Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 10:11:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/04_2023/7u05_26254_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/04_2023/7u05_26254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/04_2023/7u05_26254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/04_2023/7u05_26254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/04_2023/7u05_26254_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/04_2023/7u05_26254_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.657 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: 5 Type Number sf(0) Gaussians S 282 5.16 5 C 42170 2.51 5 N 10850 2.21 5 O 12292 1.98 5 H 62402 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ASP 506": "OD1" <-> "OD2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I ASP 160": "OD1" <-> "OD2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "B PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 605": "OE1" <-> "OE2" Residue "B PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 637": "OE1" <-> "OE2" Residue "B PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 803": "OE1" <-> "OE2" Residue "B GLU 877": "OE1" <-> "OE2" Residue "B GLU 963": "OE1" <-> "OE2" Residue "B TYR 964": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1058": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1140": "OD1" <-> "OD2" Residue "A PHE 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1157": "OD1" <-> "OD2" Residue "A GLU 1179": "OE1" <-> "OE2" Residue "A GLU 1257": "OE1" <-> "OE2" Residue "A TYR 1261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 70": "OE1" <-> "OE2" Residue "e PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 207": "OE1" <-> "OE2" Residue "e PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ASP 70": "OD1" <-> "OD2" Residue "h TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ASP 9": "OD1" <-> "OD2" Residue "l PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 292": "OE1" <-> "OE2" Residue "b TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 404": "OE1" <-> "OE2" Residue "b GLU 412": "OE1" <-> "OE2" Residue "b GLU 446": "OE1" <-> "OE2" Residue "b ASP 590": "OD1" <-> "OD2" Residue "b GLU 605": "OE1" <-> "OE2" Residue "b GLU 626": "OE1" <-> "OE2" Residue "b GLU 630": "OE1" <-> "OE2" Residue "b GLU 637": "OE1" <-> "OE2" Residue "b GLU 655": "OE1" <-> "OE2" Residue "b ASP 710": "OD1" <-> "OD2" Residue "b GLU 728": "OE1" <-> "OE2" Residue "b TYR 730": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 794": "OE1" <-> "OE2" Residue "b GLU 795": "OE1" <-> "OE2" Residue "b GLU 833": "OE1" <-> "OE2" Residue "b ASP 851": "OD1" <-> "OD2" Residue "b GLU 877": "OE1" <-> "OE2" Residue "b GLU 887": "OE1" <-> "OE2" Residue "b GLU 936": "OE1" <-> "OE2" Residue "b TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 1056": "OE1" <-> "OE2" Residue "b PHE 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 40": "OE1" <-> "OE2" Residue "a ASP 105": "OD1" <-> "OD2" Residue "a GLU 115": "OE1" <-> "OE2" Residue "a GLU 135": "OE1" <-> "OE2" Residue "a GLU 137": "OE1" <-> "OE2" Residue "a ASP 152": "OD1" <-> "OD2" Residue "a PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 403": "OD1" <-> "OD2" Residue "a GLU 433": "OE1" <-> "OE2" Residue "a TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 508": "OE1" <-> "OE2" Residue "a GLU 627": "OE1" <-> "OE2" Residue "a GLU 671": "OE1" <-> "OE2" Residue "a GLU 752": "OE1" <-> "OE2" Residue "a GLU 797": "OE1" <-> "OE2" Residue "a ASP 872": "OD1" <-> "OD2" Residue "a ASP 904": "OD1" <-> "OD2" Residue "a GLU 949": "OE1" <-> "OE2" Residue "a GLU 1014": "OE1" <-> "OE2" Residue "a TYR 1066": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1111": "OE1" <-> "OE2" Residue "a ASP 1140": "OD1" <-> "OD2" Residue "a GLU 1179": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 127996 Number of models: 1 Model: "" Number of chains: 32 Chain: "M" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1135 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 227} Link IDs: {'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 681 Unresolved non-hydrogen dihedrals: 227 Planarities with less than four sites: {'UNK:plan-1': 227} Unresolved non-hydrogen planarities: 227 Chain: "C" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4652 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 4 Chain: "D" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2262 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3430 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 Chain: "F" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2997 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain: "G" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2518 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "H" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2863 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2971 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "J" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3343 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 2 Chain: "K" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2342 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "L" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2982 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 13433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 13433 Classifications: {'peptide': 815} Link IDs: {'PTRANS': 17, 'TRANS': 797} Chain breaks: 4 Chain: "m" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1135 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 227} Link IDs: {'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 681 Unresolved non-hydrogen dihedrals: 227 Planarities with less than four sites: {'UNK:plan-1': 227} Unresolved non-hydrogen planarities: 227 Chain: "A" Number of atoms: 18376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 18376 Classifications: {'peptide': 1114} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1057} Chain breaks: 6 Chain: "c" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4652 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 4 Chain: "d" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2262 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "e" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3430 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 Chain: "f" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2997 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain: "g" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2518 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "h" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2863 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "i" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2971 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain: "j" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3343 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 2 Chain: "k" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2342 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "l" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2982 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "b" Number of atoms: 13433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 13433 Classifications: {'peptide': 815} Link IDs: {'PTRANS': 17, 'TRANS': 797} Chain breaks: 4 Chain: "a" Number of atoms: 18376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 18376 Classifications: {'peptide': 1114} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1057} Chain breaks: 6 Chain: "N" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 660 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 132 Planarities with less than four sites: {'UNK:plan-1': 132} Unresolved non-hydrogen planarities: 132 Chain: "n" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 660 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 132 Planarities with less than four sites: {'UNK:plan-1': 132} Unresolved non-hydrogen planarities: 132 Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 39.39, per 1000 atoms: 0.31 Number of scatterers: 127996 At special positions: 0 Unit cell: (360.864, 323.632, 173.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 282 16.00 O 12292 8.00 N 10850 7.00 C 42170 6.00 H 62402 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 76.65 Conformation dependent library (CDL) restraints added in 7.8 seconds 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16100 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 206 helices and 78 sheets defined 40.4% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.84 Creating SS restraints... Processing helix chain 'C' and resid 138 through 146 removed outlier: 4.663A pdb=" N GLU C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 146 " --> pdb=" O TYR C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 247 removed outlier: 3.516A pdb=" N GLU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS C 246 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 498 Processing helix chain 'C' and resid 550 through 555 removed outlier: 3.581A pdb=" N GLY C 554 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 555 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing helix chain 'c' and resid 138 through 146 Processing helix chain 'c' and resid 237 through 247 removed outlier: 3.861A pdb=" N GLU c 241 " --> pdb=" O SER c 237 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS c 245 " --> pdb=" O GLU c 241 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS c 246 " --> pdb=" O GLN c 242 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE c 247 " --> pdb=" O LEU c 243 " (cutoff:3.500A) Processing helix chain 'c' and resid 481 through 498 Processing helix chain 'c' and resid 550 through 555 removed outlier: 3.805A pdb=" N ASN c 553 " --> pdb=" O GLU c 550 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY c 554 " --> pdb=" O VAL c 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.804A pdb=" N LYS D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.870A pdb=" N LEU D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 91 through 96' Processing helix chain 'D' and resid 98 through 122 Processing helix chain 'D' and resid 129 through 146 removed outlier: 3.580A pdb=" N ILE D 133 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 47 removed outlier: 3.587A pdb=" N LYS d 35 " --> pdb=" O ASN d 31 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP d 45 " --> pdb=" O ASN d 41 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR d 46 " --> pdb=" O ILE d 42 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE d 47 " --> pdb=" O SER d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 96 removed outlier: 4.047A pdb=" N LEU d 95 " --> pdb=" O GLU d 91 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 91 through 96' Processing helix chain 'd' and resid 98 through 122 removed outlier: 3.633A pdb=" N ASN d 122 " --> pdb=" O ARG d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 146 removed outlier: 3.573A pdb=" N ILE d 133 " --> pdb=" O ASP d 129 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE d 146 " --> pdb=" O ASP d 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 64 removed outlier: 3.605A pdb=" N TYR E 45 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Proline residue: E 54 - end of helix removed outlier: 3.805A pdb=" N GLU E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 111 removed outlier: 3.571A pdb=" N HIS E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 142 removed outlier: 4.185A pdb=" N GLU E 136 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 169 removed outlier: 3.837A pdb=" N ILE E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP E 165 " --> pdb=" O CYS E 161 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.868A pdb=" N GLU E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Proline residue: E 213 - end of helix removed outlier: 4.258A pdb=" N GLU E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) Proline residue: E 218 - end of helix removed outlier: 4.326A pdb=" N SER E 228 " --> pdb=" O GLY E 224 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 237 removed outlier: 4.139A pdb=" N VAL