Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 03:51:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xey_22156/08_2023/6xey_22156.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xey_22156/08_2023/6xey_22156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xey_22156/08_2023/6xey_22156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xey_22156/08_2023/6xey_22156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xey_22156/08_2023/6xey_22156.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xey_22156/08_2023/6xey_22156.pdb" } resolution = 3.25 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= 0.008 sd= 0.026 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 135 5.16 5 C 18106 2.51 5 N 4672 2.21 5 O 5569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "G TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 101": "OD1" <-> "OD2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 28482 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7663 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 982} Chain breaks: 6 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 490 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 5, 'ASN:plan1': 9, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 210 Chain: "B" Number of atoms: 7630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7630 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 982} Chain breaks: 6 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 518 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 252 Chain: "C" Number of atoms: 7683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7683 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Chain breaks: 6 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 208 Chain: "F" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 850 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "G" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 698 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "H" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 857 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "J" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 848 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "K" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 692 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 694 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 14.15, per 1000 atoms: 0.50 Number of scatterers: 28482 At special positions: 0 Unit cell: (148.12, 140.714, 197.846, 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 135 16.00 O 5569 8.00 N 4672 7.00 C 18106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A 801 " " NAG A1314 " - " ASN A 709 " " NAG A1315 " - " ASN A 657 " " NAG A1316 " - " ASN A 616 " " NAG A1317 " - " ASN A 603 " " NAG A1318 " - " ASN A 331 " " NAG A1319 " - " ASN A 165 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 657 " " NAG B1306 " - " ASN B 331 " " NAG B1312 " - " ASN B1134 " " NAG B1313 " - " ASN B 234 " " NAG B1314 " - " ASN B 709 " " NAG B1315 " - " ASN B 165 " " NAG B1316 " - " ASN B1098 " " NAG B1317 " - " ASN B 801 " " NAG B1318 " - " ASN B1074 " " NAG B1319 " - " ASN B 616 " " NAG C1301 " - " ASN C 657 " " NAG C1305 " - " ASN C 331 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 603 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C1098 " " NAG C1315 " - " ASN C 165 " " NAG C1316 " - " ASN C 616 " " NAG C1317 " - " ASN C 709 " " NAG C1318 " - " ASN C 801 " " NAG C1319 " - " ASN C 282 " " NAG D 1 " - " ASN A 481 " " NAG E 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 717 " " NAG M 1 " - " ASN B 481 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN C 343 " " NAG Q 1 " - " ASN C 481 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN F 58 " " NAG T 1 " - " ASN H 58 " " NAG U 1 " - " ASN J 58 " Time building additional restraints: 11.54 Conformation dependent library (CDL) restraints added in 4.6 seconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7018 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 64 sheets defined 20.9% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.819A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.674A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.568A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.900A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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 783 removed outlier: 3.822A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.787A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.643A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.012A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.714A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.703A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.739A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 4.330A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.567A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.632A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.503A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.762A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.731A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.595A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 removed outlier: 3.574A pdb=" N ALA B 944 " --> pdb=" O THR B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 4.655A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.518A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.767A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.770A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.321A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.510A pdb=" N