdb=" O ARG Z 500 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN Z 505 " --> pdb=" O ASN Z 501 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN Z 506 " --> pdb=" O ALA Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 513 through 522 removed outlier: 3.563A pdb=" N PHE Z 518 " --> pdb=" O ILE Z 514 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 539 removed outlier: 3.651A pdb=" N TYR Z 532 " --> pdb=" O ALA Z 528 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 100 Processing helix chain 'R' and resid 106 through 121 removed outlier: 3.591A pdb=" N GLU R 111 " --> pdb=" O PRO R 107 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS R 112 " --> pdb=" O THR R 108 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'L' and resid 106 through 112 removed outlier: 5.265A pdb=" N GLU L 107 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL L 98 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN L 144 " --> pdb=" O PRO L 91 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS L 93 " --> pdb=" O LEU L 142 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N ARG L 133 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 10.657A pdb=" N ARG L 70 " --> pdb=" O ARG L 133 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE L 135 " --> pdb=" O PHE L 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.652A pdb=" N GLY A 507 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU A 497 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 18 through 19 removed outlier: 5.927A pdb=" N ARG A 594 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP A 589 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR A 596 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE A 587 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU A 598 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA7, first strand: chain 'A' and resid 125 through 132 Processing sheet with id=AA8, first strand: chain 'A' and resid 177 through 182 Processing sheet with id=AA9, first strand: chain 'A' and resid 237 through 238 removed outlier: 6.697A pdb=" N VAL A 224 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N HIS A 411 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LYS A 226 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N TRP A 413 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 268 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR A 414 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N HIS A 266 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 255 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 249 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET A 257 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.836A pdb=" N LYS A 440 " --> pdb=" O PHE A 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.836A pdb=" N LYS A 440 " --> pdb=" O PHE A 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 860 through 862 removed outlier: 6.316A pdb=" N TYR A 860 " --> pdb=" O THR A 897 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1047 through 1048 removed outlier: 6.714A pdb=" N VAL A1047 " --> pdb=" O ARG A1110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1572 through 1574 Processing sheet with id=AB6, first strand: chain 'A' and resid 1655 through 1656 removed outlier: 4.334A pdb=" N THR A1655 " --> pdb=" O LEU A1619 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1647 through 1652 removed outlier: 6.968A pdb=" N LEU A1633 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A1668 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU A1635 " --> pdb=" O ILE A1666 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE A1666 " --> pdb=" O GLU A1635 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR A1637 " --> pdb=" O LYS A1664 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A1676 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 590 through 591 removed outlier: 6.744A pdb=" N GLY N 590 " --> pdb=" O TRP C 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'N' and resid 635 through 636 Processing sheet with id=AC1, first strand: chain 'N' and resid 655 through 656 removed outlier: 3.586A pdb=" N ASP N 647 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 4 " --> pdb=" O ASP N 647 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 12 through 15 removed outlier: 5.566A pdb=" N VAL I 13 " --> pdb=" O GLU I 745 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU I 745 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY I 15 " --> pdb=" O VAL I 743 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL I 730 " --> pdb=" O ASN I 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 23 through 28 removed outlier: 6.726A pdb=" N ALA I 38 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU I 26 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA I 36 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP I 56 " --> pdb=" O LEU I 46 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 68 through 73 removed outlier: 4.101A pdb=" N CYS I 70 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS I 89 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 110 through 117 removed outlier: 6.984A pdb=" N GLY I 179 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET I 113 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL I 177 " --> pdb=" O MET I 113 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TRP I 115 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE I 175 " --> pdb=" O TRP I 115 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE I 185 " --> pdb=" O ARG I 197 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG I 197 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU I 187 " --> pdb=" O ILE I 195 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 204 through 210 removed outlier: 5.172A pdb=" N CYS I 205 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU I 222 " --> pdb=" O CYS I 205 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA I 207 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER I 229 " --> pdb=" O ARG I 558 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG I 558 " --> pdb=" O SER I 229 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL I 231 " --> pdb=" O LEU I 556 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 574 through 578 removed outlier: 11.711A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG I 632 " --> pdb=" O PHE I 623 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 574 through 578 removed outlier: 11.711A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ARG I 703 " --> pdb=" O LEU I 615 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA I 617 " --> pdb=" O ARG I 703 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET I 705 " --> pdb=" O ALA I 617 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS I 619 " --> pdb=" O MET I 705 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE I 707 " --> pdb=" O LYS I 619 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N GLY I 621 " --> pdb=" O PHE I 707 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 636 through 645 removed outlier: 6.903A pdb=" N VAL I 652 " --> pdb=" O LEU I 639 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA I 641 " --> pdb=" O THR I 650 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR I 650 " --> pdb=" O ALA I 641 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N PHE I 643 " --> pdb=" O THR I 648 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR I 648 " --> pdb=" O PHE I 643 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 13 through 14 removed outlier: 4.199A pdb=" N MET O 13 " --> pdb=" O GLY V 139 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY V 139 " --> pdb=" O MET O 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'R' and resid 174 through 177 removed outlier: 5.143A pdb=" N THR R 466 " --> pdb=" O ALA R 462 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA R 462 " --> pdb=" O THR R 466 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA R 459 " --> pdb=" O LEU R 449 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEU R 449 " --> pdb=" O ALA R 459 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA R 461 " --> pdb=" O LEU R 447 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 191 through 192 removed outlier: 3.884A pdb=" N VAL R 200 " --> pdb=" O TYR R 207 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR R 207 " --> pdb=" O VAL R 200 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL R 206 " --> pdb=" O LEU R 219 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 229 through 234 removed outlier: 6.023A pdb=" N VAL R 250 " --> pdb=" O ASN R 263 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN R 263 " --> pdb=" O VAL R 250 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU R 252 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 274 through 276 Processing sheet with id=AD6, first strand: chain 'R' and resid 312 through 317 removed outlier: 3.507A pdb=" N GLN R 349 " --> pdb=" O VAL R 335 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 360 through 363 removed outlier: 3.713A pdb=" N ALA R 360 " --> pdb=" O GLY R 374 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE R 382 " --> pdb=" O ALA R 395 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA R 395 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE R 384 " --> pdb=" O LEU R 393 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 402 through 408 removed outlier: 3.726A pdb=" N SER R 404 " --> pdb=" O GLY R 417 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE R 427 " --> pdb=" O ALA R 437 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA R 437 " --> pdb=" O ILE R 427 " (cutoff:3.500A) 3865 hydrogen bonds defined for protein. 11377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.89 Time building geometry restraints manager: 22.