E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 232 through 237' Processing helix chain 'e' and resid 41 through 64 removed outlier: 4.328A pdb=" N MET e 52 " --> pdb=" O LEU e 48 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL e 53 " --> pdb=" O LEU e 49 " (cutoff:3.500A) Proline residue: e 54 - end of helix removed outlier: 3.530A pdb=" N GLU e 60 " --> pdb=" O ALA e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 100 through 111 removed outlier: 3.639A pdb=" N LEU e 104 " --> pdb=" O ARG e 100 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE e 105 " --> pdb=" O SER e 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS e 106 " --> pdb=" O HIS e 102 " (cutoff:3.500A) Processing helix chain 'e' and resid 112 through 142 removed outlier: 4.064A pdb=" N GLU e 136 " --> pdb=" O LEU e 132 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU e 137 " --> pdb=" O LYS e 133 " (cutoff:3.500A) Processing helix chain 'e' and resid 152 through 169 removed outlier: 3.784A pdb=" N ILE e 156 " --> pdb=" O ASP e 152 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TRP e 165 " --> pdb=" O CYS e 161 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS e 166 " --> pdb=" O ARG e 162 " (cutoff:3.500A) Processing helix chain 'e' and resid 203 through 230 removed outlier: 4.052A pdb=" N GLU e 207 " --> pdb=" O ALA e 203 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU e 208 " --> pdb=" O LYS e 204 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS e 209 " --> pdb=" O ASN e 205 " (cutoff:3.500A) Proline residue: e 213 - end of helix removed outlier: 4.366A pdb=" N GLU e 216 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE e 217 " --> pdb=" O PRO e 213 " (cutoff:3.500A) Proline residue: e 218 - end of helix removed outlier: 4.345A pdb=" N SER e 228 " --> pdb=" O GLY e 224 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU e 229 " --> pdb=" O VAL e 225 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY e 230 " --> pdb=" O LEU e 226 " (cutoff:3.500A) Processing helix chain 'e' and resid 232 through 237 removed outlier: 3.944A pdb=" N VAL e 236 " --> pdb=" O SER e 232 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE e 237 " --> pdb=" O SER e 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 232 through 237' Processing helix chain 'F' and resid 9 through 21 removed outlier: 3.607A pdb=" N ASN F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 46 removed outlier: 3.967A pdb=" N GLU F 46 " --> pdb=" O CYS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 68 removed outlier: 3.803A pdb=" N VAL F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 75 Processing helix chain 'F' and resid 82 through 99 removed outlier: 4.418A pdb=" N ALA F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N PHE F 95 " --> pdb=" O SER F 91 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS F 96 " --> pdb=" O LYS F 92 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 137 removed outlier: 4.908A pdb=" N LYS F 136 " --> pdb=" O MET F 132 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER F 137 " --> pdb=" O ASP F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 156 removed outlier: 3.967A pdb=" N CYS F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL F 155 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 21 removed outlier: 3.857A pdb=" N ASN f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 46 removed outlier: 3.802A pdb=" N GLU f 46 " --> pdb=" O CYS f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 68 removed outlier: 3.705A pdb=" N VAL f 52 " --> pdb=" O ASP f 48 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN f 53 " --> pdb=" O PHE f 49 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASP f 54 " --> pdb=" O ASN f 50 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS f 55 " --> pdb=" O LYS f 51 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG f 66 " --> pdb=" O ASN f 62 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 75 Processing helix chain 'f' and resid 82 through 99 removed outlier: 4.584A pdb=" N ALA f 94 " --> pdb=" O LEU f 90 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE f 95 " --> pdb=" O SER f 91 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS f 96 " --> pdb=" O LYS f 92 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE f 98 " --> pdb=" O ALA f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 131 through 137 removed outlier: 4.983A pdb=" N LYS f 136 " --> pdb=" O MET f 132 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER f 137 " --> pdb=" O ASP f 133 " (cutoff:3.500A) Processing helix chain 'f' and resid 141 through 156 removed outlier: 4.012A pdb=" N CYS f 145 " --> pdb=" O SER f 141 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET f 154 " --> pdb=" O GLY f 150 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN f 156 " --> pdb=" O LEU f 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 59 removed outlier: 3.915A pdb=" N GLU G 38 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA G 41 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS G 42 " --> pdb=" O GLU G 38 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU G 44 " --> pdb=" O ASP G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 109 Processing helix chain 'G' and resid 142 through 155 Proline residue: G 155 - end of helix Processing helix chain 'G' and resid 110 through 118 removed outlier: 4.302A pdb=" N VAL G 115 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASN G 118 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 59 removed outlier: 3.964A pdb=" N GLU g 38 " --> pdb=" O SER g 34 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP g 40 " --> pdb=" O GLN g 36 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA g 41 " --> pdb=" O ASN g 37 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS g 42 " --> pdb=" O GLU g 38 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU g 43 " --> pdb=" O GLU g 39 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU g 44 " --> pdb=" O ASP g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 99 through 109 Processing helix chain 'g' and resid 142 through 155 Proline residue: g 155 - end of helix Processing helix chain 'g' and resid 110 through 118 removed outlier: 4.305A pdb=" N VAL g 115 " --> pdb=" O ILE g 110 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN g 118 " --> pdb=" O LYS g 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 51 removed outlier: 3.627A pdb=" N SER H 48 " --> pdb=" O PHE H 44 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU H 50 " --> pdb=" O ILE H 46 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 58 removed outlier: 3.970A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 66 removed outlier: 4.233A pdb=" N ASN H 65 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 66' Processing helix chain 'H' and resid 167 through 193 removed outlier: 6.540A pdb=" N ALA H 171 " --> pdb=" O THR H 167 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS H 192 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP H 193 " --> pdb=" O TYR H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 219 removed outlier: 5.118A pdb=" N ASP H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU H 209 " --> pdb=" O ASN H 205 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN H 217 " --> pdb=" O LYS H 213 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU H 218 " --> pdb=" O MET H 214 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN H 219 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 51 removed outlier: 3.685A pdb=" N TYR h 33 " --> pdb=" O ASN h 29 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU h 34 " --> pdb=" O SER h 30 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE h 35 " --> pdb=" O ASN h 31 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN h 49 " --> pdb=" O ALA h 45 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU h 50 " --> pdb=" O ILE h 46 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR h 51 " --> pdb=" O ALA h 47 " (cutoff:3.500A) Processing helix chain 'h' and resid 52 through 58 removed outlier: 4.043A pdb=" N LEU h 57 " --> pdb=" O LYS h 53 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR h 58 " --> pdb=" O ALA h 54 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 66 removed outlier: 4.264A pdb=" N ASN h 65 " --> pdb=" O THR h 61 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR h 66 " --> pdb=" O ASN h 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 61 through 66' Processing helix chain 'h' and resid 167 through 193 removed outlier: 6.626A pdb=" N ALA h 171 " --> pdb=" O THR h 167 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE h 172 " --> pdb=" O SER h 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN h 173 " --> pdb=" O ASN h 169 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET h 191 " --> pdb=" O SER h 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS h 192 " --> pdb=" O ASP h 188 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASP h 193 " --> pdb=" O TYR h 189 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 219 removed outlier: 4.728A pdb=" N ASP h 208 " --> pdb=" O SER h 204 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU h 209 " --> pdb=" O ASN h 205 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN h 219 " --> pdb=" O VAL h 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 20 removed outlier: 5.616A pdb=" N MET I 13 " --> pdb=" O SER I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 46 removed outlier: 3.692A pdb=" N PHE I 30 " --> pdb=" O ASN I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 68 removed outlier: 3.787A pdb=" N ARG I 66 " --> pdb=" O ASN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 75 removed outlier: 6.053A pdb=" N THR I 75 " --> pdb=" O PHE I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 99 removed outlier: 5.814A pdb=" N THR I 86 " --> pdb=" O ASN I 82 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER I 87 " --> pdb=" O LEU I 83 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA I 94 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS I 96 " --> pdb=" O LYS I 92 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU I 99 " --> pdb=" O PHE I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 156 removed outlier: 4.597A pdb=" N CYS I 145 " --> pdb=" O SER I 141 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY I 146 " --> pdb=" O ASN I 142 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 20 removed outlier: 5.775A pdb=" N MET i 13 " --> pdb=" O SER i 9 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 46 removed outlier: 3.870A pdb=" N PHE i 30 " --> pdb=" O ASN i 26 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 68 Processing helix chain 'i' and resid 70 through 75 removed outlier: 6.114A pdb=" N THR i 75 " --> pdb=" O PHE i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 99 removed outlier: 5.751A pdb=" N THR i 86 " --> pdb=" O ASN i 82 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER i 87 " --> pdb=" O LEU i 83 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA i 94 " --> pdb=" O LEU i 90 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE i 95 " --> pdb=" O SER i 91 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS i 96 " --> pdb=" O LYS i 92 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE i 98 " --> pdb=" O ALA i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 141 through 156 removed outlier: 4.497A pdb=" N CYS i 145 " --> pdb=" O SER i 141 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY i 146 " --> pdb=" O ASN i 142 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL i 155 " --> pdb=" O SER i 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN i 156 " --> pdb=" O LEU i 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 48 removed outlier: 6.511A pdb=" N SER J 47 " --> pdb=" O SER J 43 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 43 through 48' Processing helix chain 'J' and resid 58 through 77 removed outlier: 3.770A pdb=" N MET J 62 " --> pdb=" O SER J 58 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR J 76 " --> pdb=" O GLN J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 107 removed outlier: 3.943A pdb=" N ILE J 94 