ASP C 571 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 568 through 572' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 749 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.270A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.680A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.681A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.079A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.274A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.719A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.172A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.666A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.952A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.816A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.767A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.837A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.710A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.116A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.951A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.939A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 126 through 130 removed outlier: 3.696A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 319 removed outlier: 5.424A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.521A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.308A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.976A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.978A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.644A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.644A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.049A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.237A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.559A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.851A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.755A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.539A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.631A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.633A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.145A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 728 removed outlier: 6.185A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B1049 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.328A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.806A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.865A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 65 through 66 removed outlier: 4.045A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.803A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.381A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.214A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.613A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.695A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.803A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.215A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.897A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AF4, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.717A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.717A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.638A pdb=" N ALA G 11 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 18 through 24 removed outlier: 3.587A pdb=" N SER G 65 " --> pdb=" O SER G 72 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER G 63 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.615A pdb=" N SER G 90 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL G 97 " --> pdb=" O SER G 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN H 58 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AG4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.817A pdb=" N MET J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 9 through 11 removed outlier: 6.603A pdb=" N TRP K 35 " --> pdb=" O MET K 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 18 through 23 removed outlier: 3.607A pdb=" N SER K 72 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 89 through 90 removed outlier: 3.511A pdb=" N SER K 90 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL K 97 " --> pdb=" O SER K 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.711A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.505A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.637A pdb=" N ALA L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 2928 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: 13.14 Time building geometry restraints manager: 12.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9118 1.34 - 1.46: 7559 1.46 - 1.59: 12289 1.59 - 1.71: 0 1.71 - 1.83: 178 Bond restraints: 29144 Sorted by residual: bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.43e+00 bond pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.78e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.67e+00 bond pdb=" C1 BMA M 2 " pdb=" C2 BMA M 2 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" CB THR C1077 " pdb=" CG2 THR C1077 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 ... (remaining 29139 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.09: 593 105.09 - 112.41: 14872 112.41 - 119.72: 9324 119.72 - 127.04: 14803 127.04 - 134.36: 306 Bond angle restraints: 39898 Sorted by residual: angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 111.36 104.35 7.01 1.09e+00 8.42e-01 4.13e+01 angle pdb=" N VAL G 51 " pdb=" CA VAL G 51 " pdb=" C VAL G 51 " ideal model delta sigma weight residual 109.34 121.50 -12.16 2.08e+00 2.31e-01 3.42e+01 angle pdb=" N GLY F 44 " pdb=" CA GLY F 44 " pdb=" C GLY F 44 " ideal model delta sigma weight residual 