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17501 1.33 - 1.45: 13408 1.45 - 1.57: 37879 1.57 - 1.69: 1 1.69 - 1.82: 630 Bond restraints: 69419 Sorted by residual: bond pdb=" C HIS A1591 " pdb=" N PHE A1592 " ideal model delta sigma weight residual 1.331 1.220 0.111 2.83e-02 1.25e+03 1.55e+01 bond pdb=" C LEU A 629 " pdb=" N PRO A 630 " ideal model delta sigma weight residual 1.331 1.368 -0.036 1.21e-02 6.83e+03 9.05e+00 bond pdb=" C SER K 297 " pdb=" N ASN K 298 " ideal model delta sigma weight residual 1.335 1.242 0.093 3.59e-02 7.76e+02 6.73e+00 bond pdb=" C THR I 144 " pdb=" N LEU I 145 " ideal model delta sigma weight residual 1.333 1.266 0.067 2.74e-02 1.33e+03 5.95e+00 bond pdb=" CA LYS J 650 " pdb=" CB LYS J 650 " ideal model delta sigma weight residual 1.526 1.490 0.036 1.51e-02 4.39e+03 5.82e+00 ... (remaining 69414 not shown) Histogram of bond angle deviations from ideal: 95.89 - 104.03: 946 104.03 - 112.17: 34201 112.17 - 120.30: 32503 120.30 - 128.44: 25749 128.44 - 136.58: 629 Bond angle restraints: 94028 Sorted by residual: angle pdb=" C HIS A 758 " pdb=" N ILE A 759 " pdb=" CA ILE A 759 " ideal model delta sigma weight residual 120.24 124.35 -4.11 6.30e-01 2.52e+00 4.25e+01 angle pdb=" C SER A1596 " pdb=" N THR A1597 " pdb=" CA THR A1597 " ideal model delta sigma weight residual 126.45 136.58 -10.13 1.77e+00 3.19e-01 3.27e+01 angle pdb=" C SER K 62 " pdb=" N ARG K 63 " pdb=" CA ARG K 63 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 angle pdb=" C LEU A1921 " pdb=" N LYS A1922 " pdb=" CA LYS A1922 " ideal model delta sigma weight residual 122.46 129.65 -7.19 1.41e+00 5.03e-01 2.60e+01 angle pdb=" CG1 ILE Z 334 " pdb=" CB ILE Z 334 " pdb=" CG2 ILE Z 334 " ideal model delta sigma weight residual 110.70 95.89 14.81 3.00e+00 1.11e-01 2.44e+01 ... (remaining 94023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 36905 18.33 - 36.67: 4132 36.67 - 55.00: 613 55.00 - 73.33: 145 73.33 - 91.67: 55 Dihedral angle restraints: 41850 sinusoidal: 16625 harmonic: 25225 Sorted by residual: dihedral pdb=" CA ASP A 969 " pdb=" C ASP A 969 " pdb=" N TRP A 970 " pdb=" CA TRP A 970 " ideal model delta harmonic sigma weight residual -180.00 -121.27 -58.73 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA GLU O 123 " pdb=" C GLU O 123 " pdb=" N PRO O 124 " pdb=" CA PRO O 124 " ideal model delta harmonic sigma weight residual -180.00 -141.07 -38.93 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA LEU R 202 " pdb=" C LEU R 202 " pdb=" N ASP R 203 " pdb=" CA ASP R 203 " ideal model delta harmonic sigma weight residual -180.00 -143.34 -36.66 0 5.00e+00 4.00e-02 5.38e+01 ... (remaining 41847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 9882 0.101 - 0.202: 613 0.202 - 0.303: 25 0.303 - 0.405: 4 0.405 - 0.506: 1 Chirality restraints: 10525 Sorted by residual: chirality pdb=" CB ILE U 297 " pdb=" CA ILE U 297 " pdb=" CG1 ILE U 297 " pdb=" CG2 ILE U 297 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CB ILE R 427 " pdb=" CA ILE R 427 " pdb=" CG1 ILE R 427 " pdb=" CG2 ILE R 427 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB ILE A 133 " pdb=" CA ILE A 133 " pdb=" CG1 ILE A 133 " pdb=" CG2 ILE A 133 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 10522 not shown) Planarity restraints: 11956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 970 " -0.095 5.00e-02 4.00e+02 1.45e-01 3.37e+01 pdb=" N PRO A 971 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO A 971 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO A 971 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO Y 73 " -0.064 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO Y 74 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO Y 74 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO Y 74 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1386 " -0.025 2.00e-02 2.50e+03 1.96e-02 9.58e+00 pdb=" CG TRP A1386 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A1386 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A1386 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1386 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1386 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1386 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1386 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1386 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1386 " -0.001 2.00e-02 2.50e+03 ... (remaining 11953 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 12241 2.76 - 3.30: 64888 3.30 - 3.83: 118870 3.83 - 4.37: 138963 4.37 - 4.90: 233930 Nonbonded interactions: 568892 Sorted by model distance: nonbonded pdb=" OH TYR K 487 " pdb=" O ASP W 15 " model vdw 2.226 2.440 nonbonded pdb=" OD1 ASP Z 517 " pdb=" OH TYR Z 532 " model vdw 2.239 2.440 nonbonded pdb=" O ASP L 86 " pdb=" OG1 THR L 90 " model vdw 2.242 2.440 nonbonded pdb=" OD1 ASP Y 85 " pdb=" OH TYR Y 100 " model vdw 2.250 2.440 nonbonded pdb=" O ASP G 15 " pdb=" OH TYR Q 487 " model vdw 2.254 2.440 ... (remaining 568887 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 'G' and resid 1 through 26) selection = (chain 'W' and (resid 1 through 23 or (resid 24 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26)) } ncs_group { reference = (chain 'J' and (resid 5 through 170 or (resid 452 and (name N or name CA or name \ C or name O or name CB )) or resid 453 through 766 or (resid 767 through 768 an \ d (name N or name CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 5 through 170 or resid 452 through 768)) } ncs_group { reference = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 221 or (resid 222 and (name N or name CA or name C or name \ O or name CB )) or resid 223 through 528 or (resid 548 and (name N or name CA or \ name C or name O or name CB )) or (resid 560 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'Q' and (resid 2 through 94 or resid 127 through 436 or (resid 437 throug \ h 438 and (name N or name CA or name C or name O or name CB )) or resid 439 thro \ ugh 530)) } ncs_group { reference = (chain 'U' and (resid 26 through 108 or (resid 109 and (name N or name CA or nam \ e C or name O or name CB )) or resid 110 through 507 or (resid 508 through 509 a \ nd (name N or name CA or name C or name O or name CB )) or resid 510 through 513 \ or (resid 514 and (name N or name CA or name C or name O or name CB )) or resid \ 515 through 554)) selection = (chain 'V' and (resid 26 through 135 or (resid 147 and (name N or name CA or nam \ e C or name O or name CB )) or resid 148 through 280 or (resid 281 through 282 a \ nd (name N or name CA or name C or name O or name CB )) or resid 283 through 496 \ or (resid 497 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 498 through 508 or (resid 509 and (name N or name CA or \ name C or name O or name CB )) or resid 510 through 536 or (resid 537 through 54 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 546 or (resi \ d 547 through 554 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'Y' and (resid 36 through 499 or resid 501 through 540)) selection = (chain 'Z' and (resid 36 through 110 or resid 132 through 263 or (resid 264 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 499 or \ resid 501 through 540)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 15.390 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 144.400 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.007 0.111 69419 Z= 0.434 Angle : 0.873 16.958 94028 Z= 0.479 Chirality : 0.053 0.506 10525 Planarity : 0.006 0.145 11956 Dihedral : 15.560 91.666 25502 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.25 % Allowed : 8.00 % Favored : 91.75 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.62 % Twisted General : 0.05 % 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: -3.85 (0.07), residues: 8427 helix: -2.43 (0.05), residues: 5276 sheet: -1.57 (0.20), residues: 521 loop : -2.59 (0.10), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1386 HIS 0.023 0.002 HIS N 266 PHE 0.033 0.002 PHE I 255 TYR 0.021 0.002 TYR O 296 ARG 0.012 0.001 ARG O 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 620 time to evaluate : 5.924 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: L 53 TYR cc_start: 0.8661 (p90) cc_final: 0.8440 (p90) REVERT: L 75 LYS cc_start: 0.9324 (tttt) cc_final: 0.9122 (ttmt) REVERT: L 112 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7731 (mm-30) REVERT: L 157 LYS cc_start: 0.9359 (mttt) cc_final: 0.8988 (mttm) REVERT: D 29 GLU cc_start: 0.8543 (pt0) cc_final: 0.8178 (pt0) REVERT: D 36 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8788 (tm-30) REVERT: A 619 GLN cc_start: 0.8967 (tt0) cc_final: 0.8623 (mt0) REVERT: A 1320 ASN cc_start: 0.8468 (t0) cc_final: 0.8260 (t0) REVERT: A 1752 GLU cc_start: 0.8834 (tt0) cc_final: 0.8358 (tp30) REVERT: A 1761 MET cc_start: 0.6593 (mtt) cc_final: 0.6157 (mtt) REVERT: A 1858 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8410 (tm-30) REVERT: N 540 ARG cc_start: 0.8461 (mmp80) cc_final: 0.8201 (tpt90) REVERT: I 19 LEU cc_start: 0.8708 (tp) cc_final: 0.8426 (tp) REVERT: I 305 MET cc_start: 0.9175 (tpp) cc_final: 0.8766 (mmm) REVERT: I 548 MET cc_start: 0.9095 (mtt) cc_final: 0.8734 (mpp) REVERT: I 669 LEU cc_start: 0.8466 (mp) cc_final: 0.7996 (tt) REVERT: I 717 MET cc_start: 0.4432 (tpt) cc_final: 0.4086 (mmm) REVERT: I 752 TRP cc_start: 0.7734 (m100) cc_final: 0.7517 (m-10) REVERT: O 335 ASN cc_start: 0.8810 (p0) cc_final: 0.8340 (t0) REVERT: O 411 LYS cc_start: 0.9464 (tttt) cc_final: 0.9215 (tptt) REVERT: O 414 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.9004 (pp) REVERT: O 664 MET cc_start: 0.9472 (mmt) cc_final: 0.9243 (mmt) REVERT: K 352 GLN cc_start: 0.8902 (mp-120) cc_final: 0.8494 (mp10) REVERT: G 15 ASP cc_start: 0.8249 (m-30) cc_final: 0.7622 (m-30) REVERT: W 5 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8779 (mmmt) REVERT: M 1 MET cc_start: 0.7618 (mtm) cc_final: 0.7054 (mtm) REVERT: M 35 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8904 (mp0) REVERT: M 51 LYS cc_start: 0.9367 (tttp) cc_final: 0.9156 (tttm) REVERT: H 53 PHE cc_start: 0.8066 (m-80) cc_final: 0.7787 (m-10) REVERT: H 87 GLU cc_start: 0.8491 (mp0) cc_final: 0.8187 (mp0) REVERT: H 97 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8871 (mtpp) REVERT: J 557 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8633 (tptp) REVERT: J 562 MET cc_start: 0.9069 (ttp) cc_final: 0.8857 (ttm) REVERT: Q 164 PHE cc_start: 0.8541 (t80) cc_final: 0.8244 (t80) REVERT: Q 249 MET cc_start: 0.8194 (mmm) cc_final: 0.7953 (tpp) REVERT: Q 349 GLU cc_start: 0.8049 (tt0) cc_final: 0.7842 (tp30) REVERT: Y 148 MET cc_start: 0.9018 (mmm) cc_final: 0.8746 (mmm) REVERT: Y 427 MET cc_start: 0.8846 (mpp) cc_final: 0.8627 (mpp) REVERT: U 157 GLU cc_start: 0.8581 (tt0) cc_final: 0.8105 (mt-10) REVERT: U 435 MET cc_start: 0.8884 (mpp) cc_final: 0.8551 (mpp) REVERT: U 457 TRP cc_start: 0.8458 (m100) cc_final: 0.8027 (m-10) REVERT: V 142 GLU cc_start: 0.8664 (mp0) cc_final: 0.8072 (mp0) REVERT: V 218 MET cc_start: 0.8508 (ttm) cc_final: 0.7961 (mtp) REVERT: Z 144 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8046 (mm-30) REVERT: Z 222 MET cc_start: 0.8743 (mtp) cc_final: 0.8488 (mtt) REVERT: Z 396 PHE cc_start: 0.8004 (m-10) cc_final: 0.7793 (m-10) REVERT: Z 427 MET cc_start: 0.8197 (tpt) cc_final: 0.7953 (tpp) REVERT: R 433 MET cc_start: 0.3003 (mmt) cc_final: 0.2668 (mmp) outliers start: 16 outliers final: 6 residues processed: 635 average time/residue: 0.6911 time to fit residues: 736.5833 Evaluate side-chains 451 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 444 time to evaluate : 5.