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG J 97 " --> pdb=" O ASN J 93 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU J 100 " --> pdb=" O ILE J 96 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG J 105 " --> pdb=" O LEU J 101 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER J 107 " --> pdb=" O ASN J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 167 removed outlier: 4.607A pdb=" N TYR J 165 " --> pdb=" O SER J 161 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE J 166 " --> pdb=" O LEU J 162 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 161 through 167' Processing helix chain 'J' and resid 175 through 193 removed outlier: 3.618A pdb=" N ILE J 179 " --> pdb=" O LYS J 175 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU J 180 " --> pdb=" O ILE J 176 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU J 187 " --> pdb=" O ILE J 183 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TRP J 188 " --> pdb=" O HIS J 184 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER J 189 " --> pdb=" O GLY J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 245 removed outlier: 3.708A pdb=" N CYS J 234 " --> pdb=" O GLU J 230 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA J 244 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY J 245 " --> pdb=" O LEU J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 279 removed outlier: 4.174A pdb=" N GLY J 279 " --> pdb=" O LEU J 275 " (cutoff:3.500A) Processing helix chain 'j' and resid 43 through 48 removed outlier: 6.553A pdb=" N SER j 47 " --> pdb=" O SER j 43 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU j 48 " --> pdb=" O ARG j 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 43 through 48' Processing helix chain 'j' and resid 58 through 77 removed outlier: 3.705A pdb=" N MET j 62 " --> pdb=" O SER j 58 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG j 75 " --> pdb=" O SER j 71 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR j 76 " --> pdb=" O GLN j 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 79 through 107 removed outlier: 3.728A pdb=" N ASN j 93 " --> pdb=" O ASP j 89 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE j 94 " --> pdb=" O TYR j 90 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU j 100 " --> pdb=" O ILE j 96 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU j 101 " --> pdb=" O ARG j 97 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG j 105 " --> pdb=" O LEU j 101 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA j 106 " --> pdb=" O LEU j 102 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER j 107 " --> pdb=" O ASN j 103 " (cutoff:3.500A) Processing helix chain 'j' and resid 161 through 167 removed outlier: 4.951A pdb=" N TYR j 165 " --> pdb=" O SER j 161 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE j 166 " --> pdb=" O LEU j 162 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N THR j 167 " --> pdb=" O SER j 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 161 through 167' Processing helix chain 'j' and resid 175 through 193 removed outlier: 4.190A pdb=" N ILE j 179 " --> pdb=" O LYS j 175 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU j 180 " --> pdb=" O ILE j 176 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU j 187 " --> pdb=" O ILE j 183 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TRP j 188 " --> pdb=" O HIS j 184 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER j 189 " --> pdb=" O GLY j 185 " (cutoff:3.500A) Processing helix chain 'j' and resid 230 through 245 removed outlier: 3.722A pdb=" N CYS j 234 " --> pdb=" O GLU j 230 " (cutoff:3.500A) Processing helix chain 'j' and resid 271 through 279 Processing helix chain 'K' and resid 30 through 52 removed outlier: 6.124A pdb=" N LYS K 34 " --> pdb=" O PRO K 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU K 35 " --> pdb=" O GLN K 31 " (cutoff:3.500A) Proline residue: K 38 - end of helix removed outlier: 3.675A pdb=" N LEU K 45 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP K 46 " --> pdb=" O HIS K 42 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE K 47 " --> pdb=" O ALA K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 147 removed outlier: 4.982A pdb=" N ASN K 147 " --> pdb=" O LYS K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 173 removed outlier: 3.790A pdb=" N ARG K 170 " --> pdb=" O ARG K 166 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS K 171 " --> pdb=" O THR K 167 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS K 172 " --> pdb=" O LEU K 168 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU K 173 " --> pdb=" O ALA K 169 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 52 removed outlier: 6.184A pdb=" N LYS k 34 " --> pdb=" O PRO k 30 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU k 35 " --> pdb=" O GLN k 31 " (cutoff:3.500A) Proline residue: k 38 - end of helix removed outlier: 3.846A pdb=" N ASP k 46 " --> pdb=" O HIS k 42 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE k 47 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 126 through 147 removed outlier: 4.817A pdb=" N ASN k 147 " --> pdb=" O LYS k 143 " (cutoff:3.500A) Processing helix chain 'k' and resid 158 through 173 Processing helix chain 'L' and resid 25 through 34 removed outlier: 4.198A pdb=" N SER L 31 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG L 32 " --> pdb=" O ASN L 28 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 47 removed outlier: 4.174A pdb=" N ILE L 46 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY L 47 " --> pdb=" O LYS L 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 42 through 47' Processing helix chain 'L' and resid 76 through 84 removed outlier: 3.819A pdb=" N SER L 80 " --> pdb=" O ARG L 76 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR L 83 " --> pdb=" O THR L 79 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 114 removed outlier: 4.009A pdb=" N TYR L 101 " --> pdb=" O LYS L 97 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS L 104 " --> pdb=" O SER L 100 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN L 105 " --> pdb=" O TYR L 101 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N HIS L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 149 removed outlier: 3.578A pdb=" N GLU L 147 " --> pdb=" O ASN L 143 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN L 148 " --> pdb=" O PHE L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 179 removed outlier: 3.708A pdb=" N LYS L 165 " --> pdb=" O ASP L 161 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER L 179 " --> pdb=" O PHE L 175 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 34 removed outlier: 3.723A pdb=" N SER l 31 " --> pdb=" O SER l 27 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N PHE l 33 " --> pdb=" O LEU l 29 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N THR l 34 " --> pdb=" O LEU l 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 42 through 47 removed outlier: 3.717A pdb=" N ILE l 46 " --> pdb=" O SER l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 84 removed outlier: 3.883A pdb=" N SER l 80 " --> pdb=" O ARG l 76 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR l 83 " --> pdb=" O THR l 79 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) Processing helix chain 'l' and resid 97 through 114 removed outlier: 4.018A pdb=" N TYR l 101 " --> pdb=" O LYS l 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS l 104 " --> pdb=" O SER l 100 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN l 105 " --> pdb=" O TYR l 101 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 137 through 149 removed outlier: 3.779A pdb=" N ASN l 148 " --> pdb=" O PHE l 144 " (cutoff:3.500A) Processing helix chain 'l' and resid 161 through 179 removed outlier: 3.810A pdb=" N LYS l 165 " --> pdb=" O ASP l 161 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET l 177 " --> pdb=" O ALA l 173 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER l 179 " --> pdb=" O PHE l 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.766A pdb=" N LEU B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 317 removed outlier: 3.546A pdb=" N SER B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 removed outlier: 3.837A pdb=" N SER B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 372 removed outlier: 4.211A pdb=" N ILE B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 421 removed outlier: 4.442A pdb=" N PHE B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 443 removed outlier: 4.729A pdb=" N VAL B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.940A pdb=" N ALA B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N CYS B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 463 removed outlier: 4.570A pdb=" N GLN B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASN B 463 " --> pdb=" O TYR B 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 463' Processing helix chain 'B' and resid 464 through 482 removed outlier: 3.651A pdb=" N CYS B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.500A pdb=" N LYS B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 528 removed outlier: 3.657A pdb=" N TRP B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 873 Processing helix chain 'B' and resid 879 through 891 removed outlier: 4.612A pdb=" N PHE B 883 " --> pdb=" O ASP B 879 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 885 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS B 888 " --> pdb=" O ILE B 884 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N TRP B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 890 " --> pdb=" O PHE B 886 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THR B 891 " --> pdb=" O GLU B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 901 removed outlier: 4.669A pdb=" N LYS B 900 " --> pdb=" O GLU B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 911 Processing helix chain 'B' and resid 922 through 934 removed outlier: 3.919A pdb=" N SER B 928 " --> pdb=" O ASN B 924 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N CYS B 934 " --> pdb=" O ILE B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 953 Processing helix chain 'B' and resid 964 through 969 removed outlier: 4.791A pdb=" N LEU B 968 " --> pdb=" O TYR B 964 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL B 969 " --> pdb=" O VAL B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 964 through 969' Processing helix chain 'B' and resid 1020 through 1025 removed outlier: 5.261A pdb=" N TRP B1024 " --> pdb=" O LEU B1020 " (cutoff:3.500A) Processing helix chain 'b' and resid 273 through 289 removed outlier: 5.379A pdb=" N LEU b 277 " --> pdb=" O ASP b 273 " (cutoff:3.500A) Processing helix chain 'b' and resid 295 through 317 removed outlier: 3.645A pdb=" N GLU b 316 " --> pdb=" O SER b 312 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR b 317 " --> pdb=" O ILE b 313 " (cutoff:3.500A) Processing helix chain 'b' and resid 322 through 339 removed outlier: 3.541A pdb=" N TYR b 329 " --> pdb=" O GLU b 325 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER b 336 " --> pdb=" O THR b 332 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR b 337 " --> pdb=" O SER b 333 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE b 338 " --> pdb=" O MET b 334 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU b 339 " --> pdb=" O LEU b 335 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 372 removed outlier: 3.617A pdb=" N ALA b 369 " --> pdb=" O GLN b 365 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 421 removed outlier: 4.080A pdb=" N PHE b 402 " --> pdb=" O ASP b 398 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN b 403 " --> pdb=" O GLU b 399 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU b 404 " --> pdb=" O THR b 400 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS b 420 " --> pdb=" O LEU b 416 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU b 421 " --> pdb=" O PHE b 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 424 through 443 removed outlier: 4.695A pdb=" N VAL b 428 " --> pdb=" O ARG b 424 " (cutoff:3.500A) Processing helix chain 'b' and resid 444 through 456 removed outlier: 3.831A pdb=" N ALA b 448 " --> pdb=" O LYS b 444 