111.78 121.04 -9.26 1.69e+00 3.50e-01 3.00e+01 angle pdb=" N ILE B 805 " pdb=" CA ILE B 805 " pdb=" C ILE B 805 " ideal model delta sigma weight residual 111.90 107.77 4.13 8.10e-01 1.52e+00 2.60e+01 angle pdb=" N GLY A 476 " pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 113.79 108.32 5.47 1.17e+00 7.31e-01 2.19e+01 ... (remaining 39893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 15339 17.63 - 35.26: 926 35.26 - 52.89: 160 52.89 - 70.52: 50 70.52 - 88.15: 26 Dihedral angle restraints: 16501 sinusoidal: 5546 harmonic: 10955 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 14.65 78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -143.39 57.39 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 147.27 -54.27 1 1.00e+01 1.00e-02 3.99e+01 ... (remaining 16498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4623 0.116 - 0.231: 140 0.231 - 0.347: 16 0.347 - 0.462: 3 0.462 - 0.578: 1 Chirality restraints: 4783 Sorted by residual: chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.34e+00 chirality pdb=" CA ASN K 31 " pdb=" N ASN K 31 " pdb=" C ASN K 31 " pdb=" CB ASN K 31 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 4780 not shown) Planarity restraints: 5166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 486 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C PHE A 486 " 0.068 2.00e-02 2.50e+03 pdb=" O PHE A 486 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 487 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1041 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ASP A1041 " 0.063 2.00e-02 2.50e+03 pdb=" O ASP A1041 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A1042 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A 295 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.040 5.00e-02 4.00e+02 ... (remaining 5163 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 7402 2.79 - 3.32: 25356 3.32 - 3.85: 46652 3.85 - 4.37: 52415 4.37 - 4.90: 92148 Nonbonded interactions: 223973 Sorted by model distance: nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR L 26 " pdb=" O SER L 27A" model vdw 2.280 2.440 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR B 351 " pdb=" O ILE B 468 " model vdw 2.310 2.440 nonbonded pdb=" OG SER K 34 " pdb=" OG SER K 89 " model vdw 2.319 2.440 ... (remaining 223968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 51 or (resid 52 throu \ gh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 throu \ gh 68 or (resid 69 and (name N or name CA or name C or name O or name CB )) or r \ esid 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or \ resid 81 through 86 or (resid 87 and (name N or name CA or name C or name O or \ name CB )) or resid 88 through 94 or (resid 95 through 98 and (name N or name CA \ or name C or name O or name CB )) or resid 99 through 114 or (resid 115 and (na \ me N or name CA or name C or name O or name CB )) or resid 116 through 123 or (r \ esid 124 and (name N or name CA or name C or name O or name CB )) or resid 125 t \ hrough 133 or (resid 134 and (name N or name CA or name C or name O or name CB ) \ ) or resid 135 or (resid 136 through 138 and (name N or name CA or name C or nam \ e O or name CB )) or resid 139 through 143 or resid 158 through 160 or (resid 16 \ 1 through 164 and (name N or name CA or name C or name O or name CB )) or resid \ 165 through 205 or (resid 206 and (name N or name CA or name C or name O or name \ CB )) or resid 207 through 244 or (resid 245 through 246 and (name N or name CA \ or name C or name O or name CB )) or resid 247 through 253 or (resid 254 and (n \ ame N or name CA or name C or name O or name CB )) or resid 255 through 280 or ( \ resid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 \ through 286 or (resid 287 through 288 and (name N or name CA or name C or name O \ or name CB )) or resid 289 through 308 or (resid 309 through 310 and (name N or \ name CA or name C or name O or name CB )) or resid 311 through 323 or (resid 32 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 325 through \ 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) or re \ sid 333 through 345 or (resid 346 and (name N or name CA or name C or name O or \ name CB )) or resid 347 through 355 or (resid 356 through 357 and (name N or nam \ e CA or name C or name O or name CB )) or resid 358 through 385 or (resid 386 an \ d (name N or name CA or name C or name O or name CB )) or resid 387 or (resid 38 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 389 through \ 404 or (resid 405 through 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 through 440 or (resid 441 through 442 and (name N or name CA \ or name C or name O or name CB )) or resid 443 through 451 or (resid 452 and (n \ ame N or name CA or name C or name O or name CB )) or resid 453 through 458 or ( \ resid 459 and (name N or name CA or name C or name O or name CB )) or resid 460 \ through 477 or (resid 478 and (name N or name CA or name C or name O or name CB \ )) or resid 479 through 483 or (resid 484 and (name N or name CA or name C or na \ me O or name CB )) or resid 485 through 531 or (resid 532 and (name N or name CA \ or name C or name O or name CB )) or resid 533 through 534 or (resid 535 and (n \ ame N or name CA or name C or name O or name CB )) or resid 536 or (resid 537 an \ d (name N or name CA or name C or name O or name CB )) or resid 538 through 553 \ or (resid 554 and (name N or name CA or name C or name O or name CB )) or resid \ 555 or (resid 556 through 558 and (name N or name CA or name C or name O or name \ CB )) or resid 559 through 563 or (resid 564 and (name N or name CA or name C o \ r name O or name CB )) or