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain R residue 312 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 844 random chunks: chunk 712 optimal weight: 3.9990 chunk 639 optimal weight: 2.9990 chunk 354 optimal weight: 0.0170 chunk 218 optimal weight: 7.9990 chunk 431 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 661 optimal weight: 0.8980 chunk 255 optimal weight: 0.0570 chunk 402 optimal weight: 2.9990 chunk 492 optimal weight: 0.8980 chunk 766 optimal weight: 0.8980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 110 GLN L 144 ASN A 31 HIS A 38 GLN A 75 GLN A 125 GLN A 162 HIS A 176 GLN A 179 ASN A 215 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS A 426 GLN A 449 GLN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN A 654 HIS A 666 ASN A 716 HIS A 722 HIS A 725 ASN A 792 GLN A1130 ASN A1138 HIS A1161 ASN A1170 ASN A1192 ASN A1248 ASN A1262 GLN A1266 HIS A1309 HIS A1327 GLN A1351 GLN A1543 HIS A1559 HIS A1591 HIS ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 HIS A1604 GLN ** A1727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1813 GLN A1892 HIS N 186 GLN N 235 GLN N 248 HIS N 541 ASN I 257 HIS I 323 ASN I 345 GLN ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 503 ASN I 506 HIS ** I 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 578 ASN I 684 GLN ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN O 150 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 291 ASN ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 424 GLN O 449 ASN ** O 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 512 GLN O 526 HIS ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 565 GLN O 671 GLN O 722 HIS O 731 ASN K 16 GLN K 80 HIS K 174 HIS K 271 HIS K 318 HIS K 382 ASN C 31 ASN H 75 GLN J 103 HIS J 123 HIS J 486 ASN J 497 ASN J 583 HIS J 595 GLN J 674 HIS J 702 ASN J 708 HIS J 773 ASN P 14 GLN P 98 ASN P 100 GLN P 680 HIS P 702 ASN P 708 HIS P 759 ASN Q 16 GLN Q 17 GLN Q 58 HIS Q 80 HIS Q 342 HIS Q 503 HIS Y 66 ASN Y 151 GLN ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 338 HIS Y 395 HIS Y 431 ASN Y 442 GLN Y 506 GLN Y 523 ASN U 299 ASN U 305 ASN ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 346 GLN V 104 HIS V 202 HIS V 287 ASN V 305 ASN V 346 GLN V 373 HIS ** V 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN Z 50 HIS Z 65 ASN Z 67 ASN Z 106 GLN Z 151 GLN Z 172 ASN Z 184 GLN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 287 ASN Z 326 ASN Z 338 HIS ** Z 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 ASN ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 GLN Total number of N/Q/H flips: 121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 69419 Z= 0.149 Angle : 0.553 11.175 94028 Z= 0.286 Chirality : 0.039 0.250 10525 Planarity : 0.004 0.133 11956 Dihedral : 5.197 64.777 9295 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.08 % Allowed : 11.80 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.62 % Twisted General : 0.02 % 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: -1.59 (0.08), residues: 8427 helix: -0.43 (0.07), residues: 5318 sheet: -1.15 (0.21), residues: 532 loop : -2.14 (0.11), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP Z 239 HIS 0.015 0.001 HIS O 754 PHE 0.026 0.001 PHE N 604 TYR 0.031 0.001 TYR Z 243 ARG 0.013 0.000 ARG U 344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 530 time to evaluate : 6.093 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: L 14 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8841 (mtmm) REVERT: L 53 TYR cc_start: 0.8623 (p90) cc_final: 0.8360 (p90) REVERT: L 75 LYS cc_start: 0.9374 (tttt) cc_final: 0.9084 (ttpt) REVERT: L 80 TYR cc_start: 0.8702 (t80) cc_final: 0.8179 (t80) REVERT: L 157 LYS cc_start: 0.9347 (mttt) cc_final: 0.8891 (mttm) REVERT: D 29 GLU cc_start: 0.8560 (pt0) cc_final: 0.8207 (pt0) REVERT: D 50 ASN cc_start: 0.9136 (p0) cc_final: 0.8867 (p0) REVERT: A 11 MET cc_start: 0.7663 (mmt) cc_final: 0.7392 (mmm) REVERT: A 90 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8244 (p0) REVERT: A 161 MET cc_start: 0.8502 (mpp) cc_final: 0.8289 (mpp) REVERT: A 179 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8845 (m110) REVERT: A 619 GLN cc_start: 0.8921 (tt0) cc_final: 0.8555 (mt0) REVERT: A 665 MET cc_start: 0.8706 (mmp) cc_final: 0.8308 (mmm) REVERT: A 1078 MET cc_start: 0.8956 (mtm) cc_final: 0.8493 (mtm) REVERT: A 1323 GLU cc_start: 0.7676 (mp0) cc_final: 0.7475 (mp0) REVERT: A 1527 MET cc_start: 0.8618 (mmm) cc_final: 0.8362 (mmm) REVERT: A 1752 GLU cc_start: 0.8824 (tt0) cc_final: 0.8363 (tp30) REVERT: A 1858 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8419 (tm-30) REVERT: N 540 ARG cc_start: 0.8470 (mmp80) cc_final: 0.8204 (tpt90) REVERT: I 19 LEU cc_start: 0.8746 (tp) cc_final: 0.8467 (tp) REVERT: I 113 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7529 (ptp) REVERT: I 305 MET cc_start: 0.9141 (tpp) cc_final: 0.8576 (mmm) REVERT: I 369 MET cc_start: 0.9185 (mtt) cc_final: 0.8926 (mtt) REVERT: I 548 MET cc_start: 0.9051 (mtt) cc_final: 0.8673 (mpp) REVERT: I 717 MET cc_start: 0.4366 (tpt) cc_final: 0.3878 (tpt) REVERT: I 746 MET cc_start: 0.7174 (mmm) cc_final: 0.6748 (mpp) REVERT: O 411 LYS cc_start: 0.9429 (tttt) cc_final: 0.9223 (tptt) REVERT: O 414 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8768 (pp) REVERT: K 347 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7930 (tm-30) REVERT: K 352 GLN cc_start: 0.8852 (mp-120) cc_final: 0.8422 (mp10) REVERT: G 15 ASP cc_start: 0.8219 (m-30) cc_final: 0.7868 (m-30) REVERT: W 5 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8800 (mmmt) REVERT: W 17 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8472 (mp0) REVERT: M 35 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8772 (mp0) REVERT: M 51 LYS cc_start: 0.9255 (tttp) cc_final: 0.8876 (tttm) REVERT: M 54 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7835 (mp0) REVERT: H 80 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8208 (mm-30) REVERT: H 87 GLU cc_start: 0.8638 (mp0) cc_final: 0.8266 (mp0) REVERT: H 88 GLU cc_start: 0.8535 (mp0) cc_final: 0.8217 (mp0) REVERT: H 93 GLU cc_start: 0.8866 (tp30) cc_final: 0.8630 (tp30) REVERT: J 557 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8641 (tptp) REVERT: P 656 MET cc_start: 0.8450 (tmm) cc_final: 0.8052 (tmm) REVERT: Q 164 PHE cc_start: 0.8551 (t80) cc_final: 0.8297 (t80) REVERT: U 157 GLU cc_start: 0.8506 (tt0) cc_final: 0.8178 (mt-10) REVERT: U 435 MET cc_start: 0.8878 (mpp) cc_final: 0.8517 (mpp) REVERT: U 457 TRP cc_start: 0.8466 (m100) cc_final: 0.8033 (m-10) REVERT: V 142 GLU cc_start: 0.8685 (mp0) cc_final: 0.8088 (mp0) REVERT: V 167 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6131 (pp) REVERT: V 218 MET cc_start: 0.8470 (ttm) cc_final: 0.8002 (mtp) REVERT: Z 49 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9106 (pp) REVERT: Z 144 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8061 (mm-30) REVERT: Z 396 PHE cc_start: 0.7992 (m-10) cc_final: 0.7792 (m-10) REVERT: R 264 MET cc_start: 0.3827 (mtm) cc_final: 0.3579 (mmp) REVERT: R 433 MET cc_start: 0.2971 (mmt) cc_final: 0.2504 (mmp) outliers start: 77 outliers final: 40 residues processed: 584 average time/residue: 0.6357 time to fit residues: 652.6550 Evaluate side-chains 502 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 456 time to evaluate : 5.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 360 ASP Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 728 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 706 HIS Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 749 VAL Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 17 GLN Chi-restraints excluded: chain Q residue 451 LEU Chi-restraints excluded: chain U residue 355 GLN Chi-restraints excluded: chain V residue 107 HIS Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 521 PHE Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 492 TYR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 495 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 844 random chunks: chunk 425 optimal weight: 7.9990 chunk 237 optimal weight: 40.0000 chunk 637 optimal weight: 9.9990 chunk 521 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 767 optimal weight: 5.9990 chunk 829 optimal weight: 4.9990 chunk 683 optimal weight: 0.7980 chunk 761 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 615 optimal weight: 0.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 67 GLN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN A 981 GLN A1130 ASN A1248 ASN ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 388 HIS I 292 GLN ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 342 HIS ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 472 HIS ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 693 ASN ** O 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 557 ASN J 702 ASN P 583 HIS P 634 HIS Q 52 GLN Q 271 HIS ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 321 HIS ** V 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 151 GLN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 367 GLN Z 369 ASN ** Z 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 69419 Z= 0.258 Angle : 0.568 10.835 94028 Z= 0.292 Chirality : 0.040 0.236 10525 Planarity : 0.004 0.130 11956 Dihedral : 4.935 62.860 9295 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.59 % Allowed : 13.62 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.46 (0.09), residues: 8427 helix: 0.54 (0.07), residues: 5346 sheet: -0.89 (0.22), residues: 527 loop : -1.90 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP Z 239 HIS 0.007 0.001 HIS U 321 PHE 0.021 0.001 PHE A1821 TYR 0.018 0.001 TYR O 358 ARG 0.006 0.000 ARG Z 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 461 time to evaluate : 6.310 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: L 14 LYS cc_start: 0.9162 (mtmm) cc_final: 0.8850 (mtmm) REVERT: L 75 LYS cc_start: 0.9374 (tttt) cc_final: 0.9081 (ttpt) REVERT: L 128 HIS cc_start: 0.8568 (t-90) cc_final: 0.8277 (t70) REVERT: L 157 LYS cc_start: 0.9221 (mttt) cc_final: 0.8818 (mttm) REVERT: D 29 GLU cc_start: 0.8368 (pt0) cc_final: 0.8162 (pt0) REVERT: D 50 ASN cc_start: 0.9199 (p0) cc_final: 0.8960 (p0) REVERT: A 11 MET cc_start: 0.7621 (mmt) cc_final: 0.7366 (mmm) REVERT: A 90 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8246 (p0) REVERT: A 619 GLN cc_start: 0.8941 (tt0) cc_final: 0.8551 (mt0) REVERT: A 637 MET cc_start: 0.9235 (ttp) cc_final: 0.9002 (ptm) REVERT: A 1078 MET cc_start: 0.9167 (mtm) cc_final: 0.8937 (mtp) REVERT: A 1323 GLU cc_start: 0.7736 (mp0) cc_final: 0.7503 (mp0) REVERT: A 1752 GLU cc_start: 0.8841 (tt0) cc_final: 0.8383 (tp30) REVERT: A 1819 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8283 (tp30) REVERT: A 1858 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8412 (tm-30) REVERT: N 540 ARG cc_start: 0.8489 (mmp80) cc_final: 0.8177 (tpt90) REVERT: I 19 LEU cc_start: 0.8703 (tp) cc_final: 0.8436 (tp) REVERT: I 113 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7526 (ptp) REVERT: I 305 MET cc_start: 0.9104 (tpp) cc_final: 0.8496 (mmm) REVERT: I 369 MET cc_start: 0.9175 (mtt) cc_final: 0.8939 (mtt) REVERT: I 548 MET cc_start: 0.9070 (mtt) cc_final: 0.8651 (mpp) REVERT: I 717 MET cc_start: 0.4468 (tpt) cc_final: 0.4044 (tpt) REVERT: I 746 MET cc_start: 0.7073 (mmm) cc_final: 0.6748 (mpp) REVERT: O 335 ASN