Starting phenix.real_space_refine on Sat Mar 16 07:05:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/03_2024/7u05_26254_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/03_2024/7u05_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_26254/03_2024/7u05_26254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/03_2024/7u05_26254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/03_2024/7u05_26254_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u05_26254/03_2024/7u05_26254_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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-dev-5265/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: 39.10, 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: 69.50 Conformation dependent library (CDL) restraints added in 8.6 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 for structures that cannot fit in PDB format. 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: 33.24 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: 44.74 Time building geometry restraints manager: 74.16 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: 54824 17.99 - 35.98: 4951 35.98 - 53.98: 1025 53.98 - 71.97: 204 71.97 - 89.96: 62 Dihedral angle restraints: 61066 sinusoidal: 32074 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 61063 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: 0.000 Construct map_model_manager: 1.420 Extract box with map and model: 16.840 Check model and map are aligned: 1.410 Set scattering table: 0.830 Process input model: 302.220 Find NCS groups from input model: 3.900 Set up NCS constraints: 0.730 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 332.640 ------------------------------------------------------------------------------- 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 % Allowed : 0.33 % Favored : 99.60 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 53 HIS 0.008 0.001 HIS K 42 PHE 0.032 0.002 PHE b 475 TYR 0.023 0.002 TYR A 648 ARG 0.028 0.001 ARG J 277 *********************** 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 : 7.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 225 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6668 (tm-30) REVERT: C 263 GLU cc_start: 0.8102 (tt0) cc_final: 0.7654 (tt0) REVERT: C 312 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7520 (ttm-80) REVERT: C 417 SER cc_start: 0.9110 (p) cc_final: 0.8842 (p) REVERT: D 65 SER cc_start: 0.9624 (t) cc_final: 0.9330 (t) REVERT: D 80 LYS cc_start: 0.9022 (tttt) cc_final: 0.8758 (ttmm) REVERT: D 114 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8023 (mmmt) REVERT: D 139 ARG cc_start: 0.8387 (ptp-110) cc_final: 0.8006 (ptm160) REVERT: D 143 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7799 (tm-30) REVERT: E 42 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8478 (tm-30) REVERT: E 113 GLU cc_start: 0.8097 (pp20) cc_final: 0.7859 (pp20) REVERT: E 116 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8517 (tttm) REVERT: E 125 ASN cc_start: 0.8873 (t0) cc_final: 0.8653 (t0) REVERT: E 166 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8769 (mmmm) REVERT: E 185 TYR cc_start: 0.8437 (m-80) cc_final: 0.7581 (m-80) REVERT: F 26 ASN cc_start: 0.8458 (m-40) cc_final: 0.8188 (m110) REVERT: F 29 LEU cc_start: 0.9054 (tp) cc_final: 0.8696 (tp) REVERT: F 57 TYR cc_start: 0.8741 (t80) cc_final: 0.8360 (t80) REVERT: F 107 ASN cc_start: 0.9000 (m110) cc_final: 0.8676 (m-40) REVERT: F 113 ASP cc_start: 0.8999 (t0) cc_final: 0.8775 (t0) REVERT: F 120 ASP cc_start: 0.7844 (t0) cc_final: 0.6996 (t0) REVERT: F 121 GLU cc_start: 0.7184 (mp0) cc_final: 0.6190 (mp0) REVERT: G 80 TYR cc_start: 0.9181 (t80) cc_final: 0.8514 (t80) REVERT: G 101 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8482 (mt0) REVERT: G 118 ASN cc_start: 0.8750 (t0) cc_final: 0.8537 (t0) REVERT: G 130 ASN cc_start: 0.7996 (t0) cc_final: 0.7728 (t0) REVERT: G 144 ASN cc_start: 0.8804 (m110) cc_final: 0.8438 (m110) REVERT: G 147 SER cc_start: 0.8925 (m) cc_final: 0.8522 (m) REVERT: G 148 VAL cc_start: 0.9161 (t) cc_final: 0.8943 (t) REVERT: G 156 MET cc_start: 0.8456 (ptp) cc_final: 0.8146 (ptm) REVERT: H 18 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8255 (tm-30) REVERT: H 100 SER cc_start: 0.8055 (p) cc_final: 0.7481 (p) REVERT: I 18 TRP cc_start: 0.8454 (t60) cc_final: 0.8042 (t-100) REVERT: I 23 GLU cc_start: 0.6447 (mp0) cc_final: 0.6119 (mp0) REVERT: I 156 GLN cc_start: 0.8859 (mp10) cc_final: 0.8566 (mp10) REVERT: J 75 ARG cc_start: 0.8496 (ptp90) cc_final: 0.8071 (ptp90) REVERT: J 177 LEU cc_start: 0.9213 (tt) cc_final: 0.8995 (tt) REVERT: J 255 MET cc_start: 0.8906 (mmt) cc_final: 0.8706 (mmt) REVERT: J 257 GLN cc_start: 0.9140 (pp30) cc_final: 0.8369 (pp30) REVERT: K 22 ASN cc_start: 0.7791 (t0) cc_final: 0.7517 (t0) REVERT: K 158 SER cc_start: 0.8539 (t) cc_final: 0.8245 (t) REVERT: L 59 ASN cc_start: 0.8467 (t0) cc_final: 0.7842 (t0) REVERT: L 61 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7654 (mmtm) REVERT: L 106 HIS cc_start: 0.7895 (t-90) cc_final: 0.7117 (t70) REVERT: L 113 GLU cc_start: 0.7262 (tm-30) cc_final: 0.7018 (tm-30) REVERT: L 114 ASN cc_start: 0.8396 (t0) cc_final: 0.7462 (t0) REVERT: L 117 ASP cc_start: 0.7695 (m-30) cc_final: 0.7488 (m-30) REVERT: L 162 ASN cc_start: 0.7666 (t0) cc_final: 0.7320 (t0) REVERT: L 200 LYS cc_start: 0.8612 (tttp) cc_final: 0.8062 (ptpt) REVERT: B 276 GLN cc_start: 0.8622 (mt0) cc_final: 0.8163 (pt0) REVERT: B 339 GLU cc_start: 0.7690 (tp30) cc_final: 0.7481 (tp30) REVERT: B 349 CYS cc_start: 0.9111 (m) cc_final: 0.8883 (m) REVERT: B 357 MET cc_start: 0.9104 (ttt) cc_final: 0.8896 (ttp) REVERT: B 394 GLU cc_start: 0.7651 (tt0) cc_final: 0.7398 (pt0) REVERT: B 429 ASP cc_start: 0.8598 (m-30) cc_final: 0.8370 (m-30) REVERT: B 567 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7414 (mtmt) REVERT: B 728 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7191 (tt0) REVERT: B 812 ASP cc_start: 0.6636 (t0) cc_final: 0.5565 (m-30) REVERT: B 894 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7761 (mt-10) REVERT: B 906 ASP cc_start: 0.8563 (m-30) cc_final: 0.8354 (m-30) REVERT: B 911 ASN cc_start: 0.8842 (m-40) cc_final: 0.8214 (t0) REVERT: B 932 ASN cc_start: 0.8020 (m110) cc_final: 0.7636 (m110) REVERT: B 1009 ASN cc_start: 0.8900 (m110) cc_final: 0.8617 (m110) REVERT: B 1073 LEU cc_start: 0.9196 (mt) cc_final: 0.8994 (mt) REVERT: A 58 THR cc_start: 