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER b 450 " --> pdb=" O GLU b 446 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER b 454 " --> pdb=" O SER b 450 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS b 455 " --> pdb=" O LEU b 451 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 463 removed outlier: 4.469A pdb=" N GLN b 461 " --> pdb=" O GLU b 457 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR b 462 " --> pdb=" O TYR b 458 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASN b 463 " --> pdb=" O TYR b 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 457 through 463' Processing helix chain 'b' and resid 464 through 482 removed outlier: 3.719A pdb=" N CYS b 482 " --> pdb=" O SER b 478 " (cutoff:3.500A) Processing helix chain 'b' and resid 496 through 512 removed outlier: 3.675A pdb=" N LYS b 510 " --> pdb=" O LEU b 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 518 through 528 removed outlier: 3.608A pdb=" N TRP b 522 " --> pdb=" O LYS b 518 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP b 527 " --> pdb=" O LYS b 523 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU b 528 " --> pdb=" O LYS b 524 " (cutoff:3.500A) Processing helix chain 'b' and resid 861 through 873 Processing helix chain 'b' and resid 879 through 891 removed outlier: 4.515A pdb=" N PHE b 883 " --> pdb=" O ASP b 879 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU b 885 " --> pdb=" O GLU b 881 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS b 888 " --> pdb=" O ILE b 884 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TRP b 889 " --> pdb=" O LEU b 885 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS b 890 " --> pdb=" O PHE b 886 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR b 891 " --> pdb=" O GLU b 887 " (cutoff:3.500A) Processing helix chain 'b' and resid 896 through 901 removed outlier: 4.773A pdb=" N LYS b 900 " --> pdb=" O GLU b 896 " (cutoff:3.500A) Processing helix chain 'b' and resid 904 through 911 Processing helix chain 'b' and resid 922 through 934 removed outlier: 3.946A pdb=" N SER b 928 " --> pdb=" O ASN b 924 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS b 934 " --> pdb=" O ILE b 930 " (cutoff:3.500A) Processing helix chain 'b' and resid 936 through 953 Processing helix chain 'b' and resid 964 through 969 removed outlier: 4.567A pdb=" N LEU b 968 " --> pdb=" O TYR b 964 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL b 969 " --> pdb=" O VAL b 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 964 through 969' Processing helix chain 'b' and resid 1020 through 1025 removed outlier: 4.740A pdb=" N TRP b1024 " --> pdb=" O LEU b1020 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY b1025 " --> pdb=" O SER b1021 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 1020 through 1025' Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.513A pdb=" N LYS A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 16' Processing helix chain 'A' and resid 27 through 41 removed outlier: 4.277A pdb=" N GLU A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 removed outlier: 5.021A pdb=" N PHE A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Proline residue: A 63 - end of helix No H-bonds generated for 'chain 'A' and resid 58 through 63' Processing helix chain 'A' and resid 78 through 89 removed outlier: 6.035A pdb=" N LEU A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Proline residue: A 89 - end of helix No H-bonds generated for 'chain 'A' and resid 78 through 89' Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.674A pdb=" N PHE A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.718A pdb=" N GLN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.764A pdb=" N ALA A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 166 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 265 through 287 removed outlier: 4.438A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 307 removed outlier: 4.179A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.538A pdb=" N GLY A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.677A pdb=" N SER A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.036A pdb=" N ILE A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 408' Processing helix chain 'A' and resid 409 through 428 removed outlier: 3.945A pdb=" N LEU A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 457 removed outlier: 3.565A pdb=" N PHE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N SER A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 471 removed outlier: 3.589A pdb=" N LEU A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 removed outlier: 3.789A pdb=" N VAL A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TYR A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 497 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 525 Processing helix chain 'A' and resid 526 through 544 removed outlier: 3.696A pdb=" N THR A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 566 removed outlier: 4.369A pdb=" N ARG A 555 " --> pdb=" O HIS A 551 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.745A pdb=" N ASN A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 618 removed outlier: 3.972A pdb=" N VAL A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 643 removed outlier: 3.653A pdb=" N ILE A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Proline residue: A 638 - end of helix removed outlier: 4.199A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 4.789A pdb=" N ASN A 670 " --> pdb=" O ASP A 666 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU A 671 " --> pdb=" O PRO A 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 671' Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.584A pdb=" N LEU A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 927 Processing helix chain 'A' and resid 1016 through 1030 Processing helix chain 'A' and resid 1084 through 1089 removed outlier: 3.884A pdb=" N TYR A1088 " --> pdb=" O ASP A1084 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A1089 " --> pdb=" O TYR A1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1084 through 1089' Processing helix chain 'A' and resid 1110 through 1131 removed outlier: 3.697A pdb=" N GLU A1116 " --> pdb=" O GLU A1112 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A1127 " --> pdb=" O CYS A1123 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS A1130 " --> pdb=" O HIS A1126 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A1131 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1165 removed outlier: 4.305A pdb=" N ILE A1164 " --> pdb=" O MET A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1203 removed outlier: 3.773A pdb=" N ARG A1202 " --> pdb=" O SER A1198 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 16 removed outlier: 5.257A pdb=" N ILE a 16 " --> pdb=" O GLY a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 27 through 41 removed outlier: 4.409A pdb=" N GLU a 40 " --> pdb=" O GLN a 36 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N PHE a 41 " --> pdb=" O LYS a 37 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 63 removed outlier: 4.995A pdb=" N PHE a 62 " --> pdb=" O THR a 58 " (cutoff:3.500A) Proline residue: a 63 - end of helix No H-bonds generated for 'chain 'a' and resid 58 through 63' Processing helix chain 'a' and resid 78 through 89 removed outlier: 6.130A pdb=" N LEU a 82 " --> pdb=" O ASP a 78 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU a 84 " --> pdb=" O LEU a 80 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR a 85 " --> pdb=" O GLU a 81 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP a 86 " --> pdb=" O LEU a 82 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE a 87 " --> pdb=" O PHE a 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU a 88 " --> pdb=" O LEU a 84 " (cutoff:3.500A) Proline residue: a 89 - end of helix No H-bonds generated for 'chain 'a' and resid 78 through 89' Processing helix chain 'a' and resid 105 through 118 Proline residue: a 118 - end of helix Processing helix chain 'a' and resid 133 through 144 removed outlier: 3.767A pdb=" N GLN a 138 " --> pdb=" O LYS a 134 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR a 139 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET a 143 " --> pdb=" O THR a 139 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU a 144 " --> pdb=" O ILE a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 180 removed outlier: 3.781A pdb=" N ALA a 165 " --> pdb=" O MET a 161 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG a 166 " --> pdb=" O CYS a 162 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA a 171 " --> pdb=" O ASN a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 192 Processing helix chain 'a' and resid 265 through 287 removed outlier: 3.692A pdb=" N GLN a 269 " --> pdb=" O ASN a 265 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS a 270 " --> pdb=" O ARG a 266 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY a 273 " --> pdb=" O GLN a 269 " (cutoff:3.500A) Processing helix chain 'a' and resid 288 through 307 removed outlier: 4.186A pdb=" N ASP a 298 " --> pdb=" O ASN a 294 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG a 307 " --> pdb=" O LEU a 303 " (cutoff:3.500A) Processing helix chain 'a' and resid 308 through 330 removed outlier: 3.961A pdb=" N LEU a 312 " --> pdb=" O ASP a 308 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER a 314 " --> pdb=" O LEU a 310 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE a 323 " --> pdb=" O ILE a 319 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU a 324 " --> pdb=" O SER a 320 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU a 325 " --> pdb=" O ILE a 321 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 343 removed outlier: 3.626A pdb=" N SER a 340 " --> pdb=" O PRO a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 403 through 408 removed outlier: 3.909A pdb=" N ILE a 407 " --> pdb=" O ASP a 403 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASN a 408 " --> pdb=" O VAL a 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 403 through 408' Processing helix chain 'a' and resid 409 through 428 removed outlier: 3.941A pdb=" N LEU a 428 " --> pdb=" O TYR a 424 " (cutoff:3.500A) Processing helix chain 'a' and resid 436 through 457 removed outlier: 3.999A pdb=" N LYS a 456 " --> pdb=" O THR a 452 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER a 457 " --> pdb=" O SER a 453 " (cutoff:3.500A) Processing helix chain 'a' and resid 461 through 471 removed outlier: 3.787A pdb=" N LEU a 465 " --> pdb=" O SER a 461 " (cutoff:3.500A) Processing helix chain 'a' and resid 486 through 500 removed outlier: 3.653A pdb=" N VAL a 490 " --> pdb=" O PRO a 486 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYR a 491 " --> pdb=" O ARG a 487 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS a 496 " --> pdb=" O PHE a 492 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU a 497 " --> pdb=" O TYR a 493 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE a 498 " --> pdb=" O SER a 494 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU a 499 " --> pdb=" O ASN a 495 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU a 500 " --> pdb=" O LYS a 496 " (cutoff:3.500A) Processing helix chain 'a' and resid 506 through 525 removed outlier: 4.046A pdb=" N LYS a 512 " --> pdb=" O GLU a 508 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE a 513 " --> pdb=" O ALA a 509 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR a 514 " --> pdb=" O GLN a 510 " (cutoff:3.500A) Processing helix chain 'a' and resid 526 through 544 removed outlier: 4.326A pdb=" N THR a 544 " --> pdb=" O ALA a 540 " (cutoff:3.500A) Processing helix chain 'a' and resid 551 through 566 removed outlier: 3.871A pdb=" N ARG a 555 " --> pdb=" O HIS a 551 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU a 565 " --> pdb=" O ILE a 561 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN a 566 " --> pdb=" O ILE a 562 " (cutoff:3.500A) Processing helix chain 'a' and resid 584 through 603 removed outlier: 4.615A pdb=" N ASN a 603 " --> pdb=" O SER a 599 " (cutoff:3.500A) Processing helix chain 'a' and resid 604 through 618 removed outlier: 3.747A pdb=" N VAL a 608 " --> pdb=" O ASP a 