resid 565 through 570 or (resid 571 through 572 and (n \ ame N or name CA or name C or name O or name CB )) or resid 573 through 612 or ( \ resid 613 through 614 and (name N or name CA or name C or name O or name CB )) o \ r resid 615 through 620 or resid 641 through 676 or (resid 690 and (name N or na \ me CA or name C or name O or name CB )) or resid 691 through 736 or (resid 737 a \ nd (name N or name CA or name C or name O or name CB )) or resid 738 through 744 \ or (resid 745 and (name N or name CA or name C or name O or name CB )) or resid \ 746 through 747 or (resid 748 and (name N or name CA or name C or name O or nam \ e CB )) or resid 749 through 754 or (resid 755 and (name N or name CA or name C \ or name O or name CB )) or resid 756 through 775 or (resid 776 and (name N or na \ me CA or name C or name O or name CB )) or resid 777 through 778 or (resid 779 t \ hrough 780 and (name N or name CA or name C or name O or name CB )) or resid 781 \ through 827 or (resid 828 and (name N or name CA or name C or name O or name CB \ )) or (resid 855 and (name N or name CA or name C or name O or name CB )) or re \ sid 856 through 867 or (resid 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 938 or (resid 939 through 944 and (name N or nam \ e CA or name C or name O or name CB )) or resid 945 through 984 or (resid 985 an \ d (name N or name CA or name C or name O or name CB )) or resid 986 through 987 \ or (resid 988 through 989 and (name N or name CA or name C or name O or name CB \ )) or resid 990 through 994 or (resid 995 and (name N or name CA or name C or na \ me O or name CB )) or resid 996 through 1013 or (resid 1014 through 1016 and (na \ me N or name CA or name C or name O or name CB )) or resid 1017 through 1018 or \ (resid 1019 through 1020 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1021 through 1050 or (resid 1051 and (name N or name CA or name C or \ name O or name CB )) or resid 1052 through 1091 or (resid 1092 and (name N or na \ me CA or name C or name O or name CB )) or resid 1093 through 1110 or (resid 111 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 1112 through \ 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O or \ name CB )) or resid 1303 through 1319)) selection = (chain 'B' and (resid 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 51 or (resid 52 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 67 or (res \ id 68 through 69 and (name N or name CA or name C or name O or name CB )) or res \ id 70 through 71 or resid 81 through 86 or (resid 87 and (name N or name CA or n \ ame C or name O or name CB )) or resid 88 through 107 or (resid 108 through 113 \ and (name N or name CA or name C or name O or name CB )) or resid 114 or (resid \ 115 and (name N or name CA or name C or name O or name CB )) or resid 116 throug \ h 120 or (resid 121 through 124 and (name N or name CA or name C or name O or na \ me CB )) or resid 125 through 142 or (resid 143 through 158 and (name N or name \ CA or name C or name O or name CB )) or resid 159 through 160 or (resid 161 thro \ ugh 164 and (name N or name CA or name C or name O or name CB )) or resid 165 th \ rough 187 or (resid 188 and (name N or name CA or name C or name O or name CB )) \ or resid 189 through 199 or (resid 200 and (name N or name CA or name C or name \ O or name CB )) or resid 201 through 212 or (resid 213 through 214 and (name N \ or name CA or name C or name O or name CB )) or resid 215 through 217 or (resid \ 218 and (name N or name CA or name C or name O or name CB )) or resid 219 throug \ h 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) or \ resid 225 through 248 or (resid 249 through 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 253 or (resid 254 and (name N or n \ ame CA or name C or name O or name CB )) or resid 255 through 320 or (resid 321 \ and (name N or name CA or name C or name O or name CB )) or resid 322 or (resid \ 323 through 324 and (name N or name CA or name C or name O or name CB )) or resi \ d 325 through 331 or (resid 332 and (name N or name CA or name C or name O or na \ me CB )) or resid 333 through 356 or (resid 357 and (name N or name CA or name C \ or name O or name CB )) or resid 358 through 402 or (resid 403 and (name N or n \ ame CA or name C or name O or name CB )) or resid 404 or (resid 405 through 406 \ and (name N or name CA or name C or name O or name CB )) or resid 407 or (resid \ 408 and (name N or name CA or name C or name O or name CB )) or resid 409 throug \ h 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) or \ resid 416 through 423 or (resid 424 and (name N or name CA or name C or name O o \ r name CB )) or resid 425 through 444 or (resid 445 and (name N or name CA or na \ me C or name O or name CB )) or resid 446 through 451 or (resid 452 and (name N \ or name CA or name C or name O or name CB )) or resid 453 through 457 or (resid \ 458 through 459 and (name N or name CA or name C or name O or name CB )) or resi \ d 460 through 464 or (resid 465 and (name N or name CA or name C or name O or na \ me CB )) or resid 466 through 477 or (resid 478 and (name N or name CA or name C \ or name O or name CB )) or resid 479 through 483 or (resid 484 and (name N or n \ ame CA or name C or name O or name CB )) or resid 485 through 486 or (resid 487 \ and (name N or name CA or name C or name O or name CB )) or resid 488 through 49 \ 9 or (resid 500 and (name N or name CA or name C or name O or name CB )) or resi \ d 501 through 508 or (resid 509 and (name N or name CA or name C or name O or na \ me CB )) or resid 510 through 534 or (resid 535 and (name N or name CA or name C \ or name O or name CB )) or resid 536 through 563 or (resid 564 and (name N or n \ ame CA or name C or name O or name CB )) or resid 565 through 568 or (resid 569 \ through 572 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 3 through 579 or (resid 580 and (name N or name CA or name C or name O or name C \ B )) or resid 581 through 617 or (resid 618 and (name N or name CA or name C or \ name O or name CB )) or resid 619 through 620 or resid 641 through 747 or (resid \ 748 and (name N or name CA or name C or name O or name CB )) or resid 749 throu \ gh 818 or (resid 819 and (name N or name CA or name C or name O or name CB )) or \ resid 820 through 824 or (resid 825 and (name N or name CA or name C or name O \ or name CB )) or resid 826 through 828 or resid 855 through 917 or (resid 918 an \ d (name N or name CA or name C or name O or name CB )) or resid 919 through 920 \ or (resid 921 and (name N or name CA or name C or name O or name CB )) or resid \ 922 through 932 or (resid 933 and (name N or name CA or name C or name O or name \ CB )) or resid 934 through 935 or (resid 936 and (name N or name CA or name C o \ r name O or name CB )) or resid 937 through 940 or (resid 941 through 944 and (n \ ame N or name CA or name C or name O or name CB )) or resid 945 through 946 or ( \ resid 947 and (name N or name CA or name C or name O or name CB )) or resid 948 \ through 963 or (resid 964 and (name N or name CA or name C or name O or name CB \ )) or resid 965 through 1050 or (resid 1051 and (name N or name CA or name C or \ name O or name CB )) or resid 1052 through 1106 or (resid 1107 and (name N or na \ me CA or name C or name O or name CB )) or resid 1108 through 1110 or (resid 111 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 1112 through \ 1137 or (resid 1138 and (name N or name CA or name C or name O or name CB )) or \ resid 1139 through 1143 or (resid 1144 through 1146 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1301 through 1319)) selection = (chain 'C' and (resid 27 through 67 or (resid 68 through 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 or (resid 71 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 through 94 or (resid 95 throu \ gh 98 and (name N or name CA or name C or name O or name CB )) or resid 99 throu \ gh 107 or (resid 108 through 113 and (name N or name CA or name C or name O or n \ ame CB )) or resid 114 through 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 135 or (resid 136 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 142 o \ r (resid 143 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 58 through 175 or (resid 176 through 188 and (name N or name CA or name C or nam \ e O or name CB )) or resid 189 through 199 or (resid 200 and (name N or name CA \ or name C or name O or name CB )) or resid 201 through 205 or (resid 206 and (na \ me N or name CA or name C or name O or name CB )) or resid 207 through 217 or (r \ esid 218 and (name N or name CA or name C or name O or name CB )) or resid 219 t \ hrough 223 or (resid 224 and (name N or name CA or name C or name O or name CB ) \ ) or resid 225 through 244 or (resid 245 through 246 and (name N or name CA or n \ ame C or name O or name CB )) or resid 247 through 248 or (resid 249 through 250 \ and (name N or name CA or name C or name O or name CB )) or resid 251 through 2 \ 80 or (resid 281 and (name N or name CA or name C or name O or name CB )) or res \ id 282 through 286 or (resid 287 through 288 and (name N or name CA or name C or \ name O or name CB )) or resid 289 through 303 or (resid 304 and (name N or name \ CA or name C or name O or name CB )) or resid 305 through 308 or (resid 309 thr \ ough 310 and (name N or name CA or name C or name O or name CB )) or resid 311 t \ hrough 320 or (resid 321 and (name N or name CA or name C or name O or name CB ) \ ) or resid 322 through 323 or (resid 324 and (name N or name CA or name C or nam \ e O or name CB )) or resid 325 through 345 or (resid 346 and (name N or name CA \ or name C or name O or name CB )) or resid 347 through 368 or (resid 369 and (na \ me N or name CA or name C or name O or name CB )) or resid 370 through 385 or (r \ esid 386 and (name N or name CA or name C or name O or name CB )) or resid 387 t \ hrough 402 or (resid 403 and (name N or name CA or name C or name O or name CB ) \ ) or resid 404 through 407 or (resid 408 and (name N or name CA or name C or nam \ e O or name CB )) or resid 409 through 416 or (resid 417 and (name N or name CA \ or name C or name O or name CB )) or resid 418 through 423 or (resid 424 and (na \ me N or name CA or name C or name O or name CB )) or resid 425 through 427 or (r \ esid 428 and (name N or name CA or name C or name O or name CB )) or resid 429 t \ hrough 438 or (resid 439 through 442 and (name N or name CA or name C or name O \ or name CB )) or resid 443 through 444 or (resid 445 and (name N or name CA or n \ ame C or name O or name CB )) or resid 446 through 461 or (resid 462 and (name N \ or name CA or name C or name O or name CB )) or resid 463 through 508 or (resid \ 509 and (name N or name CA or name C or name O or name CB )) or resid 510 throu \ gh 531 or (resid 532 and (name N or name CA or name C or name O or name CB )) or \ resid 533 through 536 or (resid 537 and (name N or name CA or name C or name O \ or name CB )) or resid 538 through 556 or (resid 557 through 558 and (name N or \ name CA or name C or name O or name CB )) or resid 559 through 568 or (resid 569 \ through 572 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 73 through 612 or (resid 613 through 614 and (name N or name CA or name C or nam \ e O or name CB )) or resid 615 through 