cc_start: 0.8969 (p0) cc_final: 0.8272 (t0) REVERT: O 411 LYS cc_start: 0.9434 (tttt) cc_final: 0.9225 (tptt) REVERT: O 414 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8733 (pp) REVERT: O 557 MET cc_start: 0.9157 (mmm) cc_final: 0.8757 (mmt) REVERT: K 347 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7769 (tm-30) REVERT: K 352 GLN cc_start: 0.8947 (mp-120) cc_final: 0.8356 (mp10) REVERT: G 15 ASP cc_start: 0.8143 (m-30) cc_final: 0.7902 (m-30) REVERT: W 5 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8809 (mmmt) REVERT: W 14 ASP cc_start: 0.7849 (p0) cc_final: 0.7395 (p0) REVERT: W 17 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8438 (mp0) REVERT: M 35 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8823 (mp0) REVERT: M 51 LYS cc_start: 0.9198 (tttp) cc_final: 0.8983 (tttm) REVERT: H 53 PHE cc_start: 0.7660 (m-10) cc_final: 0.7423 (m-10) REVERT: H 87 GLU cc_start: 0.8621 (mp0) cc_final: 0.8237 (mp0) REVERT: H 88 GLU cc_start: 0.8580 (mp0) cc_final: 0.8226 (mp0) REVERT: Q 164 PHE cc_start: 0.8612 (t80) cc_final: 0.8363 (t80) REVERT: Y 142 MET cc_start: 0.9043 (mmm) cc_final: 0.8640 (mmm) REVERT: Y 148 MET cc_start: 0.9069 (mmm) cc_final: 0.8738 (mmm) REVERT: U 157 GLU cc_start: 0.8509 (tt0) cc_final: 0.8131 (mt-10) REVERT: U 435 MET cc_start: 0.8910 (mpp) cc_final: 0.8471 (mpp) REVERT: U 457 TRP cc_start: 0.8518 (m100) cc_final: 0.8023 (m-10) REVERT: V 167 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6315 (pp) REVERT: V 218 MET cc_start: 0.8508 (ttm) cc_final: 0.7982 (mtp) REVERT: Z 49 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9085 (pp) REVERT: Z 144 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7838 (mm-30) REVERT: Z 174 MET cc_start: 0.8965 (ttm) cc_final: 0.8621 (ttm) REVERT: Z 304 LEU cc_start: 0.8971 (tt) cc_final: 0.8754 (tt) REVERT: Z 396 PHE cc_start: 0.8180 (m-10) cc_final: 0.7772 (m-10) REVERT: R 264 MET cc_start: 0.3866 (mtm) cc_final: 0.3435 (mmp) REVERT: R 433 MET cc_start: 0.2921 (mmt) cc_final: 0.2491 (mmp) outliers start: 114 outliers final: 65 residues processed: 545 average time/residue: 0.6617 time to fit residues: 641.0023 Evaluate side-chains 519 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 448 time to evaluate : 6.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1805 MET Chi-restraints excluded: chain A residue 1819 GLU Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 360 ASP Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 728 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 706 HIS Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain P residue 762 TRP Chi-restraints excluded: chain P residue 765 ASP Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 107 HIS Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 219 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 414 MET Chi-restraints excluded: chain V residue 521 PHE Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 185 GLU Chi-restraints excluded: chain Z residue 434 TYR Chi-restraints excluded: chain Z residue 492 TYR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 495 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 844 random chunks: chunk 758 optimal weight: 6.9990 chunk 577 optimal weight: 1.9990 chunk 398 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 366 optimal weight: 2.9990 chunk 515 optimal weight: 0.5980 chunk 770 optimal weight: 7.9990 chunk 815 optimal weight: 50.0000 chunk 402 optimal weight: 0.0070 chunk 730 optimal weight: 0.9990 chunk 219 optimal weight: 20.0000 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN A 250 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN A1248 ASN A1558 HIS ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 639 HIS I 292 GLN ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 754 HIS K 16 GLN J 702 ASN Q 17 GLN ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 337 GLN U 197 HIS ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 69419 Z= 0.163 Angle : 0.518 10.072 94028 Z= 0.264 Chirality : 0.038 0.178 10525 Planarity : 0.004 0.126 11956 Dihedral : 4.720 63.671 9295 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.59 % Allowed : 14.76 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.09 (0.09), residues: 8427 helix: 1.00 (0.07), residues: 5350 sheet: -0.67 (0.22), residues: 526 loop : -1.77 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP Z 239 HIS 0.008 0.001 HIS U 321 PHE 0.017 0.001 PHE P 741 TYR 0.016 0.001 TYR N 336 ARG 0.006 0.000 ARG U 165 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 483 time to evaluate : 6.176 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: L 14 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8885 (mtmm) REVERT: L 75 LYS cc_start: 0.9371 (tttt) cc_final: 0.9069 (ttpt) REVERT: L 157 LYS cc_start: 0.9163 (mttt) cc_final: 0.8924 (mttm) REVERT: D 50 ASN cc_start: 0.9199 (p0) cc_final: 0.8946 (p0) REVERT: A 11 MET cc_start: 0.7673 (mmt) cc_final: 0.7388 (mmm) REVERT: A 90 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8247 (p0) REVERT: A 161 MET cc_start: 0.8661 (mpp) cc_final: 0.8120 (mpp) REVERT: A 250 ASN cc_start: 0.9398 (OUTLIER) cc_final: 0.9123 (t0) REVERT: A 619 GLN cc_start: 0.8916 (tt0) cc_final: 0.8550 (mt0) REVERT: A 637 MET cc_start: 0.9213 (ttp) cc_final: 0.8987 (ptm) REVERT: A 852 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8235 (pt) REVERT: A 1078 MET cc_start: 0.9169 (mtm) cc_final: 0.8942 (mtp) REVERT: A 1752 GLU cc_start: 0.8794 (tt0) cc_final: 0.8328 (tp30) REVERT: A 1786 MET cc_start: 0.9024 (mmm) cc_final: 0.8821 (mmt) REVERT: A 1819 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: A 1858 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8424 (tm-30) REVERT: N 540 ARG cc_start: 0.8560 (mmp80) cc_final: 0.8194 (tpt90) REVERT: I 19 LEU cc_start: 0.8724 (tp) cc_final: 0.8459 (tp) REVERT: I 305 MET cc_start: 0.9046 (tpp) cc_final: 0.8456 (mmm) REVERT: I 548 MET cc_start: 0.9037 (mtt) cc_final: 0.8658 (mpp) REVERT: I 717 MET cc_start: 0.4484 (tpt) cc_final: 0.3978 (tpt) REVERT: I 746 MET cc_start: 0.7197 (mmm) cc_final: 0.6844 (mpp) REVERT: O 335 ASN cc_start: 0.8911 (p0) cc_final: 0.8349 (t0) REVERT: O 411 LYS cc_start: 0.9430 (tttt) cc_final: 0.9225 (tptt) REVERT: O 414 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8551 (pp) REVERT: O 557 MET cc_start: 0.9205 (mmm) cc_final: 0.8968 (mmt) REVERT: K 352 GLN cc_start: 0.8898 (mp-120) cc_final: 0.8303 (mp10) REVERT: C 60 ILE cc_start: -0.1038 (OUTLIER) cc_final: -0.1264 (mp) REVERT: G 15 ASP cc_start: 0.8216 (m-30) cc_final: 0.7949 (m-30) REVERT: W 5 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8844 (mmmt) REVERT: W 17 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8466 (mp0) REVERT: M 35 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8795 (mp0) REVERT: M 56 LYS cc_start: 0.9235 (pttt) cc_final: 0.9023 (pttm) REVERT: H 87 GLU cc_start: 0.8573 (mp0) cc_final: 0.8204 (mp0) REVERT: H 88 GLU cc_start: 0.8626 (mp0) cc_final: 0.8335 (mp0) REVERT: J 557 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8610 (tppt) REVERT: Q 164 PHE cc_start: 0.8585 (t80) cc_final: 0.8350 (t80) REVERT: Y 142 MET cc_start: 0.9072 (mmm) cc_final: 0.8821 (mmm) REVERT: Y 148 MET cc_start: 0.9078 (mmm) cc_final: 0.8744 (mmm) REVERT: Y 524 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: Y 529 MET cc_start: 0.8882 (mtm) cc_final: 0.8429 (mtt) REVERT: U 157 GLU cc_start: 0.8463 (tt0) cc_final: 0.8118 (mt-10) REVERT: U 435 MET cc_start: 0.8916 (mpp) cc_final: 0.8500 (mpp) REVERT: U 457 TRP cc_start: 0.8439 (m100) cc_final: 0.8002 (m-10) REVERT: V 142 GLU cc_start: 0.8445 (mp0) cc_final: 0.8085 (mp0) REVERT: V 167 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6157 (pp) REVERT: V 218 MET cc_start: 0.8469 (ttm) cc_final: 0.7932 (mtp) REVERT: Z 49 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9037 (pp) REVERT: Z 144 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7827 (mm-30) REVERT: Z 396 PHE cc_start: 0.8201 (m-10) cc_final: 0.7812 (m-10) REVERT: Z 427 MET cc_start: 0.8126 (tpt) cc_final: 0.7833 (tpt) REVERT: R 264 MET cc_start: 0.3803 (mtm) cc_final: 0.3454 (mmp) REVERT: R 433 MET cc_start: 0.2924 (mmt) cc_final: 0.2475 (mmp) outliers start: 114 outliers final: 71 residues processed: 572 average time/residue: 0.6321 time to fit residues: 639.1735 Evaluate side-chains 530 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 450 time to evaluate : 6.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1805 MET Chi-restraints excluded: chain A residue 1819 GLU Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 360 ASP Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain N residue 641 LEU Chi-restraints excluded: chain N residue 728 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 505 GLN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain P residue 562 MET Chi-restraints excluded: chain P residue 731 GLN Chi-restraints excluded: chain P residue 762 TRP Chi-restraints excluded: chain P residue 765 ASP Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 17 GLN Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 451 LEU Chi-restraints excluded: chain Y residue 524 GLU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 355 GLN Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 107 HIS Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 219 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 521 PHE Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 185 GLU Chi-restraints excluded: chain Z residue 434 TYR Chi-restraints excluded: chain Z residue 492 TYR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 495 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 844 random chunks: chunk 679 optimal weight: 0.9990 chunk 463 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 607 optimal weight: 10.0000 chunk 336 optimal weight: 2.9990 chunk 696 optimal weight: 10.0000 chunk 563 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 416 optimal weight: 8.9990 chunk 732 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 ASN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN A1511 ASN ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1795 GLN N 639 HIS ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 639 GLN ** O 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 ASN ** P 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 GLN Q 350 HIS ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 289 ASN Z 395 HIS ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 69419 Z= 0.204 Angle : 0.533 14.223 94028 Z= 0.270 Chirality : 0.039 0.172 10525 Planarity : 0.004 0.124 11956 Dihedral : 4.623 63.148 9295 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.84 % Allowed : 15.54 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.41 (0.09), residues: 8427 helix: 1.26 (0.07), residues: 5361 sheet: -0.60 (0.22), residues: 537 loop : -1.67 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP Z 239 HIS 0.008 0.001 