604 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA a 609 " --> pdb=" O PHE a 605 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE a 614 " --> pdb=" O LYS a 610 " (cutoff:3.500A) Processing helix chain 'a' and resid 624 through 643 removed outlier: 3.705A pdb=" N ILE a 636 " --> pdb=" O PHE a 632 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLN a 637 " --> pdb=" O LYS a 633 " (cutoff:3.500A) Proline residue: a 638 - end of helix removed outlier: 3.890A pdb=" N GLU a 643 " --> pdb=" O SER a 639 " (cutoff:3.500A) Processing helix chain 'a' and resid 666 through 671 removed outlier: 4.684A pdb=" N ASN a 670 " --> pdb=" O ASP a 666 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLU a 671 " --> pdb=" O PRO a 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 666 through 671' Processing helix chain 'a' and resid 761 through 769 Processing helix chain 'a' and resid 895 through 901 removed outlier: 3.679A pdb=" N GLN a 899 " --> pdb=" O ASN a 895 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU a 901 " --> pdb=" O ILE a 897 " (cutoff:3.500A) Processing helix chain 'a' and resid 910 through 927 removed outlier: 3.683A pdb=" N GLN a 920 " --> pdb=" O ILE a 916 " (cutoff:3.500A) Processing helix chain 'a' and resid 1016 through 1030 Processing helix chain 'a' and resid 1084 through 1089 removed outlier: 3.864A pdb=" N TYR a1088 " --> pdb=" O ASP a1084 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN a1089 " --> pdb=" O TYR a1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1084 through 1089' Processing helix chain 'a' and resid 1110 through 1131 removed outlier: 3.981A pdb=" N ILE a1127 " --> pdb=" O CYS a1123 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE a1128 " --> pdb=" O ARG a1124 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER a1129 " --> pdb=" O GLU a1125 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS a1130 " --> pdb=" O HIS a1126 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU a1131 " --> pdb=" O ILE a1127 " (cutoff:3.500A) Processing helix chain 'a' and resid 1157 through 1165 removed outlier: 3.570A pdb=" N ILE a1164 " --> pdb=" O MET a1160 " (cutoff:3.500A) Processing helix chain 'a' and resid 1197 through 1203 removed outlier: 3.503A pdb=" N ARG a1201 " --> pdb=" O THR a1197 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG a1202 " --> pdb=" O SER a1198 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 213 through 223 removed outlier: 3.606A pdb=" N ASN C 214 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG C 218 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER C 231 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASP C 293 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 274 through 277 removed outlier: 4.791A pdb=" N TYR C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG C 312 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA C 318 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS C 258 " --> pdb=" O GLU C 322 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 402 through 405 removed outlier: 3.633A pdb=" N SER C 405 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL C 410 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ARG C 430 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG C 523 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 418 through 421 removed outlier: 3.982A pdb=" N ILE C 419 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 557 " --> pdb=" O TYR C 532 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 442 through 445 removed outlier: 5.702A pdb=" N ASP C 442 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 543 " --> pdb=" O ASP C 442 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 312 through 320 Processing sheet with id= 7, first strand: chain 'c' and resid 213 through 223 removed outlier: 3.692A pdb=" N ARG c 218 " --> pdb=" O SER c 231 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER c 231 " --> pdb=" O ARG c 218 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP c 293 " --> pdb=" O THR c 236 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 274 through 277 removed outlier: 4.904A pdb=" N TYR c 266 " --> pdb=" O LEU c 277 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG c 312 " --> pdb=" O ILE c 269 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA c 318 " --> pdb=" O GLN c 262 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU c 322 " --> pdb=" O LYS c 258 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LYS c 258 " --> pdb=" O GLU c 322 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU c 287 " --> pdb=" O PHE c 261 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'c' and resid 402 through 405 removed outlier: 5.314A pdb=" N VAL c 410 " --> pdb=" O SER c 405 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ARG c 430 " --> pdb=" O ILE c 415 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG c 523 " --> pdb=" O LEU c 502 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'c' and resid 418 through 421 removed outlier: 4.207A pdb=" N ILE c 419 " --> pdb=" O SER c 556 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN c 560 " --> pdb=" O VAL c 421 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'c' and resid 442 through 445 removed outlier: 5.673A pdb=" N ASP c 442 " --> pdb=" O LEU c 543 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU c 543 " --> pdb=" O ASP c 442 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'c' and resid 312 through 320 removed outlier: 3.517A pdb=" N THR c 333 " --> pdb=" O LEU c 317 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 19 through 22 removed outlier: 3.727A pdb=" N LEU D 19 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE D 7 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D 84 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'd' and resid 19 through 22 removed outlier: 3.699A pdb=" N LEU d 19 " --> pdb=" O LEU d 10 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE d 7 " --> pdb=" O GLY d 89 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU d 84 " --> pdb=" O ILE d 79 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 87 through 90 Processing sheet with id= 16, first strand: chain 'E' and resid 183 through 189 Processing sheet with id= 17, first strand: chain 'e' and resid 87 through 90 Processing sheet with id= 18, first strand: chain 'e' and resid 183 through 189 Processing sheet with id= 19, first strand: chain 'F' and resid 103 through 106 removed outlier: 5.224A pdb=" N PHE F 115 " --> pdb=" O VAL F 178 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR F 174 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU F 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP F 158 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'f' and resid 103 through 106 removed outlier: 3.628A pdb=" N THR f 106 " --> pdb=" O SER f 116 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE f 115 " --> pdb=" O VAL f 178 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR f 174 " --> pdb=" O LEU f 119 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU f 175 " --> pdb=" O VAL f 164 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP f 158 " --> pdb=" O ASN f 181 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 17 through 21 removed outlier: 6.891A pdb=" N TYR G 4 " --> pdb=" O TRP G 21 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER G 5 " --> pdb=" O LEU G 91 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'g' and resid 17 through 21 removed outlier: 6.561A pdb=" N TYR g 4 " --> pdb=" O TRP g 21 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER g 5 " --> pdb=" O LEU g 91 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 4 through 9 removed outlier: 4.279A pdb=" N LEU H 138 " --> pdb=" O THR H 134 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ARG H 120 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'h' and resid 4 through 9 removed outlier: 4.349A pdb=" N LEU h 138 " --> pdb=" O THR h 134 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ARG h 120 " --> pdb=" O ILE h 131 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 103 through 106 removed outlier: 6.727A pdb=" N ASP I 113 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR I 174 " --> pdb=" O LEU I 119 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'i' and resid 103 through 106 removed outlier: 6.888A pdb=" N ASP i 113 " --> pdb=" O LEU i 180 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR i 174 " --> pdb=" O LEU i 119 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 199 through 203 removed outlier: 3.756A pdb=" N GLU J 208 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN J 207 " --> pdb=" O PHE J 270 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N PHE J 270 " --> pdb=" O ASN J 207 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN J 269 " --> pdb=" O GLY J 249 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'j' and resid 199 through 203 removed outlier: 3.859A pdb=" N GLU j 208 " --> pdb=" O SER j 202 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ASN j 207 " --> pdb=" O PHE j 270 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE j 270 " --> pdb=" O ASN j 207 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN j 269 " --> pdb=" O GLY j 249 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 15 through 21 removed outlier: 3.605A pdb=" N TYR K 16 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N MET K 109 " --> pdb=" O SER K 105 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA K 102 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N CYS K 87 " --> pdb=" O ILE K 104 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'k' and resid 15 through 21 removed outlier: 4.761A pdb=" N MET k 109 " --> pdb=" O SER k 105 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA k 102 " --> pdb=" O LEU k 89 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N CYS k 87 " --> pdb=" O ILE k 104 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'L' and resid 48 through 56 removed outlier: 4.154A pdb=" N GLU L 49 " --> pdb=" O ASP L 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR L 12 " --> pdb=" O LYS L 61 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR L 69 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY L 20 " --> pdb=" O THR L 69 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE L 19 " --> pdb=" O LEU L 90 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA L 120 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU L 151 " --> pdb=" O VAL L 121 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'l' and resid 48 through 56 removed outlier: 4.195A pdb=" N GLU l 49 " --> pdb=" O ASP l 68 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR l 12 " --> pdb=" O LYS l 61 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR l 69 " --> pdb=" O LEU l 18 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLY l 20 " --> pdb=" O THR l 69 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE l 19 " --> pdb=" O LEU l 90 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA l 120 " --> pdb=" O VAL l 87 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU l 151 " --> pdb=" O VAL l 121 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 559 through 565 Processing sheet with id= 34, first strand: chain 'B' and resid 575 through 578 removed outlier: 3.535A pdb=" N THR B 577 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE B 599 " --> pdb=" O THR B 577 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 591 through 597 removed outlier: 6.965A pdb=" N THR B 579 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 627 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG B 581 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE B 625 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER B 583 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 623 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 658 through 664 removed outlier: 4.876A pdb=" N TYR B 672 " --> pdb=" O TYR B 729 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR B 729 " --> pdb=" O TYR B 672 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 666 through 669 removed outlier: 3.803A pdb=" N LEU B 669 " --> pdb=" O THR B 974 