662 or (resid 663 and (name N or name CA \ or name C or name O or name CB )) or resid 664 through 701 or (resid 702 and (na \ me N or name CA or name C or name O or name CB )) or resid 703 through 736 or (r \ esid 737 and (name N or name CA or name C or name O or name CB )) or resid 738 t \ hrough 739 or (resid 740 and (name N or name CA or name C or name O or name CB ) \ ) or resid 741 through 744 or (resid 745 and (name N or name CA or name C or nam \ e O or name CB )) or resid 746 through 754 or (resid 755 and (name N or name CA \ or name C or name O or name CB )) or resid 756 through 775 or (resid 776 and (na \ me N or name CA or name C or name O or name CB )) or resid 777 through 778 or (r \ esid 779 through 780 and (name N or name CA or name C or name O or name CB )) or \ resid 781 through 794 or (resid 795 and (name N or name CA or name C or name O \ or name CB )) or resid 796 through 807 or (resid 808 and (name N or name CA or n \ ame C or name O or name CB )) or resid 809 through 818 or (resid 819 and (name N \ or name CA or name C or name O or name CB )) or resid 820 through 824 or (resid \ 825 and (name N or name CA or name C or name O or name CB )) or resid 826 throu \ gh 828 or (resid 855 and (name N or name CA or name C or name O or name CB )) or \ resid 856 through 867 or (resid 868 and (name N or name CA or name C or name O \ or name CB )) or resid 869 through 917 or (resid 918 and (name N or name CA or n \ ame C or name O or name CB )) or resid 919 through 938 or (resid 939 through 944 \ and (name N or name CA or name C or name O or name CB )) or resid 945 through 9 \ 46 or (resid 947 and (name N or name CA or name C or name O or name CB )) or res \ id 948 through 963 or (resid 964 and (name N or name CA or name C or name O or n \ ame CB )) or resid 965 through 994 or (resid 995 and (name N or name CA or name \ C or name O or name CB )) or resid 996 through 1013 or (resid 1014 through 1016 \ and (name N or name CA or name C or name O or name CB )) or resid 1017 through 1 \ 018 or (resid 1019 through 1020 and (name N or name CA or name C or name O or na \ me CB )) or resid 1021 through 1072 or (resid 1073 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1074 through 1091 or (resid 1092 and (name \ N or name CA or name C or name O or name CB )) or resid 1093 through 1137 or (re \ sid 1138 and (name N or name CA or name C or name O or name CB )) or resid 1139 \ through 1140 or (resid 1141 through 1142 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1143 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1301 through 1319)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) } ncs_group { reference = chain 'E' selection = chain 'O' selection = chain 'P' } ncs_group { reference = (chain 'F' and ((resid 1 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 through 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 17 or (resid 18 through 2 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 22 through 4 \ 2 or (resid 43 and (name N or name CA or name C or name O or name CB )) or resid \ 44 through 82 or (resid 82A through 82C and (name N or name CA or name C or nam \ e O or name CB )) or resid 83 or (resid 84 through 85 and (name N or name CA or \ name C or name O or name CB )) or resid 86 or (resid 87 through 89 and (name N o \ r name CA or name C or name O or name CB )) or resid 90 through 96 or (resid 97 \ and (name N or name CA or name C or name O or name CB )) or resid 98 through 100 \ or (resid 100A and (name N or name CA or name C or name O or name CB )) or resi \ d 100B through 113)) selection = (chain 'H' and ((resid 1 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 through 13 and (name N or name CA \ or name C or name O or name CB )) or resid 14 through 29 or (resid 30 and (name \ N or name CA or name C or name O or name CB )) or resid 31 through 50 or (resid \ 51 and (name N or name CA or name C or name O or name CB )) or resid 52 through \ 52A or (resid 53 and (name N or name CA or name C or name O or name CB )) or re \ sid 54 through 67 or (resid 68 and (name N or name CA or name C or name O or nam \ e CB )) or resid 69 through 86 or (resid 87 through 89 and (name N or name CA or \ name C or name O or name CB )) or resid 90 through 95 or (resid 96 through 97 a \ nd (name N or name CA or name C or name O or name CB )) or resid 98 through 112 \ or (resid 113 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 1 through 20 or (resid 21 and (name N or name CA or name C \ or name O or name CB )) or resid 22 through 29 or (resid 30 and (name N or name \ CA or name C or name O or name CB )) or resid 31 through 42 or (resid 43 and (n \ ame N or name CA or name C or name O or name CB )) or resid 44 through 50 or (re \ sid 51 and (name N or name CA or name C or name O or name CB )) or resid 52 thro \ ugh 52A or (resid 53 and (name N or name CA or name C or name O or name CB )) or \ resid 54 through 65 or (resid 66 through 68 and (name N or name CA or name C or \ name O or name CB )) or resid 69 through 94 or (resid 95 through 97 and (name N \ or name CA or name C or name O or name CB )) or resid 98 through 113)) } ncs_group { reference = (chain 'G' and (resid 3 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 23 or (resid 24 and (name \ N or name CA or name C or name O or name CB )) or (resid 25 through 27A and (nam \ e N or name CA or name C or name O or name CB )) or resid 27B through 47 or (res \ id 48 and (name N or name CA or name C or name O or name CB )) or resid 49 throu \ gh 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or r \ esid 68 through 73 or (resid 74 through 76 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 