HIS U 321 PHE 0.016 0.001 PHE Z 332 TYR 0.015 0.001 TYR K 151 ARG 0.004 0.000 ARG U 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 459 time to evaluate : 5.985 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: L 14 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8803 (mtmm) REVERT: L 75 LYS cc_start: 0.9381 (tttt) cc_final: 0.9075 (ttpt) REVERT: L 157 LYS cc_start: 0.9148 (mttt) cc_final: 0.8690 (mptt) REVERT: D 50 ASN cc_start: 0.9231 (p0) cc_final: 0.8983 (p0) REVERT: A 11 MET cc_start: 0.7737 (mmt) cc_final: 0.7491 (mmm) REVERT: A 90 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8274 (p0) REVERT: A 161 MET cc_start: 0.8638 (mpp) cc_final: 0.8126 (mpp) REVERT: A 250 ASN cc_start: 0.9341 (OUTLIER) cc_final: 0.9129 (t0) REVERT: A 257 MET cc_start: 0.8712 (ttm) cc_final: 0.8338 (ttm) REVERT: A 619 GLN cc_start: 0.8922 (tt0) cc_final: 0.8548 (mt0) REVERT: A 637 MET cc_start: 0.9172 (ttp) cc_final: 0.8837 (ppp) REVERT: A 852 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8205 (pt) REVERT: A 857 MET cc_start: 0.8469 (tpp) cc_final: 0.8252 (tpp) REVERT: A 1078 MET cc_start: 0.9214 (mtm) cc_final: 0.8972 (mtp) REVERT: A 1307 LEU cc_start: 0.9389 (tp) cc_final: 0.8965 (mt) REVERT: A 1752 GLU cc_start: 0.8782 (tt0) cc_final: 0.8331 (tp30) REVERT: A 1819 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8342 (tp30) REVERT: A 1858 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8414 (tm-30) REVERT: I 19 LEU cc_start: 0.8735 (tp) cc_final: 0.8470 (tp) REVERT: I 305 MET cc_start: 0.9027 (tpp) cc_final: 0.8440 (mmm) REVERT: I 548 MET cc_start: 0.9025 (mtt) cc_final: 0.8625 (mpp) REVERT: I 717 MET cc_start: 0.4509 (tpt) cc_final: 0.4002 (tpt) REVERT: I 746 MET cc_start: 0.7247 (mmm) cc_final: 0.6864 (mpp) REVERT: O 335 ASN cc_start: 0.8950 (p0) cc_final: 0.8468 (t0) REVERT: O 411 LYS cc_start: 0.9431 (tttt) cc_final: 0.9229 (tptt) REVERT: O 414 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8528 (pp) REVERT: K 352 GLN cc_start: 0.8901 (mp-120) cc_final: 0.8297 (mp10) REVERT: C 60 ILE cc_start: -0.1033 (OUTLIER) cc_final: -0.1261 (mp) REVERT: G 15 ASP cc_start: 0.8252 (m-30) cc_final: 0.7981 (m-30) REVERT: W 1 MET cc_start: 0.8161 (mmm) cc_final: 0.7265 (mmm) REVERT: W 5 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8847 (mmmt) REVERT: W 17 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8480 (mp0) REVERT: M 35 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8823 (mp0) REVERT: M 54 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7799 (mp0) REVERT: M 56 LYS cc_start: 0.9177 (pttt) cc_final: 0.8960 (pttm) REVERT: H 53 PHE cc_start: 0.7546 (m-10) cc_final: 0.7185 (m-10) REVERT: H 87 GLU cc_start: 0.8570 (mp0) cc_final: 0.8194 (mp0) REVERT: H 88 GLU cc_start: 0.8634 (mp0) cc_final: 0.8325 (mp0) REVERT: P 731 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: Q 164 PHE cc_start: 0.8609 (t80) cc_final: 0.8368 (t80) REVERT: Y 142 MET cc_start: 0.9052 (mmm) cc_final: 0.8648 (mmm) REVERT: Y 148 MET cc_start: 0.9120 (mmm) cc_final: 0.8807 (mmm) REVERT: Y 524 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: U 157 GLU cc_start: 0.8495 (tt0) cc_final: 0.8131 (mt-10) REVERT: U 414 MET cc_start: 0.8023 (mmm) cc_final: 0.7786 (mmm) REVERT: U 435 MET cc_start: 0.8930 (mpp) cc_final: 0.8528 (mpp) REVERT: U 457 TRP cc_start: 0.8450 (m100) cc_final: 0.8000 (m-10) REVERT: V 142 GLU cc_start: 0.8517 (mp0) cc_final: 0.8094 (mp0) REVERT: V 167 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6222 (pp) REVERT: V 218 MET cc_start: 0.8456 (ttm) cc_final: 0.7924 (mtp) REVERT: Z 49 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9005 (pp) REVERT: Z 144 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8241 (mm-30) REVERT: Z 174 MET cc_start: 0.9013 (ttm) cc_final: 0.8636 (ttm) REVERT: Z 289 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8748 (t0) REVERT: Z 396 PHE cc_start: 0.8158 (m-10) cc_final: 0.7820 (m-10) REVERT: Z 427 MET cc_start: 0.8151 (tpt) cc_final: 0.7826 (tpt) REVERT: R 264 MET cc_start: 0.3794 (mtm) cc_final: 0.3465 (mmp) REVERT: R 433 MET cc_start: 0.2960 (mmt) cc_final: 0.2506 (mmp) outliers start: 132 outliers final: 88 residues processed: 563 average time/residue: 0.6944 time to fit residues: 699.3145 Evaluate side-chains 546 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 447 time to evaluate : 5.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1748 LEU Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1819 GLU Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 179 CYS Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 297 VAL Chi-restraints excluded: chain N residue 360 ASP Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain N residue 641 LEU Chi-restraints excluded: chain N residue 728 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 706 HIS Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 505 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain J residue 758 MET Chi-restraints excluded: chain P residue 562 MET Chi-restraints excluded: chain P residue 731 GLN Chi-restraints excluded: chain P residue 762 TRP Chi-restraints excluded: chain P residue 765 ASP Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 332 THR Chi-restraints excluded: chain Q residue 442 ASP Chi-restraints excluded: chain Q residue 451 LEU Chi-restraints excluded: chain Y residue 524 GLU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 333 THR Chi-restraints excluded: chain U residue 355 GLN Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 107 HIS Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 219 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 521 PHE Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 185 GLU Chi-restraints excluded: chain Z residue 289 ASN Chi-restraints excluded: chain Z residue 434 TYR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 495 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 844 random chunks: chunk 274 optimal weight: 7.9990 chunk 734 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 478 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 816 optimal weight: 30.0000 chunk 677 optimal weight: 2.9990 chunk 378 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 270 optimal weight: 20.0000 chunk 428 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 101 ASN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 GLN A 125 GLN A 250 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN A1248 ASN ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 550 GLN ** O 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 45 GLN K 54 HIS J 702 ASN Q 18 GLN Q 316 ASN ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 202 HIS ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 166 GLN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 69419 Z= 0.446 Angle : 0.675 14.870 94028 Z= 0.341 Chirality : 0.043 0.206 10525 Planarity : 0.004 0.124 11956 Dihedral : 4.822 60.625 9295 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.11 % Allowed : 16.61 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.37 (0.09), residues: 8427 helix: 1.21 (0.07), residues: 5369 sheet: -0.59 (0.22), residues: 538 loop : -1.66 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP Z 239 HIS 0.010 0.001 HIS P 64 PHE 0.025 0.002 PHE Z 282 TYR 0.020 0.002 TYR K 322 ARG 0.008 0.000 ARG N 540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 433 time to evaluate : 5.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 GLU cc_start: 0.9072 (tp30) cc_final: 0.8870 (tp30) REVERT: L 53 TYR cc_start: 0.8672 (p90) cc_final: 0.8388 (p90) REVERT: L 75 LYS cc_start: 0.9397 (tttt) cc_final: 0.9086 (ttpt) REVERT: L 80 TYR cc_start: 0.8945 (t80) cc_final: 0.8033 (t80) REVERT: L 130 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8115 (mmtm) REVERT: L 157 LYS cc_start: 0.9204 (mttt) cc_final: 0.8768 (mptt) REVERT: A 11 MET cc_start: 0.7624 (mmt) cc_final: 0.7392 (mmm) REVERT: A 90 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8282 (p0) REVERT: A 250 ASN cc_start: 0.9412 (OUTLIER) cc_final: 0.9125 (t0) REVERT: A 257 MET cc_start: 0.8732 (ttm) cc_final: 0.8433 (ttm) REVERT: A 619 GLN cc_start: 0.8989 (tt0) cc_final: 0.8569 (mt0) REVERT: A 637 MET cc_start: 0.9227 (ttp) cc_final: 0.8915 (ppp) REVERT: A 665 MET cc_start: 0.9023 (mmp) cc_final: 0.8681 (mmm) REVERT: A 852 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8372 (pt) REVERT: A 1078 MET cc_start: 0.9261 (mtm) cc_final: 0.8973 (mtp) REVERT: A 1652 MET cc_start: 0.8140 (tpp) cc_final: 0.7543 (tpt) REVERT: A 1752 GLU cc_start: 0.8842 (tt0) cc_final: 0.8402 (tp30) REVERT: I 19 LEU cc_start: 0.8742 (tp) cc_final: 0.8484 (tp) REVERT: I 305 MET cc_start: 0.9059 (tpp) cc_final: 0.8565 (mmm) REVERT: I 717 MET cc_start: 0.4743 (tpt) cc_final: 0.4317 (tpt) REVERT: I 746 MET cc_start: 0.7356 (mmm) cc_final: 0.6982 (mpp) REVERT: O 335 ASN cc_start: 0.8997 (p0) cc_final: 0.8505 (t0) REVERT: O 363 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7645 (t-90) REVERT: O 411 LYS cc_start: 0.9443 (tttt) cc_final: 0.9233 (tptt) REVERT: O 414 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8577 (pp) REVERT: O 557 MET cc_start: 0.9285 (mmm) cc_final: 0.9061 (mmt) REVERT: C 60 ILE cc_start: -0.1032 (OUTLIER) cc_final: -0.1271 (mp) REVERT: G 15 ASP cc_start: 0.8311 (m-30) cc_final: 0.8011 (m-30) REVERT: W 5 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8843 (mmmt) REVERT: W 17 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8461 (mp0) REVERT: M 35 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8884 (mp0) REVERT: M 54 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7637 (mp0) REVERT: H 88 GLU cc_start: 0.8652 (mp0) cc_final: 0.8336 (mp0) REVERT: P 731 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: Q 164 PHE cc_start: 0.8617 (t80) cc_final: 0.8378 (t80) REVERT: Y 142 MET cc_start: 0.9119 (mmm) cc_final: 0.8751 (mmm) REVERT: Y 148 MET cc_start: 0.9158 (mmm) cc_final: 0.8879 (mmm) REVERT: Y 524 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: U 157 GLU cc_start: 0.8577 (tt0) cc_final: 0.8133 (mt-10) REVERT: U 312 MET cc_start: 0.9069 (mpp) cc_final: 0.8858 (mpp) REVERT: U 414 MET cc_start: 0.8214 (mmm) cc_final: 0.8003 (mmm) REVERT: U 435 MET cc_start: 0.8987 (mpp) cc_final: 0.8474 (mpp) REVERT: U 457 TRP cc_start: 0.8580 (m100) cc_final: 0.7930 (m-10) REVERT: V 142 GLU cc_start: 0.8712 (mp0) cc_final: 0.8218 (mp0) REVERT: V 167 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6594 (pp) REVERT: V 218 MET cc_start: 0.8540 (ttm) cc_final: 0.7852 (mtp) REVERT: V 480 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9181 (tt) REVERT: Z 49 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9142 (pp) REVERT: Z 144 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8267 (mm-30) REVERT: Z 174 MET cc_start: 0.9025 (ttm) cc_final: 0.8684 (ttm) REVERT: Z 396 PHE cc_start: 0.8252 (m-10) cc_final: 0.7944 (m-10) REVERT: R 264 MET cc_start: 0.3900 (mtm) cc_final: 0.3526 (mmp) REVERT: R 433 MET cc_start: 0.2887 (mmt) cc_final: 0.2539 (mmp) outliers start: 152 outliers final: 99 residues processed: 553 average time/residue: 0.6202 time to fit residues: 607.3872 Evaluate side-chains 532 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 421 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1666 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1748 LEU Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1817 VAL Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 179 CYS Chi-restraints excluded: chain N residue 360 ASP Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 399 LEU Chi-restraints excluded: chain N residue 447 ASP Chi-restraints excluded: chain N residue 456 LEU Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain N residue 728 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 706 HIS Chi-restraints excluded: chain O residue 131 VAL Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 505 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 704 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 466 LEU Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain P residue 704 LEU Chi-restraints excluded: chain P residue 731 GLN Chi-restraints excluded: chain P residue 762 TRP Chi-restraints excluded: chain P residue 765 ASP Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 332 THR Chi-restraints excluded: chain Q residue 442 ASP Chi-restraints excluded: chain Y residue 524 GLU Chi-restraints excluded: chain U residue 98 GLU Chi-restraints excluded: chain U residue 183 ASP Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 333 THR Chi-restraints excluded: chain U residue 355 GLN Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 107 HIS Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 219 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 414 MET Chi-restraints excluded: chain V residue 480 LEU Chi-restraints excluded: chain V residue 521 PHE Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 185 GLU Chi-restraints excluded: chain Z residue 434 TYR Chi-restraints excluded: chain Z residue 492 TYR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 495 HIS Chi-restraints excluded: chain S residue 77 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 844 random chunks: chunk 787 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 465 optimal weight: 0.7980 chunk 596 optimal weight: 0.9980 chunk 462 optimal weight: 0.6980 chunk 687 optimal weight: 3.9990 chunk 455 optimal weight: 1.9990 chunk 813 optimal weight: 0.7980 chunk 509 optimal weight: 0.6980 chunk 495 optimal weight: 6.9990 chunk 375 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 101 ASN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A 981 GLN A1248 ASN ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 382 GLN ** O 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN J 702 ASN P 657 HIS ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 202 HIS ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 69419 Z= 0.145 Angle : 0.535 13.100 94028 Z= 0.269 Chirality : 0.038 0.171 10525 Planarity : 0.004 0.123 11956 Dihedral : 4.633 63.658 9295 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.63 % Allowed : 17.56 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.70 (0.09), residues: 8427 helix: 1.47 (0.07), residues: 5374 sheet: -0.45 (0.22), residues: 536 loop : -1.54 (0.12), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP Z 239 HIS 0.008 0.001 HIS U 321 PHE 0.027 0.001 PHE Z 282 TYR 0.020 0.001 TYR N 336 ARG 0.008 0.000 ARG V 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 465 time to evaluate : 5.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 GLU cc_start: 0.8929 (tp30) cc_final: 0.8725 (tp30) REVERT: L 53 TYR cc_start: 0.8506 (p90) cc_final: 0.8208 (p90) REVERT: L 75 LYS cc_start: 0.9386 (tttt) cc_final: 0.9074 (ttpt) REVERT: L 80 TYR cc_start: 0.8884 (t80) cc_final: 0.7977 (t80) REVERT: L 157 LYS cc_start: 0.9199 (mttt) cc_final: 0.8715 (mptt) REVERT: D 50 ASN cc_start: 0.9232 (p0) cc_final: 0.8983 (p0) REVERT: A 11 MET cc_start: 0.7754 (mmt) cc_final: 0.7549 (mmm) REVERT: A 90 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8259 (p0) REVERT: A 161 MET cc_start: 0.8495 (mpp) cc_final: 0.8193 (mpp) REVERT: A 619 GLN cc_start: 0.8936 (tt0) cc_final: 0.8560 (mt0) REVERT: A 637 MET cc_start: 0.9125 (ttp) cc_final: 0.8917 (ppp) REVERT: A 1078 MET cc_start: 0.9215 (mtm) cc_final: 0.8937 (mtp) REVERT: A 1350 TYR cc_start: 0.8813 (m-10) cc_final: 0.8454 (m-10) REVERT: A 1550 MET cc_start: 0.8637 (tpp) cc_final: 0.8344 (ttp) REVERT: A 1752 GLU cc_start: 0.8760 (tt0) cc_final: 0.8356 (tp30) REVERT: A 1858 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8394 (tm-30) REVERT: I 19 LEU cc_start: 0.8740 (tp) cc_final: 0.8481 (tp) REVERT: I 272 MET cc_start: 0.8648 (mtt) cc_final: 0.8418 (mmt) REVERT: I 305 MET cc_start: 0.8990 (tpp) cc_final: 0.8426 (mmm) REVERT: I 369 MET cc_start: 0.8992 (mtt) cc_final: 0.8770 (mtt) REVERT: I 717 MET cc_start: 0.4684 (tpt) cc_final: 0.4166 (tpt) REVERT: I 746 MET cc_start: 0.7387 (mmm) cc_final: 0.7019 (mpp) REVERT: O 335 ASN cc_start: 0.8942 (p0) cc_final: 0.8552 (t0) REVERT: O 363 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.7599 (t-90) REVERT: O 411 LYS cc_start: 0.9437 (tttt) cc_final: 0.9227 (tptt) REVERT: O 414 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8531 (pp) REVERT: O 557 MET cc_start: 0.9246 (mmm) cc_final: 0.9025 (mmt) REVERT: K 352 GLN cc_start: 0.8871 (mp-120) cc_final: 0.8238 (mp10) REVERT: C 60 ILE cc_start: -0.1042 (OUTLIER) cc_final: -0.1252 (mp) REVERT: G 15 ASP cc_start: 0.8312 (m-30) cc_final: 0.8014 (m-30) REVERT: W 17 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8529 (mp0) REVERT: M 35 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8793 (mp0) REVERT: M 54 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7631 (mp0) REVERT: H 53 PHE cc_start: 0.7383 (m-10) cc_final: 0.7133 (m-10) REVERT: H 87 GLU cc_start: 0.8570 (mp0) cc_final: 0.8180 (mp0) REVERT: H 88 GLU cc_start: 0.8669 (mp0) cc_final: 0.8352 (mp0) REVERT: P 656 MET cc_start: 0.8492 (tmm) cc_final: 0.8035 (tmm) REVERT: Q 164 PHE cc_start: 0.8662 (t80) cc_final: 0.8461 (t80) REVERT: Y 142 MET cc_start: 0.9069 (mmm) cc_final: 0.8820 (mmm) REVERT: Y 148 MET cc_start: 0.9100 (mmm) cc_final: 0.8825 (mmm) REVERT: Y 529 MET cc_start: 0.8910 (mtm) cc_final: 0.8521 (mtt) REVERT: Y 552 MET cc_start: 0.8793 (mmm) cc_final: 0.8375 (mmm) REVERT: U 157 GLU cc_start: 0.8461 (tt0) cc_final: 0.8071 (mt-10) REVERT: U 312 MET cc_start: 0.9016 (mpp) cc_final: 0.8796 (mpp) REVERT: U 414 MET cc_start: 0.7981 (mmm) cc_final: 0.7766 (mmm) REVERT: U 435 MET cc_start: 0.8942 (mpp) cc_final: 0.8490 (mpp) REVERT: U 457 TRP cc_start: 0.8453 (m100) cc_final: 0.8001 (m-10) REVERT: V 142 GLU cc_start: 0.8615 (mp0) cc_final: 0.8145 (mp0) REVERT: V 167 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6336 (pp) REVERT: V 218 MET cc_start: 0.8454 (ttm) cc_final: 0.7924 (mtp) REVERT: V 371 MET cc_start: 0.8994 (ttp) cc_final: 0.8672 (ptm) REVERT: V 480 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9188 (tt) REVERT: Z 49 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9018 (pp) REVERT: Z 144 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8153 (mm-30) REVERT: Z 174 MET cc_start: 0.8999 (ttm) cc_final: 0.8640 (ttm) REVERT: Z 308 MET cc_start: 0.8446 (mmm) cc_final: 0.8236 (mmm) REVERT: Z 396 PHE cc_start: 0.8032 (m-10) cc_final: 0.7760 (m-10) REVERT: R 264 MET cc_start: 0.4075 (mtm) cc_final: 0.3724 (mmp) REVERT: R 433 MET cc_start: 0.3105 (mmt) cc_final: 0.2675 (mmp) outliers start: 117 outliers final: 82 residues processed: 551 average time/residue: 0.6076 time to fit residues: 593.2630 Evaluate side-chains 538 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 449 time to evaluate : 5.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1748 LEU Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1794 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1900 LEU Chi-restraints excluded: chain A residue 1934 LEU Chi-restraints excluded: chain N residue 179 CYS Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 297 VAL Chi-restraints excluded: chain N residue 360 ASP Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 456 LEU Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 728 VAL Chi-restraints excluded: chain I residue 706 HIS Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 505 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain P residue 762 TRP Chi-restraints excluded: chain P residue 765 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 442 ASP Chi-restraints excluded: chain U residue 98 GLU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 355 GLN Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 107 HIS Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 219 LEU Chi-restraints excluded: chain V residue 480 LEU Chi-restraints excluded: chain V residue 521 PHE Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 185 GLU Chi-restraints excluded: chain Z residue 434 TYR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 495 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 844 random chunks: chunk 503 optimal weight: 4.9990 chunk 324 optimal weight: 3.9990 chunk 485 optimal weight: 0.9990 chunk 245 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 517 optimal weight: 1.9990 chunk 554 optimal weight: 0.9980 chunk 402 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 639 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 101 ASN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN J 702 ASN ** P 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 346 GLN ** U 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 289 ASN ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 69419 Z= 0.195 Angle : 0.547 12.920 94028 Z= 0.273 Chirality : 0.039 0.168 10525 Planarity : 0.004 0.124 11956 Dihedral : 4.545 62.984 9295 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.62 % Allowed : 17.96 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.82 (0.09), residues: 8427 helix: 1.56 (0.07), residues: 5375 sheet: -0.38 (0.22), residues: 536 loop : -1.50 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP Z 239 HIS 0.008 0.001 HIS U 321 PHE 0.032 0.001 PHE I 570 TYR 0.018 0.001 TYR Z 360 ARG 0.007 0.000 ARG V 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 448 time to evaluate : 5.