0.8686 (m) cc_final: 0.8459 (m) REVERT: A 99 LEU cc_start: 0.8669 (mt) cc_final: 0.8390 (mt) REVERT: A 317 ASP cc_start: 0.8563 (t0) cc_final: 0.8311 (t0) REVERT: A 415 CYS cc_start: 0.8773 (t) cc_final: 0.8485 (t) REVERT: A 433 GLU cc_start: 0.8069 (mp0) cc_final: 0.7290 (mp0) REVERT: A 466 ASP cc_start: 0.7272 (m-30) cc_final: 0.7058 (m-30) REVERT: A 526 TYR cc_start: 0.8359 (m-10) cc_final: 0.8017 (m-10) REVERT: A 606 GLU cc_start: 0.8014 (tt0) cc_final: 0.7482 (tt0) REVERT: A 607 TYR cc_start: 0.7196 (m-80) cc_final: 0.6530 (m-80) REVERT: A 817 ASN cc_start: 0.6700 (m110) cc_final: 0.6155 (m110) REVERT: A 846 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 867 ASP cc_start: 0.7960 (t0) cc_final: 0.7363 (t0) REVERT: A 899 GLN cc_start: 0.8040 (tt0) cc_final: 0.7426 (tm-30) REVERT: A 906 TRP cc_start: 0.9179 (p-90) cc_final: 0.8389 (p-90) REVERT: A 933 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8334 (tptt) REVERT: A 1036 ASP cc_start: 0.8079 (m-30) cc_final: 0.7602 (m-30) REVERT: A 1050 ASP cc_start: 0.7986 (m-30) cc_final: 0.7766 (m-30) REVERT: A 1069 GLU cc_start: 0.7571 (pm20) cc_final: 0.7271 (pm20) REVERT: A 1184 VAL cc_start: 0.9015 (t) cc_final: 0.8797 (p) REVERT: A 1198 SER cc_start: 0.9137 (m) cc_final: 0.8748 (p) REVERT: c 225 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6663 (tm-30) REVERT: c 300 LYS cc_start: 0.9134 (ttpt) cc_final: 0.8918 (ttpt) REVERT: c 422 ILE cc_start: 0.9148 (tp) cc_final: 0.8891 (tp) REVERT: c 425 GLU cc_start: 0.8126 (tt0) cc_final: 0.7828 (tt0) REVERT: c 523 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.7354 (mtp85) REVERT: c 556 SER cc_start: 0.9208 (m) cc_final: 0.8958 (m) REVERT: d 14 SER cc_start: 0.8456 (p) cc_final: 0.8212 (p) REVERT: d 32 ASP cc_start: 0.8101 (m-30) cc_final: 0.7481 (m-30) REVERT: d 101 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7643 (mt-10) REVERT: d 120 LYS cc_start: 0.8911 (tttm) cc_final: 0.8689 (mtpt) REVERT: e 42 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8454 (tm-30) REVERT: e 91 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7444 (mm-30) REVERT: e 109 TYR cc_start: 0.8462 (t80) cc_final: 0.7987 (t80) REVERT: e 114 GLU cc_start: 0.8200 (pp20) cc_final: 0.7978 (pp20) REVERT: e 205 ASN cc_start: 0.8445 (m-40) cc_final: 0.8242 (p0) REVERT: f 15 GLU cc_start: 0.8364 (mp0) cc_final: 0.7966 (mp0) REVERT: f 28 GLU cc_start: 0.7811 (pt0) cc_final: 0.7556 (pt0) REVERT: f 32 LEU cc_start: 0.9108 (mt) cc_final: 0.8879 (mt) REVERT: f 57 TYR cc_start: 0.8668 (t80) cc_final: 0.7729 (t80) REVERT: f 61 TYR cc_start: 0.8311 (t80) cc_final: 0.7772 (t80) REVERT: f 88 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7511 (mm-30) REVERT: f 120 ASP cc_start: 0.7886 (t70) cc_final: 0.7321 (t0) REVERT: g 50 SER cc_start: 0.9331 (t) cc_final: 0.9009 (p) REVERT: g 62 SER cc_start: 0.8978 (p) cc_final: 0.8703 (p) REVERT: g 113 LYS cc_start: 0.8333 (tttt) cc_final: 0.7952 (tttm) REVERT: g 118 ASN cc_start: 0.8257 (t0) cc_final: 0.7839 (t0) REVERT: g 130 ASN cc_start: 0.8263 (t0) cc_final: 0.7430 (t0) REVERT: g 144 ASN cc_start: 0.8559 (m110) cc_final: 0.8151 (m110) REVERT: g 148 VAL cc_start: 0.9180 (t) cc_final: 0.8973 (t) REVERT: h 33 TYR cc_start: 0.9005 (m-80) cc_final: 0.8763 (m-80) REVERT: h 75 MET cc_start: 0.7955 (pmm) cc_final: 0.7361 (pmm) REVERT: i 43 GLN cc_start: 0.7989 (tt0) cc_final: 0.7710 (tt0) REVERT: i 48 ASP cc_start: 0.7525 (t0) cc_final: 0.6971 (t0) REVERT: i 156 GLN cc_start: 0.9148 (mp10) cc_final: 0.8358 (mp10) REVERT: j 23 GLU cc_start: 0.8077 (tp30) cc_final: 0.7582 (tp30) REVERT: j 228 SER cc_start: 0.8902 (t) cc_final: 0.8615 (p) REVERT: j 255 MET cc_start: 0.8833 (mmt) cc_final: 0.8324 (mmt) REVERT: j 271 ASP cc_start: 0.7725 (t0) cc_final: 0.7453 (t0) REVERT: k 3 GLN cc_start: 0.8591 (mp10) cc_final: 0.7928 (mm-40) REVERT: k 19 GLU cc_start: 0.8203 (tt0) cc_final: 0.7955 (tt0) REVERT: k 22 ASN cc_start: 0.7876 (t0) cc_final: 0.7213 (t0) REVERT: k 157 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7623 (ptm160) REVERT: l 18 LEU cc_start: 0.8768 (tp) cc_final: 0.8525 (tp) REVERT: l 49 GLU cc_start: 0.7753 (tt0) cc_final: 0.7414 (tt0) REVERT: l 59 ASN cc_start: 0.8275 (t0) cc_final: 0.7730 (t0) REVERT: l 102 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7262 (tm-30) REVERT: l 106 HIS cc_start: 0.8057 (t-90) cc_final: 0.7703 (t70) REVERT: l 117 ASP cc_start: 0.8034 (m-30) cc_final: 0.7688 (m-30) REVERT: l 148 ASN cc_start: 0.8734 (m-40) cc_final: 0.7951 (m-40) REVERT: b 363 TRP cc_start: 0.9326 (t60) cc_final: 0.8919 (t60) REVERT: b 379 ASN cc_start: 0.7743 (t0) cc_final: 0.7299 (t0) REVERT: b 404 GLU cc_start: 0.8251 (pm20) cc_final: 0.7897 (pm20) REVERT: b 431 LEU cc_start: 0.9438 (mt) cc_final: 0.9148 (mt) REVERT: b 545 GLU cc_start: 0.7304 (pm20) cc_final: 0.7065 (pm20) REVERT: b 551 LYS cc_start: 0.6650 (pttm) cc_final: 0.6244 (pttt) REVERT: b 598 ASP cc_start: 0.7516 (m-30) cc_final: 0.6923 (t0) REVERT: b 692 GLU cc_start: 0.7642 (pt0) cc_final: 0.7412 (pt0) REVERT: b 734 GLN cc_start: 0.7701 (mm110) cc_final: 0.7451 (mm110) REVERT: b 896 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6934 (mm-30) REVERT: b 911 ASN cc_start: 0.8829 (m-40) cc_final: 0.8201 (t0) REVERT: b 926 THR cc_start: 0.9106 (m) cc_final: 0.8895 (m) REVERT: b 1060 GLU cc_start: 0.8567 (pt0) cc_final: 0.8342 (pt0) REVERT: b 1069 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8702 (mmmm) REVERT: a 30 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7733 (mm-30) REVERT: a 40 GLU cc_start: 0.8031 (tp30) cc_final: 0.7814 (tp30) REVERT: a 107 LEU cc_start: 0.8226 (mm) cc_final: 0.8003 (mm) REVERT: a 303 LEU cc_start: 0.9145 (tp) cc_final: 0.8909 (tp) REVERT: a 331 LEU cc_start: 0.8934 (mt) cc_final: 0.8695 (mt) REVERT: a 536 LEU cc_start: 0.9015 (mt) cc_final: 0.8691 (mp) REVERT: a 627 GLU cc_start: 0.8447 (mp0) cc_final: 0.7775 (mp0) REVERT: a 643 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7629 (mp0) REVERT: a 867 ASP cc_start: 0.8359 (t0) cc_final: 0.7924 (t0) REVERT: a 904 ASP cc_start: 0.7931 (p0) cc_final: 0.7558 (p0) REVERT: a 942 GLU cc_start: 0.8340 (tt0) cc_final: 0.8088 (tt0) REVERT: a 1020 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8011 (tm-30) REVERT: a 1036 ASP cc_start: 0.8399 (m-30) cc_final: 0.8176 (m-30) REVERT: a 1050 ASP cc_start: 0.8081 (m-30) cc_final: 0.7717 (m-30) REVERT: a 1064 ASN cc_start: 0.8517 (p0) cc_final: 0.8305 (p0) REVERT: a 1217 ASP cc_start: 0.8514 (t70) cc_final: 0.8210 (t0) outliers start: 5 outliers final: 1 residues processed: 3141 average time/residue: 1.3017 time to fit residues: 6942.6081 Evaluate side-chains 2771 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2770 time to evaluate : 7.