77 through 84 and (name N or name CA or name C or \ name O or name CB )) or resid 85 through 107)) selection = (chain 'K' and (resid 3 through 8 or (resid 9 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 25 or (resid 26 through 27 \ A and (name N or name CA or name C or name O or name CB )) or resid 27B through \ 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or resi \ d 77 through 95 or (resid 95A and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 101 or (resid 102 through 107 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'L' and (resid 3 through 25 or (resid 26 through 27A and (name N or name \ CA or name C or name O or name CB )) or resid 27B through 47 or (resid 48 and (n \ ame N or name CA or name C or name O or name CB )) or resid 49 through 101 or (r \ esid 102 through 107 and (name N or name CA or name C or name O or name CB )))) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 14.570 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 73.990 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.005 0.061 29144 Z= 0.354 Angle : 0.846 12.156 39898 Z= 0.484 Chirality : 0.056 0.578 4783 Planarity : 0.006 0.073 5118 Dihedral : 12.738 88.152 9348 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 3734 helix: -0.57 (0.18), residues: 691 sheet: -0.93 (0.16), residues: 905 loop : -1.62 (0.13), residues: 2138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 3.506 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 153 average time/residue: 0.3777 time to fit residues: 97.8820 Evaluate side-chains 126 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 3.521 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3015 time to fit residues: 5.4732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 340 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS C 658 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 29144 Z= 0.286 Angle : 0.598 9.930 39898 Z= 0.317 Chirality : 0.045 0.273 4783 Planarity : 0.004 0.064 5118 Dihedral : 5.368 27.838 4028 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3734 helix: 0.51 (0.20), residues: 667 sheet: -0.67 (0.17), residues: 897 loop : -1.40 (0.13), residues: 2170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 3.523 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.3875 time to fit residues: 82.9622 Evaluate side-chains 123 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 3.194 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2648 time to fit residues: 8.4424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 341 optimal weight: 7.9990 chunk 368 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 ASN C 658 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 29144 Z= 0.426 Angle : 0.636 11.034 39898 Z= 0.333 Chirality : 0.047 0.292 4783 Planarity : 0.004 0.063 5118 Dihedral : 5.299 27.011 4028 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 3734 helix: 0.78 (0.20), residues: 649 sheet: -0.60 (0.16), residues: 928 loop : -1.34 (0.13), residues: 2157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 4.796 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 136 average time/residue: 0.4222 time to fit residues: 99.7161 Evaluate side-chains 123 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 3.299 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2510 time to fit residues: 9.4371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 0.0770 chunk 256 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 229 optimal weight: 0.7980 chunk 342 optimal weight: 9.9990 chunk 362 optimal weight: 9.9990 chunk 178 optimal weight: 0.4980 chunk 324 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1088 HIS G 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 29144 Z= 0.215 Angle : 0.548 10.937 39898 Z= 0.285 Chirality : 0.045 0.280 4783 Planarity : 0.004 0.060 5118 Dihedral : 4.928 26.026 4028 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3734 helix: 1.15 (0.21), residues: 651 sheet: -0.52 (0.17), residues: 917 loop : -1.21 (0.13), residues: 2166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 3.196 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 132 average time/residue: 0.3894 time to fit residues: 88.3056 Evaluate side-chains 120 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 3.220 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2686 time to fit residues: 7.3082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 309 optimal weight: 8.9990 chunk 250 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 325 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS C 658 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN G 37 GLN ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 29144 Z= 0.401 Angle : 0.612 11.082 39898 Z= 0.317 Chirality : 0.046 0.275 4783 Planarity : 0.004 0.055 5118 Dihedral : 5.032 27.285 4028 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.81 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3734 helix: 1.06 (0.21), residues: 652 sheet: -0.53 (0.16), residues: 941 loop : -1.23 (0.14), residues: 2141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 4.565 Fit side-chains outliers start: 29 outliers final: 14 residues processed: 138 average time/residue: 0.4016 time to fit residues: 96.7653 Evaluate side-chains 126 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 3.190 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2692 time to fit residues: 11.1892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 1.9990 chunk 326 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 362 optimal weight: 9.9990 chunk 301 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 