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 14 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8876 (mtmm) REVERT: L 53 TYR cc_start: 0.8513 (p90) cc_final: 0.8244 (p90) REVERT: L 75 LYS cc_start: 0.9380 (tttt) cc_final: 0.9068 (ttpt) REVERT: L 80 TYR cc_start: 0.8903 (t80) cc_final: 0.7997 (t80) REVERT: L 157 LYS cc_start: 0.9210 (mttt) cc_final: 0.8726 (mptt) REVERT: D 50 ASN cc_start: 0.9227 (p0) cc_final: 0.8994 (p0) REVERT: A 11 MET cc_start: 0.7766 (mmt) cc_final: 0.7542 (mmm) REVERT: A 90 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8331 (p0) REVERT: A 161 MET cc_start: 0.8558 (mpp) cc_final: 0.8201 (mpp) REVERT: A 619 GLN cc_start: 0.8937 (tt0) cc_final: 0.8587 (mt0) REVERT: A 637 MET cc_start: 0.9136 (ttp) cc_final: 0.8932 (ppp) REVERT: A 1078 MET cc_start: 0.9228 (mtm) cc_final: 0.8912 (mtp) REVERT: A 1550 MET cc_start: 0.8663 (tpp) cc_final: 0.8386 (ttp) REVERT: A 1652 MET cc_start: 0.8028 (tpp) cc_final: 0.7472 (tpt) REVERT: A 1752 GLU cc_start: 0.8776 (tt0) cc_final: 0.8357 (tp30) REVERT: A 1858 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8404 (tm-30) REVERT: N 172 MET cc_start: 0.8189 (tmm) cc_final: 0.7543 (mtm) REVERT: I 19 LEU cc_start: 0.8748 (tp) cc_final: 0.8486 (tp) REVERT: I 305 MET cc_start: 0.8991 (tpp) cc_final: 0.8491 (mmm) REVERT: I 369 MET cc_start: 0.9034 (mtt) cc_final: 0.8825 (mtt) REVERT: I 548 MET cc_start: 0.8948 (mmt) cc_final: 0.8740 (mmt) REVERT: I 717 MET cc_start: 0.4705 (tpt) cc_final: 0.4169 (tpt) REVERT: I 746 MET cc_start: 0.7447 (mmm) cc_final: 0.7072 (mpp) REVERT: O 335 ASN cc_start: 0.8936 (p0) cc_final: 0.8568 (t0) REVERT: O 363 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.7592 (t-90) REVERT: O 411 LYS cc_start: 0.9435 (tttt) cc_final: 0.9229 (tptt) REVERT: O 414 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8518 (pp) REVERT: O 557 MET cc_start: 0.9272 (mmm) cc_final: 0.9019 (mmt) REVERT: K 352 GLN cc_start: 0.8896 (mp-120) cc_final: 0.8192 (mp10) REVERT: C 60 ILE cc_start: -0.1055 (OUTLIER) cc_final: -0.1288 (mp) REVERT: G 15 ASP cc_start: 0.8291 (m-30) cc_final: 0.7971 (m-30) REVERT: M 35 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8802 (mp0) REVERT: M 54 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7705 (mp0) REVERT: H 53 PHE cc_start: 0.7417 (m-10) cc_final: 0.7150 (m-10) REVERT: H 87 GLU cc_start: 0.8566 (mp0) cc_final: 0.8168 (mp0) REVERT: H 88 GLU cc_start: 0.8679 (mp0) cc_final: 0.8349 (mp0) REVERT: P 656 MET cc_start: 0.8491 (tmm) cc_final: 0.8006 (tmm) REVERT: P 731 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: Q 164 PHE cc_start: 0.8613 (t80) cc_final: 0.8395 (t80) REVERT: Y 142 MET cc_start: 0.9054 (mmm) cc_final: 0.8672 (mmm) REVERT: Y 148 MET cc_start: 0.9091 (mmm) cc_final: 0.8812 (mmm) REVERT: U 157 GLU cc_start: 0.8467 (tt0) cc_final: 0.8067 (mt-10) REVERT: U 312 MET cc_start: 0.9029 (mpp) cc_final: 0.8788 (mpp) REVERT: U 414 MET cc_start: 0.8025 (mmm) cc_final: 0.7804 (mmm) REVERT: U 435 MET cc_start: 0.8947 (mpp) cc_final: 0.8499 (mpp) REVERT: U 457 TRP cc_start: 0.8491 (m100) cc_final: 0.7918 (m-10) REVERT: V 142 GLU cc_start: 0.8637 (mp0) cc_final: 0.8185 (mp0) REVERT: V 167 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6247 (pp) REVERT: V 218 MET cc_start: 0.8444 (ttm) cc_final: 0.7919 (mtp) REVERT: V 480 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9194 (tt) REVERT: Z 49 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9001 (pp) REVERT: Z 144 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8169 (mm-30) REVERT: Z 174 MET cc_start: 0.9025 (ttm) cc_final: 0.8780 (ttm) REVERT: Z 308 MET cc_start: 0.8489 (mmm) cc_final: 0.8267 (mmm) REVERT: Z 396 PHE cc_start: 0.8102 (m-10) cc_final: 0.7889 (m-10) REVERT: R 264 MET cc_start: 0.4084 (mtm) cc_final: 0.3726 (mmp) REVERT: R 433 MET cc_start: 0.3101 (mmt) cc_final: 0.2665 (mmp) outliers start: 116 outliers final: 91 residues processed: 532 average time/residue: 0.6349 time to fit residues: 599.4243 Evaluate side-chains 540 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 441 time to evaluate : 5.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1748 LEU Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1761 MET Chi-restraints excluded: chain A residue 1786 MET Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1900 LEU Chi-restraints excluded: chain A residue 1934 LEU Chi-restraints excluded: chain N residue 179 CYS Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 297 VAL Chi-restraints excluded: chain N residue 360 ASP Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 456 LEU Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 728 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 696 GLN Chi-restraints excluded: chain I residue 706 HIS Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 505 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain J residue 758 MET Chi-restraints excluded: chain P residue 562 MET Chi-restraints excluded: chain P residue 701 LYS Chi-restraints excluded: chain P residue 704 LEU Chi-restraints excluded: chain P residue 731 GLN Chi-restraints excluded: chain P residue 762 TRP Chi-restraints excluded: chain P residue 765 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 354 MET Chi-restraints excluded: chain Q residue 442 ASP Chi-restraints excluded: chain U residue 98 GLU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 355 GLN Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 107 HIS Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 219 LEU Chi-restraints excluded: chain V residue 480 LEU Chi-restraints excluded: chain V residue 521 PHE Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 434 TYR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 495 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 844 random chunks: chunk 739 optimal weight: 0.9980 chunk 779 optimal weight: 4.9990 chunk 711 optimal weight: 6.9990 chunk 758 optimal weight: 0.9990 chunk 456 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 chunk 595 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 685 optimal weight: 0.8980 chunk 716 optimal weight: 0.8980 chunk 755 optimal weight: 30.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 101 ASN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1813 GLN ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 ASN ** P 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 69419 Z= 0.170 Angle : 0.542 12.457 94028 Z= 0.270 Chirality : 0.038 0.196 10525 Planarity : 0.003 0.127 11956 Dihedral : 4.484 62.977 9295 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.63 % Allowed : 17.97 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.31 % Twisted General : 0.02 % 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: 0.91 (0.09), residues: 8427 helix: 1.62 (0.07), residues: 5369 sheet: -0.34 (0.22), residues: 538 loop : -1.42 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP Z 239 HIS 0.008 0.001 HIS U 321 PHE 0.025 0.001 PHE Z 282 TYR 0.017 0.001 TYR N 336 ARG 0.006 0.000 ARG V 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 457 time to evaluate : 5.914 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: L 14 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8857 (mtmm) REVERT: L 53 TYR cc_start: 0.8575 (p90) cc_final: 0.8299 (p90) REVERT: L 75 LYS cc_start: 0.9370 (tttt) cc_final: 0.9070 (ttpt) REVERT: L 80 TYR cc_start: 0.8915 (t80) cc_final: 0.8034 (t80) REVERT: L 157 LYS cc_start: 0.9209 (mttt) cc_final: 0.8723 (mptt) REVERT: D 50 ASN cc_start: 0.9230 (p0) cc_final: 0.8989 (p0) REVERT: A 11 MET cc_start: 0.7770 (mmt) cc_final: 0.7541 (mmm) REVERT: A 90 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8353 (p0) REVERT: A 161 MET cc_start: 0.8544 (mpp) cc_final: 0.8209 (mpp) REVERT: A 619 GLN cc_start: 0.8945 (tt0) cc_final: 0.8606 (mt0) REVERT: A 1078 MET cc_start: 0.9167 (mtm) cc_final: 0.8891 (mtp) REVERT: A 1350 TYR cc_start: 0.8804 (m-10) cc_final: 0.8437 (m-10) REVERT: A 1550 MET cc_start: 0.8618 (tpp) cc_final: 0.8400 (ttp) REVERT: A 1652 MET cc_start: 0.7924 (tpp) cc_final: 0.7361 (tpt) REVERT: A 1858 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8395 (tm-30) REVERT: N 172 MET cc_start: 0.8157 (tmm) cc_final: 0.7545 (mtm) REVERT: I 19 LEU cc_start: 0.8774 (tp) cc_final: 0.8503 (tp) REVERT: I 272 MET cc_start: 0.8663 (mtt) cc_final: 0.8383 (mmt) REVERT: I 305 MET cc_start: 0.8974 (tpp) cc_final: 0.8485 (mmm) REVERT: I 717 MET cc_start: 0.4687 (tpt) cc_final: 0.4154 (tpt) REVERT: I 746 MET cc_start: 0.7562 (mmm) cc_final: 0.7208 (mpp) REVERT: O 335 ASN cc_start: 0.8916 (p0) cc_final: 0.8580 (t0) REVERT: O 363 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.7585 (t-90) REVERT: O 411 LYS cc_start: 0.9430 (tttt) cc_final: 0.9229 (tptt) REVERT: O 414 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8467 (pp) REVERT: O 557 MET cc_start: 0.9279 (mmm) cc_final: 0.9039 (mmt) REVERT: K 75 LEU cc_start: 0.9553 (tp) cc_final: 0.9248 (tt) REVERT: K 352 GLN cc_start: 0.8876 (mp-120) cc_final: 0.8235 (mp10) REVERT: K 364 MET cc_start: 0.8351 (mmt) cc_final: 0.7910 (mmt) REVERT: C 60 ILE cc_start: -0.1077 (OUTLIER) cc_final: -0.1308 (mp) REVERT: G 15 ASP cc_start: 0.8304 (m-30) cc_final: 0.7988 (m-30) REVERT: M 35 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8793 (mp0) REVERT: M 54 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7752 (mp0) REVERT: H 53 PHE cc_start: 0.7321 (m-10) cc_final: 0.7067 (m-10) REVERT: H 88 GLU cc_start: 0.8690 (mp0) cc_final: 0.8411 (mp0) REVERT: P 582 GLU cc_start: 0.8460 (mp0) cc_final: 0.8022 (mp0) REVERT: P 656 MET cc_start: 0.8505 (tmm) cc_final: 0.8042 (tmm) REVERT: Q 164 PHE cc_start: 0.8636 (t80) cc_final: 0.8422 (t80) REVERT: Y 142 MET cc_start: 0.9064 (mmm) cc_final: 0.8638 (mmm) REVERT: Y 148 MET cc_start: 0.9081 (mmm) cc_final: 0.8805 (mmm) REVERT: Y 552 MET cc_start: 0.8789 (mmm) cc_final: 0.8379 (mmm) REVERT: U 312 MET cc_start: 0.9012 (mpp) cc_final: 0.8761 (mpp) REVERT: U 435 MET cc_start: 0.8948 (mpp) cc_final: 0.8485 (mpp) REVERT: U 457 TRP cc_start: 0.8488 (m100) cc_final: 0.7917 (m-10) REVERT: V 142 GLU cc_start: 0.8666 (mp0) cc_final: 0.8229 (mp0) REVERT: V 167 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6212 (pp) REVERT: V 218 MET cc_start: 0.8429 (ttm) cc_final: 0.7896 (mtp) REVERT: V 246 GLU cc_start: 0.8291 (mp0) cc_final: 0.8067 (mp0) REVERT: V 371 MET cc_start: 0.8988 (ttp) cc_final: 0.8746 (ptm) REVERT: V 480 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9200 (tt) REVERT: Z 49 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9000 (pp) REVERT: Z 144 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8167 (mm-30) REVERT: Z 148 MET cc_start: 0.8912 (mmm) cc_final: 0.8631 (mmm) REVERT: Z 174 MET cc_start: 0.9042 (ttm) cc_final: 0.8777 (ttm) REVERT: Z 308 MET cc_start: 0.8470 (mmm) cc_final: 0.8264 (mmm) REVERT: R 264 MET cc_start: 0.4048 (mtm) cc_final: 0.3711 (mmp) REVERT: R 433 MET cc_start: 0.3088 (mmt) cc_final: 0.2643 (mmp) outliers start: 117 outliers final: 90 residues processed: 545 average time/residue: 0.6128 time to fit residues: 594.0301 Evaluate side-chains 541 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 444 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1748 LEU Chi-restraints excluded: chain A residue 1749 SER Chi-restraints excluded: chain A residue 1786 MET Chi-restraints excluded: chain A residue 1794 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1900 LEU Chi-restraints excluded: chain A residue 1934 LEU Chi-restraints