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 25 ASN 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: 1.9990 chunk 332 optimal weight: 1.9990 chunk 644 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 391 optimal weight: 0.4980 chunk 479 optimal weight: 0.9990 chunk 746 optimal weight: 0.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 F 53 ASN G 142 ASN H 31 ASN J 184 HIS ** K 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 181 GLN k 42 HIS k 172 HIS l 65 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 66826 Z= 0.241 Angle : 0.575 7.247 90446 Z= 0.305 Chirality : 0.040 0.197 10438 Planarity : 0.004 0.060 11462 Dihedral : 5.111 58.866 8940 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.54 % Favored : 90.37 % Rotamer: Outliers : 2.13 % Allowed : 14.81 % Favored : 83.06 % 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: -1.33 (0.10), residues: 7496 helix: 1.10 (0.11), residues: 2514 sheet: -0.86 (0.14), residues: 1482 loop : -2.48 (0.10), residues: 3500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 18 HIS 0.004 0.001 HIS B 987 PHE 0.021 0.001 PHE B 525 TYR 0.019 0.001 TYR e 109 ARG 0.009 0.001 ARG b 816 *********************** 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 2912 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 2762 time to evaluate : 7.925 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: C 263 GLU cc_start: 0.8167 (tt0) cc_final: 0.7654 (tt0) REVERT: C 312 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7579 (ttm-80) REVERT: C 417 SER cc_start: 0.9126 (p) cc_final: 0.8854 (p) REVERT: D 16 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8339 (tptp) REVERT: D 64 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8750 (mmmm) REVERT: D 65 SER cc_start: 0.9646 (t) cc_final: 0.9377 (t) REVERT: D 80 LYS cc_start: 0.8999 (tttt) cc_final: 0.8766 (ttmm) REVERT: D 106 ASN cc_start: 0.8925 (t0) cc_final: 0.8691 (t0) REVERT: D 143 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7949 (tm-30) REVERT: E 42 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8449 (tm-30) REVERT: E 113 GLU cc_start: 0.7581 (pp20) cc_final: 0.7290 (pp20) REVERT: E 116 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8322 (tttm) REVERT: E 185 TYR cc_start: 0.8414 (m-80) cc_final: 0.7345 (m-80) REVERT: F 28 GLU cc_start: 0.7817 (pt0) cc_final: 0.7593 (pm20) REVERT: F 113 ASP cc_start: 0.9082 (t0) cc_final: 0.8839 (t0) REVERT: F 120 ASP cc_start: 0.7939 (t0) cc_final: 0.7000 (t0) REVERT: F 121 GLU cc_start: 0.7026 (mp0) cc_final: 0.5960 (mp0) REVERT: F 132 MET cc_start: 0.8637 (mmm) cc_final: 0.8407 (mmp) REVERT: F 136 LYS cc_start: 0.8795 (pttm) cc_final: 0.8469 (ptmm) REVERT: G 80 TYR cc_start: 0.9189 (t80) cc_final: 0.8320 (t80) REVERT: G 101 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8491 (mt0) REVERT: G 130 ASN cc_start: 0.8240 (t0) cc_final: 0.7985 (t0) REVERT: G 144 ASN cc_start: 0.8840 (m110) cc_final: 0.8341 (m110) REVERT: G 156 MET cc_start: 0.8361 (ptp) cc_final: 0.8079 (ptm) REVERT: H 18 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8280 (tm-30) REVERT: H 100 SER cc_start: 0.7582 (p) cc_final: 0.7184 (p) REVERT: H 115 ASN cc_start: 0.8831 (p0) cc_final: 0.8590 (p0) REVERT: I 23 GLU cc_start: 0.6268 (mp0) cc_final: 0.5973 (mp0) REVERT: I 156 GLN cc_start: 0.8827 (mp10) cc_final: 0.8491 (mp10) REVERT: J 68 GLU cc_start: 0.8395 (tp30) cc_final: 0.8146 (tp30) REVERT: J 255 MET cc_start: 0.8932 (mmt) cc_final: 0.8606 (mmt) REVERT: K 25 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8985 (p0) REVERT: K 139 GLU cc_start: 0.8584 (tp30) cc_final: 0.8008 (tp30) REVERT: L 58 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8636 (mt-10) REVERT: L 59 ASN cc_start: 0.8482 (t0) cc_final: 0.7870 (t0) REVERT: L 61 LYS cc_start: 0.7859 (mmtm) cc_final: 0.7605 (mmtm) REVERT: L 106 HIS cc_start: 0.7895 (t70) cc_final: 0.7158 (t70) REVERT: L 113 GLU cc_start: 0.7254 (tm-30) cc_final: 0.7016 (tm-30) REVERT: L 114 ASN cc_start: 0.8326 (t0) cc_final: 0.7379 (t0) REVERT: L 117 ASP cc_start: 0.8104 (m-30) cc_final: 0.7848 (m-30) REVERT: L 200 LYS cc_start: 0.8620 (tttp) cc_final: 0.8093 (ptpt) REVERT: B 276 GLN cc_start: 0.8635 (mt0) cc_final: 0.8187 (pt0) REVERT: B 349 CYS cc_start: 0.9215 (m) cc_final: 0.8900 (m) REVERT: B 355 LEU cc_start: 0.9231 (tp) cc_final: 0.8930 (mp) REVERT: B 356 LEU cc_start: 0.8699 (mt) cc_final: 0.8450 (mt) REVERT: B 453 LEU cc_start: 0.9340 (mt) cc_final: 0.9100 (mt) REVERT: B 567 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7519 (mtpt) REVERT: B 734 GLN cc_start: 0.7884 (mm110) cc_final: 0.7609 (mm110) REVERT: B 894 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7903 (mt-10) REVERT: B 911 ASN cc_start: 0.8835 (m-40) cc_final: 0.8142 (t0) REVERT: B 932 ASN cc_start: 0.8068 (m110) cc_final: 0.7673 (m110) REVERT: B 985 PHE cc_start: 0.8539 (t80) cc_final: 0.8261 (t80) REVERT: B 1009 ASN cc_start: 0.8952 (m110) cc_final: 0.8526 (m110) REVERT: B 1102 PHE cc_start: 0.7494 (t80) cc_final: 0.7169 (t80) REVERT: A 58 THR cc_start: 0.8656 (m) cc_final: 0.8416 (m) REVERT: A 99 LEU cc_start: 0.8440 (mt) cc_final: 0.8151 (mt) REVERT: A 154 GLN cc_start: 0.7421 (mp-120) cc_final: 0.7131 (mp10) REVERT: A 157 ILE cc_start: 0.9410 (tp) cc_final: 0.9155 (tp) REVERT: A 317 ASP cc_start: 0.8577 (t0) cc_final: 0.8281 (t0) REVERT: A 415 CYS cc_start: 0.8842 (t) cc_final: 0.8524 (t) REVERT: A 466 ASP cc_start: 0.7236 (m-30) cc_final: 0.7017 (m-30) REVERT: A 563 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7532 (tm-30) REVERT: A 607 TYR cc_start: 0.7361 (m-80) cc_final: 0.6849 (m-80) REVERT: A 817 ASN cc_start: 0.6820 (m110) cc_final: 0.6284 (m110) REVERT: A 867 ASP cc_start: 0.8033 (t0) cc_final: 0.7411 (t0) REVERT: A 899 GLN cc_start: 0.8079 (tt0) cc_final: 0.7307 (tm-30) REVERT: A 933 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8318 (tptt) REVERT: A 994 THR cc_start: 0.8724 (p) cc_final: 0.8345 (p) REVERT: A 1036 ASP cc_start: 0.8120 (m-30) cc_final: 0.7624 (m-30) REVERT: A 1069 GLU cc_start: 0.7533 (pm20) cc_final: 0.7250 (pm20) REVERT: A 1198 SER cc_start: 0.9063 (m) cc_final: 0.8720 (p) REVERT: c 225 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6951 (tm-30) REVERT: c 300 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8646 (ttpt) REVERT: c 312 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7766 (ttm-80) REVERT: c 338 GLU cc_start: 0.9123 (pm20) cc_final: 0.8869 (pm20) REVERT: c 506 ASP cc_start: 0.7084 (m-30) cc_final: 0.6835 (m-30) REVERT: d 32 ASP cc_start: 0.8204 (m-30) cc_final: 0.7581 (m-30) REVERT: d 64 LYS cc_start: 0.9041 (mmmm) cc_final: 0.8815 (mmmm) REVERT: d 101 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7609 (mt-10) REVERT: d 120 LYS cc_start: 0.8884 (tttm) cc_final: 0.8676 (mtpt) REVERT: d 139 ARG cc_start: 0.8460 (ptm160) cc_final: 0.8234 (ptp-110) REVERT: e 42 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8385 (tm-30) REVERT: e 91 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7917 (mm-30) REVERT: f 15 GLU cc_start: 0.8182 (mp0) cc_final: 0.7856 (mp0) REVERT: f 57 TYR cc_start: 0.8705 (t80) cc_final: 0.7653 (t80) REVERT: f 88 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7571 (mm-30) REVERT: f 120 ASP cc_start: 0.7865 (t70) cc_final: 0.7266 (t0) REVERT: g 113 LYS cc_start: 0.8390 (tttt) cc_final: 0.7971 (tttm) REVERT: g 118 ASN cc_start: 0.8575 (t0) cc_final: 0.8256 (t0) REVERT: g 130 ASN cc_start: 0.8271 (t0) cc_final: 0.7969 (t0) REVERT: g 144 ASN cc_start: 0.8719 (m110) cc_final: 0.8185 (m110) REVERT: h 75 MET cc_start: 0.8005 (pmm) cc_final: 0.7305 (pmm) REVERT: h 115 ASN cc_start: 0.8956 (p0) cc_final: 0.8494 (p0) REVERT: h 123 CYS cc_start: 0.8443 (m) cc_final: 0.8094 (m) REVERT: i 72 LEU cc_start: 0.8589 (tt) cc_final: 0.8346 (tt) REVERT: i 156 GLN cc_start: 0.9208 (mp10) cc_final: 0.8372 (mp10) REVERT: j 23 GLU cc_start: 0.8175 (tp30) cc_final: 0.7776 (tp30) REVERT: j 189 SER cc_start: 0.9112 (p) cc_final: 0.8819 (p) REVERT: j 228 SER cc_start: 0.9112 (t) cc_final: 0.8700 (p) REVERT: j 255 MET cc_start: 0.8825 (mmt) cc_final: 0.8292 (mmt) REVERT: j 271 ASP cc_start: 0.7689 (t0) cc_final: 0.7280 (t0) REVERT: k 3 GLN cc_start: 0.8710 (mp10) cc_final: 0.8000 (mm-40) REVERT: k 22 ASN cc_start: 0.7814 (t0) cc_final: 0.7129 (t0) REVERT: k 24 GLU cc_start: 0.6632 (pm20) cc_final: 0.6299 (mp0) REVERT: k 35 GLU cc_start: 0.8397 (tt0) cc_final: 0.8191 (tp30) REVERT: k 126 ASP cc_start: 0.8280 (t0) cc_final: 0.7967 (t0) REVERT: k 136 GLU cc_start: 0.8182 (tp30) cc_final: 0.7732 (tp30) REVERT: k 157 ARG cc_start: 0.8129 (ptm160) cc_final: 0.7753 (ptm160) REVERT: l 18 LEU cc_start: 0.9047 (tp) cc_final: 0.8845 (tp) REVERT: l 49 GLU cc_start: 0.7492 (tt0) cc_final: 0.7204 (tt0) REVERT: l 59 ASN cc_start: 0.8320 (t0) cc_final: 0.7786 (t0) REVERT: l 102 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7189 (tm-30) REVERT: l 106 HIS cc_start: 0.7797 (t-90) cc_final: 0.7532 (t70) REVERT: l 117 ASP cc_start: 0.8126 (m-30) cc_final: 0.7820 (m-30) REVERT: l 127 LYS cc_start: 0.7595 (mttm) cc_final: 0.7349 (mttp) REVERT: l 148 ASN cc_start: 0.8652 (m-40) cc_final: 0.7821 (m-40) REVERT: b 363 TRP cc_start: 0.9395 (t60) cc_final: 0.9018 (t60) REVERT: b 458 TYR cc_start: 0.8295 (t80) cc_final: 0.7958 (t80) REVERT: b 535 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7626 (t-90) REVERT: b 551 LYS cc_start: 0.7032 (pttm) cc_final: 0.6567 (pttt) REVERT: b 692 GLU cc_start: 0.7588 (pt0) cc_final: 0.7334 (pt0) REVERT: b 728 GLU cc_start: 0.7985 (tt0) cc_final: 0.7673 (tt0) REVERT: b 734 GLN cc_start: 0.7776 (mm110) cc_final: 0.7510 (mm110) REVERT: b 816 ARG cc_start: 0.7191 (ttp80) cc_final: 0.6595 (ttp80) REVERT: b 877 GLU cc_start: 0.7479 (pm20) cc_final: 0.7178 (pm20) REVERT: b 896 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6993 (mm-30) REVERT: b 911 ASN cc_start: 0.8862 (m-40) cc_final: 0.8211 (t0) REVERT: b 926 THR cc_start: 0.9064 (m) cc_final: 0.8846 (m) REVERT: b 1102 PHE cc_start: 0.7780 (t80) cc_final: 0.7418 (t80) REVERT: a 303 LEU cc_start: 0.8749 (tp) cc_final: 0.8432 (tp) REVERT: a 309 TYR cc_start: 0.8609 (m-10) cc_final: 0.8208 (m-10) REVERT: a 536 LEU cc_start: 0.8988 (mt) cc_final: 0.8674 (mp) REVERT: a 582 SER cc_start: 0.8886 (t) cc_final: 0.8674 (t) REVERT: a 867 ASP cc_start: 0.8382 (t0) cc_final: 0.7936 (t0) REVERT: a 1002 ILE cc_start: 0.8399 (mm) cc_final: 0.7817 (mm) REVERT: a 1014 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7926 (pt0) REVERT: a 1020 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7942 (tm-30) REVERT: a 1036 ASP cc_start: 0.8524 (m-30) cc_final: 0.8304 (m-30) REVERT: a 1050 ASP cc_start: 0.8075 (m-30) cc_final: 0.7829 (m-30) REVERT: a 1114 THR cc_start: 0.9016 (t) cc_final: 0.8691 (p) REVERT: a 1217 ASP cc_start: 0.8527 (t70) cc_final: 0.8296 (t0) outliers start: 150 outliers final: 129 residues processed: 2793 average time/residue: 1.3964 time to fit residues: 6645.8824 Evaluate side-chains 2828 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 2697 time to evaluate : 7.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 142 ASN Chi-restraints excluded: chain H residue 29 ASN Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 455 CYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 653 CYS Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 987 HIS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 559 ILE Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 134 ILE Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 126 ILE Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 118 ILE Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain g residue 3 ILE Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 182 VAL Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 32 ILE Chi-restraints excluded: chain j residue 88 SER Chi-restraints excluded: chain j residue 197 ASP Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain j residue 264 THR Chi-restraints excluded: chain k residue 25 ASN Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain b residue 320 SER Chi-restraints excluded: chain b residue 438 LEU Chi-restraints excluded: chain b residue 455 CYS Chi-restraints excluded: chain b residue 457 GLU Chi-restraints excluded: chain b residue 535 HIS Chi-restraints excluded: chain b residue 592 ILE Chi-restraints excluded: chain b residue 653 CYS Chi-restraints excluded: chain b residue 844 ASN Chi-restraints excluded: chain b residue 947 LEU Chi-restraints excluded: chain b residue 987 HIS Chi-restraints excluded: chain b residue 988 VAL Chi-restraints excluded: chain a residue 2 ASN Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 