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 715 through 719 removed outlier: 4.616A pdb=" N SER B 686 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN B 688 " --> pdb=" O SER B 745 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN B 694 " --> pdb=" O ASP B 739 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP B 739 " --> pdb=" O GLN B 694 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 757 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 746 " --> pdb=" O PHE B 755 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 768 through 778 removed outlier: 4.255A pdb=" N PHE B 835 " --> pdb=" O LEU B 788 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 796 through 800 Processing sheet with id= 41, first strand: chain 'B' and resid 1034 through 1038 removed outlier: 4.962A pdb=" N TYR B1034 " --> pdb=" O ILE B1054 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS B1050 " --> pdb=" O ILE B1038 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 1044 through 1047 removed outlier: 3.512A pdb=" N PHE B1061 " --> pdb=" O VAL B1015 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER B1012 " --> pdb=" O MET B 993 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B 987 " --> pdb=" O GLU B1018 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE B 990 " --> pdb=" O SER B1093 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 1071 through 1074 removed outlier: 3.962A pdb=" N GLY B1071 " --> pdb=" O ILE B1101 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE B1101 " --> pdb=" O GLY B1071 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 559 through 565 removed outlier: 3.531A pdb=" N SER b 560 " --> pdb=" O CYS b 612 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 575 through 578 removed outlier: 3.882A pdb=" N PHE b 599 " --> pdb=" O THR b 577 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'b' and resid 591 through 597 removed outlier: 6.922A pdb=" N THR b 579 " --> pdb=" O ILE b 627 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE b 627 " --> pdb=" O THR b 579 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG b 581 " --> pdb=" O PHE b 625 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE b 625 " --> pdb=" O ARG b 581 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER b 583 " --> pdb=" O LEU b 623 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU b 623 " --> pdb=" O PHE b 638 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 658 through 664 removed outlier: 4.702A pdb=" N TYR b 672 " --> pdb=" O TYR b 729 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR b 729 " --> pdb=" O TYR b 672 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'b' and resid 666 through 669 removed outlier: 3.732A pdb=" N THR b 974 " --> pdb=" O LEU b 667 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU b 669 " --> pdb=" O THR b 974 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'b' and resid 715 through 719 removed outlier: 3.969A pdb=" N SER b 686 " --> pdb=" O THR b 747 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN b 688 " --> pdb=" O SER b 745 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN b 694 " --> pdb=" O ASP b 739 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP b 739 " --> pdb=" O GLN b 694 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU b 757 " --> pdb=" O THR b 744 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE b 746 " --> pdb=" O PHE b 755 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'b' and resid 768 through 778 removed outlier: 4.173A pdb=" N PHE b 835 " --> pdb=" O LEU b 788 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'b' and resid 796 through 800 Processing sheet with id= 52, first strand: chain 'b' and resid 1034 through 1038 removed outlier: 4.712A pdb=" N TYR b1034 " --> pdb=" O ILE b1054 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE b1054 " --> pdb=" O TYR b1034 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS b1050 " --> pdb=" O ILE b1038 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'b' and resid 1044 through 1047 removed outlier: 5.566A pdb=" N SER b1012 " --> pdb=" O MET b 993 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU b1018 " --> pdb=" O HIS b 987 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE b 990 " --> pdb=" O SER b1093 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'b' and resid 1071 through 1074 removed outlier: 3.889A pdb=" N GLY b1071 " --> pdb=" O ILE b1101 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE b1101 " --> pdb=" O GLY b1071 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'A' and resid 42 through 46 removed outlier: 3.513A pdb=" N VAL A 95 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 21 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASN A 145 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'A' and resid 656 through 661 removed outlier: 3.980A pdb=" N GLU A 656 " --> pdb=" O ARG A 734 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 729 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 785 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER A 777 " --> pdb=" O ASN A 737 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'A' and resid 720 through 724 Processing sheet with id= 58, first strand: chain 'A' and resid 743 through 746 removed outlier: 3.731A pdb=" N PHE A 743 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'A' and resid 747 through 751 removed outlier: 3.887A pdb=" N ASP A 747 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP A 751 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS A 800 " --> pdb=" O ASP A 751 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 801 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 813 " --> pdb=" O LEU A 801 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'A' and resid 853 through 856 removed outlier: 7.168A pdb=" N HIS A 874 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 947 " --> pdb=" O ILE A 932 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 932 " --> pdb=" O ASP A 947 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASP A 951 " --> pdb=" O CYS A 928 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS A 928 " --> pdb=" O ASP A 951 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'A' and resid 861 through 865 removed outlier: 5.580A pdb=" N ASN A 861 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 863 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 963 " --> pdb=" O MET A 894 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET A 894 " --> pdb=" O ASP A 963 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 965 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 892 " --> pdb=" O LEU A 965 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 890 " --> pdb=" O GLU A 967 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'A' and resid 994 through 997 removed outlier: 5.125A pdb=" N THR A 994 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A1047 " --> pdb=" O THR A 994 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE A1037 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A1039 " --> pdb=" O ILE A1003 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE A1003 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A1041 " --> pdb=" O ASP A1001 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A1001 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'A' and resid 1065 through 1069 removed outlier: 7.444A pdb=" N GLY A1051 " --> pdb=" O THR A1138 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A1055 " --> pdb=" O ASN A1134 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'A' and resid 1171 through 1175 removed outlier: 4.082A pdb=" N GLU A1195 " --> pdb=" O GLY A1172 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A1190 " --> pdb=" O LEU A1251 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU A1252 " --> pdb=" O ASN A1234 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN A1234 " --> pdb=" O GLU A1252 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ARG A1230 " --> pdb=" O ILE A1256 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'A' and resid 1209 through 1217 removed outlier: 3.950A pdb=" N VAL A1214 " --> pdb=" O SER A1264 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE A1216 " --> pdb=" O GLU A1262 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'A' and resid 1036 through 1045 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 'a' and resid 42 through 46 removed outlier: 4.083A pdb=" N VAL a 95 " --> pdb=" O ARG a 17 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE a 96 " --> pdb=" O SER a 122 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASN a 145 " --> pdb=" O PRO a 123 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 656 through 661 removed outlier: 4.208A pdb=" N GLU a 656 " --> pdb=" O ARG a 734 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA a 729 " --> pdb=" O LEU a 785 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU a 785 " --> pdb=" O ALA a 729 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER a 777 " --> pdb=" O ASN a 737 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 720 through 724 Processing sheet with id= 70, first strand: chain 'a' and resid 743 through 746 removed outlier: 3.994A pdb=" N PHE a 743 " --> pdb=" O VAL a 773 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'a' and resid 747 through 751 removed outlier: 4.074A pdb=" N ASP a 747 " --> pdb=" O SER a 804 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP a 751 " --> pdb=" O CYS a 800 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N CYS a 800 " --> pdb=" O ASP a 751 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU a 801 " --> pdb=" O PHE a 813 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE a 813 " --> pdb=" O LEU a 801 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'a' and resid 853 through 856 removed outlier: 3.884A pdb=" N SER a 854 " --> pdb=" O THR a 876 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N HIS a 874 " --> pdb=" O SER a 856 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP a 947 " --> pdb=" O ILE a 932 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE a 932 " --> pdb=" O ASP a 947 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP a 951 " --> pdb=" O CYS a 928 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N CYS a 928 " --> pdb=" O ASP a 951 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'a' and resid 861 through 865 removed outlier: 5.481A pdb=" N ASN a 861 " --> pdb=" O PRO a 986 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP a 863 " --> pdb=" O GLU a 988 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP a 963 " --> pdb=" O MET a 894 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET a 894 " --> pdb=" O ASP a 963 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU a 965 " --> pdb=" O ILE a 892 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS a 890 " --> pdb=" O GLU a 967 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS a 888 " --> pdb=" O GLY a 969 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'a' and resid 994 through 997 removed outlier: 5.417A pdb=" N THR a 994 " --> pdb=" O SER a1047 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER a1047 " --> pdb=" O THR a 994 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE a1037 " --> pdb=" O LEU a1005 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU a1039 " --> pdb=" O ILE a1003 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE a1003 " --> pdb=" O LEU a1039 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU a1041 " --> pdb=" O ASP a1001 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP a1001 " --> pdb=" O LEU a1041 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'a' and resid 1065 through 1069 removed outlier: 7.369A pdb=" N GLY a1051 " --> pdb=" O THR a1138 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN a1055 " --> pdb=" O ASN a1134 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'a' and resid 1171 through 1175 removed outlier: 4.079A pdb=" N GLU a1195 " --> pdb=" O GLY a1172 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE a1253 " --> pdb=" O ILE a1188 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU a1190 " --> pdb=" O LEU a1251 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU a1252 " --> pdb=" O ASN a1234 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN a1234 " --> pdb=" O GLU a1252 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG a1230 " --> pdb=" O ILE a1256 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'a' and resid 1209 through 1217 removed outlier: 3.915A pdb=" N VAL a1214 " --> pdb=" O SER a1264 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE a1216 " --> pdb=" O GLU a1262 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'a' and resid 1036 through 1045 No H-bonds generated for sheet with id= 78 2502 hydrogen bonds defined for protein. 