190 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A1005 GLN B 703 ASN B 777 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN G 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 29144 Z= 0.153 Angle : 0.528 11.100 39898 Z= 0.273 Chirality : 0.044 0.286 4783 Planarity : 0.004 0.054 5118 Dihedral : 4.650 22.927 4028 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3734 helix: 1.36 (0.21), residues: 654 sheet: -0.42 (0.17), residues: 912 loop : -1.12 (0.14), residues: 2168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 3.665 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 139 average time/residue: 0.3933 time to fit residues: 93.5366 Evaluate side-chains 124 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 3.505 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2681 time to fit residues: 9.9976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 361 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 777 ASN C 658 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 29144 Z= 0.400 Angle : 0.606 10.976 39898 Z= 0.312 Chirality : 0.046 0.265 4783 Planarity : 0.004 0.052 5118 Dihedral : 4.864 25.424 4028 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.29 % Favored : 93.68 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3734 helix: 1.16 (0.21), residues: 653 sheet: -0.50 (0.17), residues: 938 loop : -1.17 (0.14), residues: 2143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 3.457 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 125 average time/residue: 0.3774 time to fit residues: 81.4005 Evaluate side-chains 116 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 3.252 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2608 time to fit residues: 7.6677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 246 optimal weight: 0.0010 chunk 178 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 284 optimal weight: 0.9980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 777 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 29144 Z= 0.157 Angle : 0.530 11.488 39898 Z= 0.273 Chirality : 0.044 0.283 4783 Planarity : 0.004 0.053 5118 Dihedral : 4.548 22.862 4028 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3734 helix: 1.50 (0.21), residues: 645 sheet: -0.38 (0.17), residues: 920 loop : -1.07 (0.14), residues: 2169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 3.180 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 123 average time/residue: 0.3933 time to fit residues: 82.7318 Evaluate side-chains 119 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2783 time to fit residues: 7.4821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 10.0000 chunk 346 optimal weight: 3.9990 chunk 315 optimal weight: 7.9990 chunk 336 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 335 optimal weight: 0.2980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN G 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 29144 Z= 0.288 Angle : 0.560 11.189 39898 Z= 0.287 Chirality : 0.045 0.255 4783 Planarity : 0.004 0.051 5118 Dihedral : 4.626 22.584 4028 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.48 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3734 helix: 1.35 (0.21), residues: 653 sheet: -0.44 (0.17), residues: 939 loop : -1.08 (0.14), residues: 2142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 3.463 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 113 average time/residue: 0.3862 time to fit residues: 75.7285 Evaluate side-chains 112 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2837 time to fit residues: 6.5813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.0060 chunk 356 optimal weight: 1.9990 chunk 217 optimal weight: 0.0020 chunk 168 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 373 optimal weight: 0.8980 chunk 343 optimal weight: 20.0000 chunk 297 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 229 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 29144 Z= 0.136 Angle : 0.524 12.158 39898 Z= 0.268 Chirality : 0.044 0.279 4783 Planarity : 0.003 0.053 5118 Dihedral : 4.411 21.325 4028 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.31 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3734 helix: 1.66 (0.22), residues: 641 sheet: -0.36 (0.17), residues: 907 loop : -0.99 (0.14), residues: 2186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 3.289 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 113 average time/residue: 0.3894 time to fit residues: 75.7206 Evaluate side-chains 112 residues out of total 3266 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 3.338 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2594 time to fit residues: 5.8108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 6.9990 chunk 316 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 297 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 305 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.048765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.040100 restraints weight = 147110.641| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.46 r_work: 0.2997 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 29144 Z= 0.190 Angle : 0.525 10.828 39898 Z= 0.268 Chirality : 0.044 0.260 4783 Planarity : 0.003 0.051 5118 Dihedral : 4.380 21.163 4028 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.97 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3734 helix: 1.54 (0.21), residues: 654 sheet: -0.33 (0.17), residues: 897 loop : -0.99 (0.14), residues: 2183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4185.06 seconds wall clock time: 78 minutes 28.45 seconds (4708.45 seconds total)