278 ILE Chi-restraints excluded: chain a residue 306 VAL Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 342 ILE Chi-restraints excluded: chain a residue 421 LEU Chi-restraints excluded: chain a residue 427 SER Chi-restraints excluded: chain a residue 452 THR Chi-restraints excluded: chain a residue 533 VAL Chi-restraints excluded: chain a residue 538 MET Chi-restraints excluded: chain a residue 804 SER Chi-restraints excluded: chain a residue 852 LEU Chi-restraints excluded: chain a residue 892 ILE Chi-restraints excluded: chain a residue 1001 ASP Chi-restraints excluded: chain a residue 1003 ILE Chi-restraints excluded: chain a residue 1024 SER Chi-restraints excluded: chain a residue 1034 SER Chi-restraints excluded: chain a residue 1198 SER 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: 2.9990 chunk 508 optimal weight: 0.9990 chunk 205 optimal weight: 0.0020 chunk 747 optimal weight: 0.8980 chunk 807 optimal weight: 50.0000 chunk 665 optimal weight: 0.0970 chunk 741 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 599 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 K 22 ASN B 362 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 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** i 181 ASN j 30 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 66826 Z= 0.180 Angle : 0.539 7.451 90446 Z= 0.283 Chirality : 0.040 0.194 10438 Planarity : 0.003 0.050 11462 Dihedral : 4.895 59.259 8940 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.14 % Favored : 90.76 % Rotamer: Outliers : 2.43 % Allowed : 17.08 % Favored : 80.49 % 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: 1.23 (0.11), residues: 2532 sheet: -0.82 (0.13), residues: 1496 loop : -2.43 (0.10), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 889 HIS 0.005 0.001 HIS K 42 PHE 0.021 0.001 PHE C 151 TYR 0.015 0.001 TYR b 445 ARG 0.010 0.000 ARG k 164 *********************** 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 2927 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 2756 time to evaluate : 7.427 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: C 263 GLU cc_start: 0.8132 (tt0) cc_final: 0.7629 (tt0) REVERT: C 312 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7576 (ttm-80) REVERT: C 417 SER cc_start: 0.9109 (p) cc_final: 0.8837 (p) REVERT: C 492 TYR cc_start: 0.8665 (m-10) cc_final: 0.8447 (m-10) REVERT: D 16 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8239 (tptp) REVERT: D 64 LYS cc_start: 0.9041 (mmtp) cc_final: 0.8702 (mmtp) REVERT: D 65 SER cc_start: 0.9617 (t) cc_final: 0.9341 (t) REVERT: D 80 LYS cc_start: 0.8980 (tttt) cc_final: 0.8745 (ttmm) REVERT: D 139 ARG cc_start: 0.8460 (ptm160) cc_final: 0.7945 (ptp-110) REVERT: D 143 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7881 (tm-30) REVERT: E 42 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8425 (tm-30) REVERT: E 113 GLU cc_start: 0.7684 (pp20) cc_final: 0.7359 (pp20) REVERT: E 116 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8386 (tttm) REVERT: E 185 TYR cc_start: 0.8417 (m-80) cc_final: 0.7298 (m-80) REVERT: F 113 ASP cc_start: 0.9101 (t0) cc_final: 0.8850 (t0) REVERT: F 120 ASP cc_start: 0.7929 (t0) cc_final: 0.7021 (t0) REVERT: F 121 GLU cc_start: 0.7003 (mp0) cc_final: 0.5940 (mp0) REVERT: F 136 LYS cc_start: 0.8783 (pttm) cc_final: 0.8452 (ptmm) REVERT: G 80 TYR cc_start: 0.9175 (t80) cc_final: 0.8187 (t80) REVERT: G 101 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8491 (mt0) REVERT: G 130 ASN cc_start: 0.8193 (t0) cc_final: 0.7803 (t0) REVERT: G 144 ASN cc_start: 0.8851 (m110) cc_final: 0.8525 (m110) REVERT: H 18 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8141 (tm-30) REVERT: H 100 SER cc_start: 0.7904 (p) cc_final: 0.7330 (p) REVERT: H 115 ASN cc_start: 0.8865 (p0) cc_final: 0.8568 (p0) REVERT: I 23 GLU cc_start: 0.6171 (mp0) cc_final: 0.5809 (mp0) REVERT: I 26 ASN cc_start: 0.8837 (t0) cc_final: 0.8533 (t0) REVERT: I 156 GLN cc_start: 0.8859 (mp10) cc_final: 0.8403 (mp10) REVERT: J 56 GLU cc_start: 0.7213 (mt-10) cc_final: 0.7007 (mt-10) REVERT: J 68 GLU cc_start: 0.8391 (tp30) cc_final: 0.8154 (tp30) REVERT: J 75 ARG cc_start: 0.8426 (ptp90) cc_final: 0.8122 (ptp-170) REVERT: J 255 MET cc_start: 0.8964 (mmt) cc_final: 0.8701 (mmt) REVERT: J 257 GLN cc_start: 0.9241 (pp30) cc_final: 0.9030 (pp30) REVERT: K 22 ASN cc_start: 0.7825 (t160) cc_final: 0.7557 (t160) REVERT: K 25 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8967 (p0) REVERT: K 113 MET cc_start: 0.8560 (tpp) cc_final: 0.8337 (tpp) REVERT: L 18 LEU cc_start: 0.8913 (tp) cc_final: 0.8672 (tp) REVERT: L 58 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8474 (mt-10) REVERT: L 59 ASN cc_start: 0.8463 (t0) cc_final: 0.7857 (t0) REVERT: L 61 LYS cc_start: 0.7849 (mmtm) cc_final: 0.7565 (mmtm) REVERT: L 101 TYR cc_start: 0.7678 (t80) cc_final: 0.6644 (t80) REVERT: L 113 GLU cc_start: 0.7260 (tm-30) cc_final: 0.7011 (tm-30) REVERT: L 114 ASN cc_start: 0.8273 (t0) cc_final: 0.7304 (t0) REVERT: L 174 ILE cc_start: 0.8437 (mt) cc_final: 0.8210 (mt) REVERT: L 200 LYS cc_start: 0.8631 (tttp) cc_final: 0.8089 (ptpt) REVERT: B 276 GLN cc_start: 0.8645 (mt0) cc_final: 0.8151 (pt0) REVERT: B 349 CYS cc_start: 0.9205 (m) cc_final: 0.8897 (m) REVERT: B 355 LEU cc_start: 0.9209 (tp) cc_final: 0.8907 (mp) REVERT: B 356 LEU cc_start: 0.8673 (mt) cc_final: 0.8408 (mt) REVERT: B 567 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7475 (mtpt) REVERT: B 734 GLN cc_start: 0.7958 (mm110) cc_final: 0.7667 (mm110) REVERT: B 780 ASP cc_start: 0.8745 (p0) cc_final: 0.8315 (p0) REVERT: B 894 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7898 (mt-10) REVERT: B 911 ASN cc_start: 0.8785 (m-40) cc_final: 0.8116 (t0) REVERT: B 932 ASN cc_start: 0.7971 (m110) cc_final: 0.7537 (m110) REVERT: B 1009 ASN cc_start: 0.8957 (m110) cc_final: 0.8487 (m110) REVERT: B 1043 GLU cc_start: 0.8855 (pt0) cc_final: 0.8552 (pt0) REVERT: B 1102 PHE cc_start: 0.7201 (t80) cc_final: 0.6949 (t80) REVERT: A 58 THR cc_start: 0.8652 (m) cc_final: 0.8398 (m) REVERT: A 99 LEU cc_start: 0.8474 (mt) cc_final: 0.8173 (mt) REVERT: A 154 GLN cc_start: 0.7352 (mp-120) cc_final: 0.7105 (mp10) REVERT: A 317 ASP cc_start: 0.8558 (t0) cc_final: 0.8234 (t0) REVERT: A 415 CYS cc_start: 0.8845 (t) cc_final: 0.8474 (t) REVERT: A 466 ASP cc_start: 0.7220 (m-30) cc_final: 0.7013 (m-30) REVERT: A 501 GLN cc_start: 0.8745 (tp40) cc_final: 0.8005 (tm-30) REVERT: A 563 