7437 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: 51.92 Time building geometry restraints manager: 81.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 62282 1.03 - 1.23: 194 1.23 - 1.42: 27562 1.42 - 1.62: 38750 1.62 - 1.82: 440 Bond restraints: 129228 Sorted by residual: bond pdb=" C HIS A 551 " pdb=" N PRO A 552 " ideal model delta sigma weight residual 1.334 1.351 -0.018 8.40e-03 1.42e+04 4.43e+00 bond pdb=" CA GLU I 187 " pdb=" CB GLU I 187 " ideal model delta sigma weight residual 1.536 1.620 -0.084 4.10e-02 5.95e+02 4.18e+00 bond pdb=" CB MET a1023 " pdb=" CG MET a1023 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.83e+00 bond pdb=" C1 PLM I 201 " pdb=" C2 PLM I 201 " ideal model delta sigma weight residual 1.542 1.581 -0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" SD MET a1023 " pdb=" CE MET a1023 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.66e+00 ... (remaining 129223 not shown) Histogram of bond angle deviations from ideal: 94.52 - 102.44: 159 102.44 - 110.35: 124319 110.35 - 118.26: 49098 118.26 - 126.17: 57836 126.17 - 134.08: 1046 Bond angle restraints: 232458 Sorted by residual: angle pdb=" N VAL F 155 " pdb=" CA VAL F 155 " pdb=" C VAL F 155 " ideal model delta sigma weight residual 111.91 107.11 4.80 8.90e-01 1.26e+00 2.91e+01 angle pdb=" CA ARG J 277 " pdb=" CB ARG J 277 " pdb=" CG ARG J 277 " ideal model delta sigma weight residual 114.10 123.92 -9.82 2.00e+00 2.50e-01 2.41e+01 angle pdb=" CA ARG G 133 " pdb=" CB ARG G 133 " pdb=" CG ARG G 133 " ideal model delta sigma weight residual 114.10 123.81 -9.71 2.00e+00 2.50e-01 2.36e+01 angle pdb=" N ARG G 133 " pdb=" CA ARG G 133 " pdb=" CB ARG G 133 " ideal model delta sigma weight residual 111.19 104.30 6.89 1.47e+00 4.63e-01 2.20e+01 angle pdb=" C ARG G 133 " pdb=" CA ARG G 133 " pdb=" CB ARG G 133 " ideal model delta sigma weight residual 112.07 119.11 -7.04 1.54e+00 4.22e-01 2.09e+01 ... (remaining 232453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 47628 17.99 - 35.98: 4512 35.98 - 53.98: 616 53.98 - 71.97: 114 71.97 - 89.96: 62 Dihedral angle restraints: 52932 sinusoidal: 23940 harmonic: 28992 Sorted by residual: dihedral pdb=" CA ILE L 46 " pdb=" C ILE L 46 " pdb=" N GLY L 47 " pdb=" CA GLY L 47 " ideal model delta harmonic sigma weight residual 180.00 151.42 28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA LYS f 51 " pdb=" C LYS f 51 " pdb=" N VAL f 52 " pdb=" CA VAL f 52 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA LEU j 101 " pdb=" C LEU j 101 " pdb=" N LEU j 102 " pdb=" CA LEU j 102 " ideal model delta harmonic sigma weight residual 180.00 153.25 26.75 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 52929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 8630 0.056 - 0.111: 1463 0.111 - 0.167: 330 0.167 - 0.223: 12 0.223 - 0.278: 3 Chirality restraints: 10438 Sorted by residual: chirality pdb=" CB ILE A1213 " pdb=" CA ILE A1213 " pdb=" CG1 ILE A1213 " pdb=" CG2 ILE A1213 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB ILE d 20 " pdb=" CA ILE d 20 " pdb=" CG1 ILE d 20 " pdb=" CG2 ILE d 20 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE a1213 " pdb=" CA ILE a1213 " pdb=" CG1 ILE a1213 " pdb=" CG2 ILE a1213 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 10435 not shown) Planarity restraints: 18750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 650 " 0.063 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 651 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 651 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 651 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR a 58 " -0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO a 59 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO a 59 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO a 59 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG a1168 " -0.221 9.50e-02 1.11e+02 7.41e-02 6.73e+00 pdb=" NE ARG a1168 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG a1168 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG a1168 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG a1168 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG a1168 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG a1168 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG a1168 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG a1168 " 0.000 2.00e-02 2.50e+03 ... (remaining 18747 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 1030 2.07 - 2.70: 199262 2.70 - 3.34: 354268 3.34 - 3.97: 446049 3.97 - 4.60: 696586 Nonbonded interactions: 1697195 Sorted by model distance: nonbonded pdb=" O ASN E 145 " pdb="HD21 ASN E 145 " model vdw 1.439 1.850 nonbonded pdb=" O ASN e 145 " pdb="HD21 ASN e 145 " model vdw 1.587 1.850 nonbonded pdb=" O ASN K 25 " pdb="HD21 ASN K 25 " model vdw 1.618 1.850 nonbonded pdb=" O ASN j 207 " pdb="HD21 ASN j 207 " model vdw 1.641 1.850 nonbonded pdb="HH22 ARG J 172 " pdb=" O GLN K 52 " model vdw 1.658 1.850 ... (remaining 1697190 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' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ or name HH11 or name HH12 or name HH21 or name HH22)) or resid 9 through 191 or \ resid 201)) selection = chain 'I' selection = (chain 'f' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ or name HH11 or name HH12 or name HH21 or name HH22)) or resid 9 through 191 or \ resid 201)) selection = chain 'i' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.140 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: 1.430 Extract box with map and model: 20.400 Check model and map are aligned: 1.350 Set scattering table: 0.820 Process input model: 305.200 Find NCS groups from input model: 4.410 Set up NCS constraints: 0.750 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 339.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.004 0.084 66826 Z= 0.282 Angle : 0.808 11.019 90446 Z= 0.414 Chirality : 0.045 0.278 10438 Planarity : 0.005 0.097 11462 Dihedral : 14.139 89.961 24378 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.70 % Favored : 90.21 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.55 (0.10), residues: 7496 helix: 0.81 (0.10), residues: 2484 sheet: -0.99 (0.14), residues: 1482 loop : -2.49 (0.10), residues: 3530 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Evaluate side-chains 3146 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 3141 time to evaluate : 7.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 3141 average time/residue: 1.3392 time to fit residues: 7096.2071 Evaluate side-chains 2757 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2756 time to evaluate : 7.531 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0373 time to fit residues: 11.6340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 694 optimal weight: 1.9990 chunk 623 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 420 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 644 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 391 optimal weight: 0.6980 chunk 479 optimal weight: 2.9990 chunk 746 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 489 HIS D 41 ASN D 68 GLN E 145 ASN E 167 GLN F 53 ASN H 31 ASN J 184 HIS L 59 ASN L 106 HIS B 362 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 HIS A1234 ASN c 262 GLN e 145 ASN ** f 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 181 ASN j 30 GLN j 181 GLN k 22 ASN k 42 HIS k 172 HIS l 65 GLN ** l 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 106 HIS ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 66826 Z= 0.291 Angle : 0.596 7.194 90446 Z= 0.319 Chirality : 0.041 0.208 10438 Planarity : 0.004 0.060 11462 Dihedral : 5.143 59.889 8938 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.94 % Favored : 89.97 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.42 (0.10), residues: 7496 helix: 1.03 (0.10), residues: 2524 sheet: -0.92 (0.13), residues: 1506 loop : -2.55 (0.10), residues: 3466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Evaluate side-chains 2908 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 2749 time to evaluate : 7.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 137 residues processed: 2787 average time/residue: 1.3161 time to fit residues: 6182.5247 Evaluate side-chains 2795 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 2658 time to evaluate : 7.532 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 137 outliers final: 1 residues processed: 137 average time/residue: 1.0557 time to fit residues: 280.2727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 414 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 621 optimal weight: 1.9990 chunk 508 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 747 optimal weight: 0.3980 chunk 807 optimal weight: 50.0000 chunk 665 optimal weight: 0.7980 chunk 741 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 599 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN H 31 ASN H 49 GLN B 362 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 HIS e 129 GLN e 145 ASN ** f 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 130 ASN h 133 GLN i 181 ASN ** l 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 535 HIS b 987 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 66826 Z= 0.204 Angle : 0.555 8.253 90446 Z= 0.292 Chirality : 0.040 0.178 10438 Planarity : 0.003 0.052 11462 Dihedral : 4.959 58.025 8938 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.41 % Favored : 90.49 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.10), residues: 7496 helix: 1.14 (0.10), residues: 2550 sheet: -0.87 (0.13), residues: 1508 loop : -2.51 (0.10), residues: 3438 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Evaluate side-chains 2796 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 2713 time to evaluate : 7.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 56 residues processed: 2739 average time/residue: 1.5283 time to fit residues: 7121.5498 Evaluate side-chains 2714 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 2658 time to evaluate : 7.427 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 2 residues processed: 56 average time/residue: 1.2888 time to fit residues: 142.5730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 738 optimal weight: 2.9990 chunk 562 optimal weight: 1.9990 chunk 388 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 356 optimal weight: 0.9990 chunk 502 optimal weight: 0.8980 chunk 750 optimal weight: 1.9990 chunk 794 optimal weight: 0.9990 chunk 392 optimal weight: 0.9990 chunk 711 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN H 31 ASN H 49 GLN B 362 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 HIS d 41 ASN e 129 GLN e 145 ASN ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 362 ASN b 535 HIS ** b 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 275 GLN ** a 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 66826 Z= 0.251 Angle : 0.552 7.855 90446 Z= 0.293 Chirality : 0.040 0.168 10438 Planarity : 0.003 0.053 11462 Dihedral : 4.892 54.514 8938 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.13 % Favored : 89.77 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.10), residues: 7496 helix: 1.17 (0.10), residues: 2556 sheet: -0.93 (0.13), residues: 1544 loop : -2.51 (0.10), residues: 3396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Evaluate side-chains 2824 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 2698 time to evaluate : 7.