excluded: chain N residue 179 CYS Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 297 VAL Chi-restraints excluded: chain N residue 360 ASP Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 456 LEU Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain N residue 728 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 696 GLN Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 505 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain J residue 758 MET Chi-restraints excluded: chain P residue 562 MET Chi-restraints excluded: chain P residue 701 LYS Chi-restraints excluded: chain P residue 704 LEU Chi-restraints excluded: chain P residue 731 GLN Chi-restraints excluded: chain P residue 762 TRP Chi-restraints excluded: chain P residue 765 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 354 MET Chi-restraints excluded: chain Q residue 442 ASP Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 355 GLN Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 107 HIS Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 219 LEU Chi-restraints excluded: chain V residue 480 LEU Chi-restraints excluded: chain V residue 521 PHE Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 434 TYR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 495 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 844 random chunks: chunk 497 optimal weight: 4.9990 chunk 801 optimal weight: 9.9990 chunk 489 optimal weight: 0.9990 chunk 380 optimal weight: 1.9990 chunk 557 optimal weight: 8.9990 chunk 840 optimal weight: 40.0000 chunk 773 optimal weight: 0.0010 chunk 669 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 517 optimal weight: 0.9980 chunk 410 optimal weight: 0.8980 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 101 ASN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1727 ASN N 319 ASN ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 702 ASN ** P 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 488 GLN ** V 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 69419 Z= 0.153 Angle : 0.542 12.221 94028 Z= 0.269 Chirality : 0.038 0.188 10525 Planarity : 0.004 0.128 11956 Dihedral : 4.416 62.847 9295 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.51 % Allowed : 18.16 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.31 % Twisted General : 0.02 % 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 (0.10), residues: 8427 helix: 1.67 (0.07), residues: 5367 sheet: -0.27 (0.22), residues: 538 loop : -1.38 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP Z 239 HIS 0.008 0.001 HIS U 321 PHE 0.025 0.001 PHE Z 282 TYR 0.018 0.001 TYR N 336 ARG 0.017 0.000 ARG G 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16854 Ramachandran restraints generated. 8427 Oldfield, 0 Emsley, 8427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 459 time to evaluate : 5.937 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: L 14 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8851 (mtmm) REVERT: L 53 TYR cc_start: 0.8608 (p90) cc_final: 0.8351 (p90) REVERT: L 75 LYS cc_start: 0.9365 (tttt) cc_final: 0.9014 (ttmm) REVERT: L 80 TYR cc_start: 0.8909 (t80) cc_final: 0.7984 (t80) REVERT: L 157 LYS cc_start: 0.9211 (mttt) cc_final: 0.8734 (mptt) REVERT: D 50 ASN cc_start: 0.9220 (p0) cc_final: 0.8975 (p0) REVERT: A 11 MET cc_start: 0.7816 (mmt) cc_final: 0.7593 (mmm) REVERT: A 90 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8336 (p0) REVERT: A 161 MET cc_start: 0.8516 (mpp) cc_final: 0.8201 (mpp) REVERT: A 257 MET cc_start: 0.8631 (ttm) cc_final: 0.8399 (ttm) REVERT: A 619 GLN cc_start: 0.8940 (tt0) cc_final: 0.8611 (mt0) REVERT: A 665 MET cc_start: 0.9002 (mmp) cc_final: 0.8646 (mmm) REVERT: A 1078 MET cc_start: 0.9186 (mtm) cc_final: 0.8879 (mtp) REVERT: A 1130 ASN cc_start: 0.8228 (t0) cc_final: 0.7926 (t0) REVERT: A 1307 LEU cc_start: 0.9320 (tp) cc_final: 0.8909 (mt) REVERT: A 1350 TYR cc_start: 0.8786 (m-10) cc_final: 0.8413 (m-10) REVERT: A 1652 MET cc_start: 0.7843 (tpp) cc_final: 0.7294 (tpt) REVERT: A 1858 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8389 (tm-30) REVERT: N 172 MET cc_start: 0.8171 (tmm) cc_final: 0.7556 (mtm) REVERT: I 19 LEU cc_start: 0.8768 (tp) cc_final: 0.8495 (tp) REVERT: I 272 MET cc_start: 0.8684 (mtt) cc_final: 0.8399 (mmt) REVERT: I 305 MET cc_start: 0.8954 (tpp) cc_final: 0.8461 (mmm) REVERT: I 428 MET cc_start: 0.7703 (mtm) cc_final: 0.7482 (ptt) REVERT: I 548 MET cc_start: 0.8584 (tpp) cc_final: 0.7964 (mmt) REVERT: I 717 MET cc_start: 0.4836 (tpt) cc_final: 0.4291 (tpt) REVERT: I 746 MET cc_start: 0.7610 (mmm) cc_final: 0.7240 (mpp) REVERT: O 335 ASN cc_start: 0.8897 (p0) cc_final: 0.8587 (t0) REVERT: O 414 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8442 (pp) REVERT: O 557 MET cc_start: 0.9295 (mmm) cc_final: 0.9072 (mmt) REVERT: K 352 GLN cc_start: 0.8861 (mp-120) cc_final: 0.8021 (mp10) REVERT: K 364 MET cc_start: 0.8379 (mmt) cc_final: 0.7938 (mmt) REVERT: C 60 ILE cc_start: -0.1069 (OUTLIER) cc_final: -0.1298 (mp) REVERT: G 15 ASP cc_start: 0.8334 (m-30) cc_final: 0.8037 (m-30) REVERT: M 35 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8746 (mp0) REVERT: M 54 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7751 (mp0) REVERT: H 53 PHE cc_start: 0.7291 (m-10) cc_final: 0.7060 (m-10) REVERT: H 88 GLU cc_start: 0.8689 (mp0) cc_final: 0.8395 (mp0) REVERT: P 582 GLU cc_start: 0.8480 (mp0) cc_final: 0.8043 (mp0) REVERT: P 656 MET cc_start: 0.8499 (tmm) cc_final: 0.8040 (tmm) REVERT: Q 164 PHE cc_start: 0.8597 (t80) cc_final: 0.8392 (t80) REVERT: Y 102 MET cc_start: 0.9090 (mtm) cc_final: 0.8866 (mtm) REVERT: Y 142 MET cc_start: 0.9150 (mmm) cc_final: 0.8683 (mmm) REVERT: Y 148 MET cc_start: 0.9068 (mmm) cc_final: 0.8795 (mmm) REVERT: Y 552 MET cc_start: 0.8773 (mmm) cc_final: 0.8471 (mmm) REVERT: U 312 MET cc_start: 0.9023 (mpp) cc_final: 0.8764 (mpp) REVERT: U 435 MET cc_start: 0.8951 (mpp) cc_final: 0.8492 (mpp) REVERT: U 457 TRP cc_start: 0.8465 (m100) cc_final: 0.7887 (m-10) REVERT: V 142 GLU cc_start: 0.8659 (mp0) cc_final: 0.8229 (mp0) REVERT: V 167 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6184 (pp) REVERT: V 218 MET cc_start: 0.8434 (ttm) cc_final: 0.7912 (mtp) REVERT: V 246 GLU cc_start: 0.8211 (mp0) cc_final: 0.7897 (mp0) REVERT: V 371 MET cc_start: 0.8995 (ttp) cc_final: 0.8751 (ptm) REVERT: Z 49 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8985 (pp) REVERT: Z 144 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8155 (mm-30) REVERT: Z 148 MET cc_start: 0.8920 (mmm) cc_final: 0.8670 (mmm) REVERT: Z 174 MET cc_start: 0.9029 (ttm) cc_final: 0.8767 (ttm) REVERT: R 264 MET cc_start: 0.3987 (mtm) cc_final: 0.3669 (mmp) REVERT: R 433 MET cc_start: 0.3052 (mmt) cc_final: 0.2569 (mmp) outliers start: 108 outliers final: 90 residues processed: 541 average time/residue: 0.6068 time to fit residues: 583.4653 Evaluate side-chains 538 residues out of total 7487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 443 time to evaluate : 5.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 ASP Chi-restraints excluded: chain L residue 65 ASN Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 176 ILE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1108 THR Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1244 ASP Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1455 GLU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1786 MET Chi-restraints excluded: chain A residue 1794 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1900 LEU Chi-restraints excluded: chain A residue 1934 LEU Chi-restraints excluded: chain N residue 179 CYS Chi-restraints excluded: chain N residue 243 LEU Chi-restraints excluded: chain N residue 297 VAL Chi-restraints excluded: chain N residue 360 ASP Chi-restraints excluded: chain N residue 368 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 456 LEU Chi-restraints excluded: chain N residue 518 GLU Chi-restraints excluded: chain N residue 609 LEU Chi-restraints excluded: chain N residue 728 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 363 HIS Chi-restraints excluded: chain O residue 387 GLN Chi-restraints excluded: chain O residue 408 LEU Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 505 GLN Chi-restraints excluded: chain O residue 532 VAL Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 332 THR Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 614 THR Chi-restraints excluded: chain P residue 701 LYS Chi-restraints excluded: chain P residue 704 LEU Chi-restraints excluded: chain P residue 762 TRP Chi-restraints excluded: chain P residue 765 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 354 MET Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 355 GLN Chi-restraints excluded: chain U residue 446 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 107 HIS Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 219 LEU Chi-restraints excluded: chain V residue 521 PHE Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain V residue 550 LEU Chi-restraints excluded: chain V residue 554 LEU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 434 TYR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 495 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 844 random chunks: chunk 531 optimal weight: 0.0000 chunk 713 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 617 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 670 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 688 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 overall best weight: 3.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 101 ASN L 104 ASN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 ASN ** A1595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 319 ASN ** I 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 696 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 352 GLN J 702 ASN ** P 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 426 HIS ** V 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 477 HIS ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.076335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.049696 restraints weight = 351743.147| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.18 r_work: 0.2814 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 69419 Z= 0.301 Angle : 0.604 12.931 94028 Z= 0.302 Chirality : 0.041 0.196 10525 Planarity : 0.004 0.128 11956 Dihedral : 4.476 60.780 9294 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.51 % Allowed : 18.30 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.97 (0.10), residues: 8427 helix: 1.64 (0.07), residues: 5375 sheet: -0.26 (0.22), residues: 533 loop : -1.37 (0.13), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP Z 239 HIS 0.008 0.001 HIS U 321 PHE 0.026 0.001 PHE P 741 TYR 0.015 0.001 TYR K 322 ARG 0.015 0.000 ARG G 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14544.83 seconds wall clock time: 265 minutes 58.14 seconds (15958.14 seconds total)