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 607 TYR cc_start: 0.7432 (m-80) cc_final: 0.6907 (m-80) REVERT: A 817 ASN cc_start: 0.6678 (m110) cc_final: 0.6175 (m110) REVERT: A 867 ASP cc_start: 0.7998 (t0) cc_final: 0.7400 (t0) REVERT: A 899 GLN cc_start: 0.8058 (tt0) cc_final: 0.7345 (tm-30) REVERT: A 908 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8528 (mmmm) REVERT: A 913 ASP cc_start: 0.7893 (m-30) cc_final: 0.7607 (m-30) REVERT: A 933 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8308 (tptt) REVERT: A 994 THR cc_start: 0.8765 (p) cc_final: 0.8410 (p) REVERT: A 1002 ILE cc_start: 0.8080 (mm) cc_final: 0.7633 (mm) REVERT: A 1036 ASP cc_start: 0.8105 (m-30) cc_final: 0.7602 (m-30) REVERT: A 1069 GLU cc_start: 0.7527 (pm20) cc_final: 0.7249 (pm20) REVERT: A 1181 LYS cc_start: 0.8460 (mmmm) cc_final: 0.7947 (mmmm) REVERT: A 1198 SER cc_start: 0.9042 (m) cc_final: 0.8711 (p) REVERT: c 312 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7771 (ttm-80) REVERT: c 338 GLU cc_start: 0.9127 (pm20) cc_final: 0.8847 (pm20) REVERT: c 409 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7609 (t0) REVERT: c 506 ASP cc_start: 0.6964 (m-30) cc_final: 0.6648 (m-30) REVERT: d 32 ASP cc_start: 0.8282 (m-30) cc_final: 0.7545 (m-30) REVERT: d 101 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7591 (mt-10) REVERT: d 139 ARG cc_start: 0.8459 (ptm160) cc_final: 0.8216 (ptp-110) REVERT: e 42 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8409 (tm-30) REVERT: e 91 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7586 (mm-30) REVERT: e 92 GLU cc_start: 0.8390 (pm20) cc_final: 0.8183 (pm20) REVERT: f 57 TYR cc_start: 0.8727 (t80) cc_final: 0.7597 (t80) REVERT: f 88 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7563 (mm-30) REVERT: f 120 ASP cc_start: 0.7901 (t70) cc_final: 0.7268 (t0) REVERT: g 118 ASN cc_start: 0.8557 (t0) cc_final: 0.8179 (t0) REVERT: g 130 ASN cc_start: 0.8010 (t0) cc_final: 0.7717 (t0) REVERT: g 144 ASN cc_start: 0.8770 (m110) cc_final: 0.8287 (m110) REVERT: h 75 MET cc_start: 0.8051 (pmm) cc_final: 0.7280 (pmm) REVERT: h 123 CYS cc_start: 0.8416 (m) cc_final: 0.8075 (m) REVERT: i 156 GLN cc_start: 0.9191 (mp10) cc_final: 0.8350 (mp10) REVERT: j 23 GLU cc_start: 0.8139 (tp30) cc_final: 0.7750 (tp30) REVERT: j 189 SER cc_start: 0.9101 (p) cc_final: 0.8799 (p) REVERT: j 228 SER cc_start: 0.9127 (t) cc_final: 0.8704 (p) REVERT: j 255 MET cc_start: 0.8811 (mmt) cc_final: 0.8277 (mmt) REVERT: j 271 ASP cc_start: 0.7638 (t0) cc_final: 0.7231 (t0) REVERT: k 3 GLN cc_start: 0.8728 (mp10) cc_final: 0.8017 (mm-40) REVERT: k 19 GLU cc_start: 0.8172 (tt0) cc_final: 0.7909 (tt0) REVERT: k 22 ASN cc_start: 0.7822 (t0) cc_final: 0.7110 (t0) REVERT: k 24 GLU cc_start: 0.6604 (pm20) cc_final: 0.6265 (mp0) REVERT: k 35 GLU cc_start: 0.8373 (tt0) cc_final: 0.8148 (tp30) REVERT: k 126 ASP cc_start: 0.8294 (t0) cc_final: 0.7965 (t0) REVERT: k 136 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: k 157 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7732 (ptm160) REVERT: l 49 GLU cc_start: 0.7425 (tt0) cc_final: 0.7153 (tt0) REVERT: l 59 ASN cc_start: 0.8315 (t0) cc_final: 0.7785 (t0) REVERT: l 102 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7167 (tm-30) REVERT: l 106 HIS cc_start: 0.7839 (t-90) cc_final: 0.7447 (t70) REVERT: l 117 ASP cc_start: 0.8024 (m-30) cc_final: 0.7773 (m-30) REVERT: l 127 LYS cc_start: 0.7632 (mttm) cc_final: 0.7367 (mttp) REVERT: l 148 ASN cc_start: 0.8737 (m-40) cc_final: 0.7797 (m110) REVERT: b 363 TRP cc_start: 0.9413 (t60) cc_final: 0.8967 (t60) REVERT: b 429 ASP cc_start: 0.8336 (m-30) cc_final: 0.7928 (m-30) REVERT: b 510 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9035 (pttp) REVERT: b 535 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7655 (t-90) REVERT: b 551 LYS cc_start: 0.6990 (pttm) cc_final: 0.6444 (pttt) REVERT: b 692 GLU cc_start: 0.7587 (pt0) cc_final: 0.7333 (pt0) REVERT: b 728 GLU cc_start: 0.7950 (tt0) cc_final: 0.7613 (tt0) REVERT: b 734 GLN cc_start: 0.7840 (mm110) cc_final: 0.7550 (mm110) REVERT: b 747 THR cc_start: 0.8754 (m) cc_final: 0.8536 (p) REVERT: b 896 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6995 (mm-30) REVERT: b 911 ASN cc_start: 0.8840 (m-40) cc_final: 0.8207 (t0) REVERT: b 926 THR cc_start: 0.9054 (m) cc_final: 0.8848 (m) REVERT: a 303 LEU cc_start: 0.8682 (tp) cc_final: 0.8376 (tp) REVERT: a 466 ASP cc_start: 0.7933 (m-30) cc_final: 0.7704 (m-30) REVERT: a 536 LEU cc_start: 0.8968 (mt) cc_final: 0.8665 (mp) REVERT: a 563 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7522 (tm-30) REVERT: a 582 SER cc_start: 0.8879 (t) cc_final: 0.8676 (t) REVERT: a 867 ASP cc_start: 0.8330 (t0) cc_final: 0.7925 (t0) REVERT: a 1002 ILE cc_start: 0.8332 (mm) cc_final: 0.7743 (mm) REVERT: a 1020 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7945 (tm-30) REVERT: a 1036 ASP cc_start: 0.8483 (m-30) cc_final: 0.8264 (m-30) REVERT: a 1050 ASP cc_start: 0.8080 (m-30) cc_final: 0.7825 (m-30) REVERT: a 1217 ASP cc_start: 0.8507 (t70) cc_final: 0.8272 (t0) outliers start: 171 outliers final: 145 residues processed: 2794 average time/residue: 1.3093 time to fit residues: 6204.6282 Evaluate side-chains 2828 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 2678 time to evaluate : 7.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 106 HIS Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 653 CYS Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 987 HIS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 244 THR Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 409 ASN Chi-restraints excluded: chain c residue 559 ILE Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 134 ILE Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 106 THR Chi-restraints excluded: chain f residue 118 ILE Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 38 GLU Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 32 ILE Chi-restraints excluded: chain j residue 88 SER Chi-restraints excluded: chain j residue 179 ILE Chi-restraints excluded: chain j residue 197 ASP Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 25 ASN Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 105 SER Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain b residue 313 ILE Chi-restraints excluded: chain b residue 320 SER Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 457 GLU Chi-restraints excluded: chain b residue 482 