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 105 residues processed: 2724 average time/residue: 1.4603 time to fit residues: 6756.2398 Evaluate side-chains 2752 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 2647 time to evaluate : 7.353 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 2 residues processed: 105 average time/residue: 1.1746 time to fit residues: 239.3758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 661 optimal weight: 1.9990 chunk 451 optimal weight: 0.7980 chunk 11 optimal weight: 40.0000 chunk 591 optimal weight: 2.9990 chunk 327 optimal weight: 0.5980 chunk 678 optimal weight: 1.9990 chunk 549 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 405 optimal weight: 1.9990 chunk 713 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN D 41 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN F 53 ASN H 31 ASN H 49 GLN I 55 HIS B 362 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 HIS ** d 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 129 GLN e 145 ASN g 14 ASN g 37 ASN ** j 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 535 HIS b 811 ASN ** b 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 66826 Z= 0.348 Angle : 0.582 7.727 90446 Z= 0.312 Chirality : 0.041 0.161 10438 Planarity : 0.004 0.056 11462 Dihedral : 4.960 56.112 8938 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.82 % Favored : 89.06 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.10), residues: 7496 helix: 1.10 (0.10), residues: 2562 sheet: -1.05 (0.13), residues: 1548 loop : -2.55 (0.10), residues: 3386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Evaluate side-chains 2863 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 2723 time to evaluate : 7.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 140 outliers final: 105 residues processed: 2755 average time/residue: 1.4073 time to fit residues: 6543.4281 Evaluate side-chains 2772 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 2667 time to evaluate : 7.551 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 2 residues processed: 105 average time/residue: 1.1110 time to fit residues: 227.0931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 267 optimal weight: 2.9990 chunk 715 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 466 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 795 optimal weight: 2.9990 chunk 660 optimal weight: 1.9990 chunk 368 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 263 optimal weight: 0.9980 chunk 417 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN F 53 ASN H 31 ASN H 49 GLN B 362 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 HIS e 145 ASN f 50 ASN ** j 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 535 HIS ** b 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 66826 Z= 0.288 Angle : 0.569 8.357 90446 Z= 0.303 Chirality : 0.041 0.183 10438 Planarity : 0.004 0.062 11462 Dihedral : 4.925 49.191 8938 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.43 % Favored : 89.45 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.10), residues: 7496 helix: 1.17 (0.10), residues: 2558 sheet: -1.09 (0.13), residues: 1554 loop : -2.54 (0.10), residues: 3384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Evaluate side-chains 2873 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 2750 time to evaluate : 7.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 99 residues processed: 2772 average time/residue: 1.4512 time to fit residues: 6804.2781 Evaluate side-chains 2790 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 2691 time to evaluate : 7.392 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 3 residues processed: 99 average time/residue: 1.1410 time to fit residues: 221.2632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 766 optimal weight: 0.0070 chunk 89 optimal weight: 1.9990 chunk 453 optimal weight: 0.7980 chunk 580 optimal weight: 1.9990 chunk 449 optimal weight: 0.5980 chunk 669 optimal weight: 4.9990 chunk 444 optimal weight: 1.9990 chunk 792 optimal weight: 0.8980 chunk 495 optimal weight: 1.9990 chunk 483 optimal weight: 0.9990 chunk 365 optimal weight: 1.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN E 172 GLN F 53 ASN H 31 ASN H 49 GLN I 181 ASN K 54 GLN B 362 ASN B 811 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 HIS d 68 GLN e 129 GLN e 145 ASN ** j 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 362 ASN b 535 HIS ** b 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1089 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 66826 Z= 0.198 Angle : 0.549 7.769 90446 Z= 0.290 Chirality : 0.040 0.171 10438 Planarity : 0.003 0.051 11462 Dihedral : 4.811 50.010 8938 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.70 % Favored : 90.19 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.10), residues: 7496 helix: 1.31 (0.11), residues: 2554 sheet: -0.97 (0.13), residues: 1550 loop : -2.44 (0.10), residues: 3392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Evaluate side-chains 2851 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 2780 time to evaluate : 7.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 52 residues processed: 2794 average time/residue: 1.3713 time to fit residues: 6448.6425 Evaluate side-chains 2751 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 2699 time to evaluate : 7.491 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 3 residues processed: 52 average time/residue: 1.1184 time to fit residues: 117.0261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 490 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 chunk 473 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 503 optimal weight: 0.6980 chunk 539 optimal weight: 1.9990 chunk 391 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 622 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN E 172 GLN H 31 ASN L 106 HIS B 362 ASN B 481 HIS B 811 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 HIS d 41 ASN d 68 GLN e 145 ASN f 50 ASN g 14 ASN g 33 ASN ** j 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 143 ASN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 362 ASN b 535 HIS ** b 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 111 ASN ** a 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 66826 Z= 0.368 Angle : 0.597 7.581 90446 Z= 0.320 Chirality : 0.041 0.172 10438 Planarity : 0.004 0.065 11462 Dihedral : 4.913 53.430 8938 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.37 % Favored : 88.51 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.10), residues: 7496 helix: 1.14 (0.10), residues: 2560 sheet: -1.08 (0.13), residues: 1592 loop : -2.60 (0.10), residues: 3344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Evaluate side-chains 2806 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 2699 time to evaluate : 7.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 85 residues processed: 2714 average time/residue: 1.4357 time to fit residues: 6574.7286 Evaluate side-chains 2740 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 2655 time to evaluate : 7.580 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 4 residues processed: 85 average time/residue: 1.1522 time to fit residues: 190.6489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 720 optimal weight: 0.1980 chunk 759 optimal weight: 1.9990 chunk 692 optimal weight: 2.9990 chunk 738 optimal weight: 2.9990 chunk 758 optimal weight: 0.4980 chunk 444 optimal weight: 0.4980 chunk 321 optimal weight: 0.6980 chunk 579 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 667 optimal weight: 2.9990 chunk 698 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN H 31 ASN L 106 HIS B 362 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** B1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 HIS e 129 GLN e 145 ASN f 50 ASN g 33 ASN h 126 GLN ** j 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 535 HIS ** b 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 66826 Z= 0.180 Angle : 0.558 8.061 90446 Z= 0.294 Chirality : 0.041 0.249 10438 Planarity : 0.003 0.046 11462 Dihedral : 4.807 54.905 8938 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.50 % Favored : 90.39 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.10), residues: 7496 helix: 1.30 (0.11), residues: 2554 sheet: -0.97 (0.13), residues: 1548 loop : -2.43 (0.10), residues: 3394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Evaluate side-chains 2818 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 2768 time to evaluate : 7.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 38 residues processed: 2779 average time/residue: 1.4093 time to fit residues: 6602.0082 Evaluate side-chains 2761 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 2723 time to evaluate : 7.499 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 3 residues processed: 38 average time/residue: 1.1687 time to fit residues: 90.2541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 735 optimal weight: 0.9980 chunk 484 optimal weight: 1.9990 chunk 780 optimal weight: 1.9990 chunk 476 optimal weight: 1.9990 chunk 370 optimal weight: 1.9990 chunk 542 optimal weight: 0.6980 chunk 818 optimal weight: 9.9990 chunk 753 optimal weight: 0.4980 chunk 652 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 503 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS B 362 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 485 GLN d 41 ASN e 145 ASN f 50 ASN g 33 ASN h 177 ASN ** j 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 362 ASN b 535 HIS ** b 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 987 HIS ** a 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 66826 Z= 0.218 Angle : 0.563 7.437 90446 Z= 0.297 Chirality : 0.040 0.252 10438 Planarity : 0.003 0.072 11462 Dihedral : 4.765 59.012 8938 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.38 % Favored : 89.50 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.10), residues: 7496 helix: 1.30 (0.11), residues: 2554 sheet: -0.90 (0.14), residues: 1516 loop : -2.45 (0.10), residues: 3426 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14992 Ramachandran restraints generated. 7496 Oldfield, 0 Emsley, 7496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue SER 168 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Evaluate side-chains 2753 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 2715 time to evaluate : 7.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 30 residues processed: 2720 average time/residue: 1.4259 time to fit residues: 6521.2922 Evaluate side-chains 2735 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 2705 time to evaluate : 7.471 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 3 residues processed: 30 average time/residue: 1.1472 time to fit residues: 72.4256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 399 optimal weight: 0.9980 chunk 517 optimal weight: 2.9990 chunk 694 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 601 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 653 optimal weight: 0.6980 chunk 273 optimal weight: 0.8980 chunk 670 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS B 362 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 485 GLN e 129 GLN e 145 ASN f 50 ASN g 33 ASN h 126 GLN ** l 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 362 ASN b 481 HIS b 535 HIS ** b 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 510 GLN ** a 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.128971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.098156 restraints weight = 305939.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.102835 restraints weight = 129610.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.105952 restraints weight = 76773.674| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 66826 Z= 0.282 Angle : 0.579 7.435 90446 Z= 0.308 Chirality : 0.041 0.256 10438 Planarity : 0.004 0.048 11462 Dihedral : 4.794 55.047 8938 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.67 % Favored : 89.22 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.10), residues: 7496 helix: 1.24 (0.11), residues: 2558 sheet: -0.90 (0.13), residues: 1538 loop : -2.51 (0.10), residues: 3400 =============================================================================== Job complete usr+sys time: 74940.36 seconds wall clock time: 1275 minutes 35.08 seconds (76535.08 seconds total)