CYS Chi-restraints excluded: chain b residue 510 LYS Chi-restraints excluded: chain b residue 535 HIS Chi-restraints excluded: chain b residue 592 ILE Chi-restraints excluded: chain b residue 653 CYS Chi-restraints excluded: chain b residue 690 GLU Chi-restraints excluded: chain b residue 844 ASN Chi-restraints excluded: chain b residue 895 LEU Chi-restraints excluded: chain b residue 987 HIS Chi-restraints excluded: chain b residue 988 VAL Chi-restraints excluded: chain a residue 2 ASN Chi-restraints excluded: chain a residue 96 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 278 ILE Chi-restraints excluded: chain a residue 320 SER Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 342 ILE Chi-restraints excluded: chain a residue 416 ILE Chi-restraints excluded: chain a residue 421 LEU Chi-restraints excluded: chain a residue 427 SER Chi-restraints excluded: chain a residue 452 THR Chi-restraints excluded: chain a residue 533 VAL Chi-restraints excluded: chain a residue 804 SER Chi-restraints excluded: chain a residue 816 ILE Chi-restraints excluded: chain a residue 852 LEU Chi-restraints excluded: chain a residue 882 LEU Chi-restraints excluded: chain a residue 892 ILE Chi-restraints excluded: chain a residue 994 THR Chi-restraints excluded: chain a residue 1001 ASP Chi-restraints excluded: chain a residue 1034 SER Chi-restraints excluded: chain a residue 1212 ASP Chi-restraints excluded: chain a residue 1236 SER 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: 1.9990 chunk 82 optimal weight: 1.9990 chunk 356 optimal weight: 0.9980 chunk 502 optimal weight: 0.4980 chunk 750 optimal weight: 0.9990 chunk 794 optimal weight: 1.9990 chunk 392 optimal weight: 0.9990 chunk 711 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 I 55 HIS B 362 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 41 ASN e 129 GLN e 145 ASN g 130 ASN h 133 GLN b 362 ASN b 535 HIS b 811 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 66826 Z= 0.240 Angle : 0.541 7.549 90446 Z= 0.286 Chirality : 0.040 0.162 10438 Planarity : 0.003 0.053 11462 Dihedral : 4.824 55.929 8940 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.71 % Favored : 90.18 % Rotamer: Outliers : 3.00 % Allowed : 17.92 % Favored : 79.08 % 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: -1.17 (0.10), residues: 7496 helix: 1.27 (0.11), residues: 2548 sheet: -0.83 (0.13), residues: 1520 loop : -2.43 (0.10), residues: 3428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 649 HIS 0.005 0.001 HIS B 987 PHE 0.017 0.001 PHE b 746 TYR 0.018 0.001 TYR a 309 ARG 0.007 0.000 ARG g 133 *********************** 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 2918 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 2707 time to evaluate : 7.457 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 GLU cc_start: 0.8092 (tt0) cc_final: 0.7600 (tt0) REVERT: C 312 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7565 (ttm-80) REVERT: C 417 SER cc_start: 0.9111 (p) cc_final: 0.8840 (p) REVERT: C 492 TYR cc_start: 0.8686 (m-10) cc_final: 0.8466 (m-10) REVERT: D 16 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8170 (tptp) REVERT: D 65 SER cc_start: 0.9609 (t) cc_final: 0.9347 (t) REVERT: D 80 LYS cc_start: 0.9031 (tttt) cc_final: 0.8778 (ttmm) REVERT: D 139 ARG cc_start: 0.8446 (ptm160) cc_final: 0.8078 (ptp-110) REVERT: D 143 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7867 (tm-30) REVERT: E 42 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8406 (tm-30) REVERT: E 91 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7474 (mm-30) REVERT: E 113 GLU cc_start: 0.7683 (pp20) cc_final: 0.7379 (pp20) REVERT: E 166 LYS cc_start: 0.8866 (tptp) cc_final: 0.8653 (tppt) REVERT: E 185 TYR cc_start: 0.8453 (m-80) cc_final: 0.7276 (m-80) REVERT: F 86 THR cc_start: 0.9426 (m) cc_final: 0.9206 (m) REVERT: F 113 ASP cc_start: 0.9106 (t0) cc_final: 0.8871 (t0) REVERT: F 120 ASP cc_start: 0.7907 (t0) cc_final: 0.7016 (t0) REVERT: F 121 GLU cc_start: 0.6978 (mp0) cc_final: 0.5940 (mp0) REVERT: F 136 LYS cc_start: 0.8802 (pttm) cc_final: 0.8474 (ptmm) REVERT: G 80 TYR cc_start: 0.9184 (t80) cc_final: 0.8196 (t80) REVERT: G 101 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8502 (mt0) REVERT: G 130 ASN cc_start: 0.8433 (t0) cc_final: 0.8042 (t0) REVERT: G 144 ASN cc_start: 0.8807 (m110) cc_final: 0.8307 (m110) REVERT: H 100 SER cc_start: 0.7994 (p) cc_final: 0.7365 (p) REVERT: H 115 ASN cc_start: 0.8918 (p0) cc_final: 0.8626 (p0) REVERT: I 23 GLU cc_start: 0.6153 (mp0) cc_final: 0.5752 (mp0) REVERT: I 156 GLN cc_start: 0.8868 (mp10) cc_final: 0.8391 (mp10) REVERT: J 48 GLU cc_start: 0.8532 (tp30) cc_final: 0.8202 (tp30) REVERT: J 68 GLU cc_start: 0.8399 (tp30) cc_final: 0.8163 (tp30) REVERT: J 75 ARG cc_start: 0.8445 (ptp90) cc_final: 0.8114 (ptp90) REVERT: J 255 MET cc_start: 0.8960 (mmt) cc_final: 0.8706 (mmt) REVERT: J 257 GLN cc_start: 0.9267 (pp30) cc_final: 0.9035 (pp30) REVERT: K 22 ASN cc_start: 0.7900 (t160) cc_final: 0.7571 (t160) REVERT: K 25 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8961 (p0) REVERT: K 113 MET cc_start: 0.8737 (tpp) cc_final: 0.8494 (tpp) REVERT: L 18 LEU cc_start: 0.8901 (tp) cc_final: 0.8667 (tp) REVERT: L 58 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8510 (mt-10) REVERT: L 59 ASN cc_start: 0.8486 (t0) cc_final: 0.7842 (t0) REVERT: L 61 LYS cc_start: 0.7842 (mmtm) cc_final: 0.7537 (mmtm) REVERT: L 101 TYR cc_start: 0.7687 (t80) cc_final: 0.6638 (t80) REVERT: L 113 GLU cc_start: 0.7314 (tm-30) cc_final: 0.7047 (tm-30) REVERT: L 114 ASN cc_start: 0.8291 (t0) cc_final: 0.7308 (t0) REVERT: L 174 ILE cc_start: 0.8423 (mt) cc_final: 0.8194 (mt) REVERT: L 200 LYS cc_start: 0.8644 (tttp) cc_final: 0.8140 (ptpt) REVERT: B 276 GLN cc_start: 0.8678 (mt0) cc_final: 0.8170 (pt0) REVERT: B 349 CYS cc_start: 0.9215 (m) cc_final: 0.8896 (m) REVERT: B 355 LEU cc_start: 0.9183 (tp) cc_final: 0.8863 (mp) REVERT: B 567 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7507 (mtpt) REVERT: B 734 GLN cc_start: 0.8016 (mm110) cc_final: 0.7743 (mm110) REVERT: B 780 ASP cc_start: 0.8701 (p0) cc_final: 0.8248 (p0) REVERT: B 911 ASN cc_start: 0.8795 (m-40) cc_final: 0.8114 (t0) REVERT: B 932 ASN cc_start: 0.7985 (m110) cc_final: 0.7546 (m110) REVERT: B 985 PHE cc_start: 0.8474 (t80) cc_final: 0.8267 (t80) REVERT: B 1009 ASN cc_start: 0.8950 (m110) cc_final: 0.8468 (m110) REVERT: B 1102 PHE cc_start: 0.7268 (t80) cc_final: 0.7066 (t80) REVERT: A 58 THR cc_start: 0.8677 (m) cc_final: 0.8422 (m) REVERT: A 99 LEU cc_start: 0.8434 (mt) cc_final: 0.8128 (mt) REVERT: A 157 ILE cc_start: 0.9460 (tp) cc_final: 0.9228 (tp) REVERT: A 317 ASP cc_start: 0.8577 (t0) cc_final: 0.8234 (t0) REVERT: A 415 CYS cc_start: 0.8868 (t) cc_final: 0.8472 (t) REVERT: A 501 GLN cc_start: 0.8776 (tp40) cc_final: 0.7978 (tm-30) REVERT: A 563 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 607 TYR cc_start: 0.7829 (m-80) cc_final: 0.7497 (m-80) REVERT: A 817 ASN cc_start: 0.6841 (m110) cc_final: 0.6339 (m110) REVERT: A 867 ASP cc_start: 0.8022 (t0) cc_final: 0.7460 (t0) REVERT: A 899 GLN cc_start: 0.8098 (tt0) cc_final: 0.7476 (tm-30) REVERT: A 913 ASP cc_start: 0.7968 (m-30) cc_final: 0.7656 (m-30) REVERT: A 933 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8328 (tptt) REVERT: A 994 THR cc_start: 0.8810 (p) cc_final: 0.8488 (p) REVERT: A 1002 ILE cc_start: 0.8251 (mm) cc_final: 0.7691 (mm) REVERT: A 1036 ASP cc_start: 0.8112 (m-30) cc_final: 0.7607 (m-30) REVERT: A 1069 GLU cc_start: 0.7531 (pm20) cc_final: 0.7247 (pm20) REVERT: A 1198 SER cc_start: 0.9032 (m) cc_final: 0.8692 (p) REVERT: c 312 ARG cc_start: 0.8243 (ttm110) cc_final: 0.7787 (ttm-80) REVERT: c 338 GLU cc_start: 0.9131 (pm20) cc_final: 0.8869 (pm20) REVERT: c 409 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7705 (t0) REVERT: c 506 ASP cc_start: 0.6891 (m-30) cc_final: 0.6561 (m-30) REVERT: d 32 ASP cc_start: 0.8286 (m-30) cc_final: 0.7523 (m-30) REVERT: d 101 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7600 (mt-10) REVERT: d 139 ARG cc_start: 0.8417 (ptm160) cc_final: 0.8175 (ptp-110) REVERT: e 42 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8441 (tm-30) REVERT: e 91 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7612 (mm-30) REVERT: e 206 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7617 (mm-30) REVERT: f 57 TYR cc_start: 0.8759 (t80) cc_final: 0.7582 (t80) REVERT: f 88 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7577 (mm-30) REVERT: f 120 ASP cc_start: 0.7920 (t70) cc_final: 0.7312 (t0) REVERT: g 118 ASN cc_start: 0.8614 (t0) cc_final: 0.8205 (t0) REVERT: g 130 ASN cc_start: 0.8455 (t0) cc_final: 0.8127 (t0) REVERT: g 144 ASN cc_start: 0.8779 (m110) cc_final: 0.8294 (m110) REVERT: h 18 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8204 (tm-30) REVERT: h 123 CYS cc_start: 0.8379 (m) cc_final: 0.8004 (m) REVERT: i 156 GLN cc_start: 0.9204 (mp10) cc_final: 0.8301 (mp10) REVERT: j 23 GLU cc_start: 0.8317 (tp30) cc_final: 0.7762 (tp30) REVERT: j 189 SER cc_start: 0.9104 (p) cc_final: 0.8806 (p) REVERT: j 228 SER cc_start: 0.9165 (t) cc_final: 0.8695 (p) REVERT: j 255 MET cc_start: 0.8829 (mmt) cc_final: 0.8288 (mmt) REVERT: j 271 ASP cc_start: 0.7820 (t0) cc_final: 0.7431 (t0) REVERT: k 3 GLN cc_start: 0.8820 (mp10) cc_final: 0.8060 (mm-40) REVERT: k 22 ASN cc_start: 0.7848 (t0) cc_final: 0.7135 (t0) REVERT: k 24 GLU cc_start: 0.6696 (pm20) cc_final: 0.6349 (mp0) REVERT: k 35 GLU cc_start: 0.8385 (tt0) cc_final: 0.8148 (tp30) REVERT: k 126 ASP cc_start: 0.8334 (t0) cc_final: 0.8004 (t0) REVERT: k 136 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: l 49 GLU cc_start: 0.7586 (tt0) cc_final: 0.7196 (tt0) REVERT: l 59 ASN cc_start: 0.8355 (t0) cc_final: 0.7831 (t0) REVERT: l 102 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7177 (tm-30) REVERT: l 106 HIS cc_start: 0.7802 (t-90) cc_final: 0.7415 (t70) REVERT: l 117 ASP cc_start: 0.8023 (m-30) cc_final: 0.7773 (m-30) REVERT: l 148 ASN cc_start: 0.8689 (m-40) cc_final: 0.7749 (m110) REVERT: b 362 ASN cc_start: 0.9151 (t0) cc_final: 0.8935 (t0) REVERT: b 363 TRP cc_start: 0.9430 (t60) cc_final: 0.8993 (t60) REVERT: b 429 ASP cc_start: 0.8577 (m-30) cc_final: 0.8255 (m-30) REVERT: b 505 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: b 510 LYS cc_start: 0.9265 (pttp) cc_final: 0.9056 (pttp) REVERT: b 535 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7590 (t-90) REVERT: b 551 LYS cc_start: 0.6957 (pttm) cc_final: 0.6433 (pttt) REVERT: b 692 GLU cc_start: 0.7543 (pt0) cc_final: 0.7273 (pt0) REVERT: b 700 MET cc_start: 0.7460 (pmm) cc_final: 0.6971 (mmm) REVERT: b 728 GLU cc_start: 0.7975 (tt0) cc_final: 0.7582 (tt0) REVERT: b 734 GLN cc_start: 0.7872 (mm110) cc_final: 0.7624 (mm-40) REVERT: b 896 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7033 (mm-30) REVERT: b 911 ASN cc_start: 0.8884 (m-40) cc_final: 0.8281 (t0) REVERT: b 926 THR cc_start: 0.9070 (m) cc_final: 0.8853 (m) REVERT: a 37 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8392 (ttmm) REVERT: a 536 LEU cc_start: 0.8941 (mt) cc_final: 0.8627 (mp) REVERT: a 582 SER cc_start: 0.8904 (t) cc_final: 0.8701 (t) REVERT: a 867 ASP cc_start: 0.8355 (t0) cc_final: 0.7952 (t0) REVERT: a 1002 ILE cc_start: 0.8331 (mm) cc_final: 0.7764 (mm) REVERT: a 1020 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8009 (tm-30) REVERT: a 1036 ASP cc_start: 0.8424 (m-30) cc_final: 0.8203 (m-30) REVERT: a 1050 ASP cc_start: 0.8088 (m-30) cc_final: 0.7847 (m-30) REVERT: a 1217 ASP cc_start: 0.8516 (t70) cc_final: 0.8256 (t0) outliers start: 211 outliers final: 189 residues processed: 2759 average time/residue: 1.4192 time to fit residues: 6677.4767 Evaluate side-chains 2860 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 2666 time to evaluate : 7.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 106 HIS Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 455 CYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 653 CYS Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 813 TYR Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 987 HIS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1236 SER Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 244 THR Chi-restraints excluded: chain c residue 263 GLU Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 409 ASN Chi-restraints excluded: chain c residue 517 THR Chi-restraints excluded: chain c residue 559 ILE Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 73 SER Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain e residue 259 SER Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 88 SER Chi-restraints excluded: chain j residue 179 ILE Chi-restraints excluded: chain j residue 197 ASP Chi-restraints excluded: chain j residue 210 MET Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 25 ASN Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 105 SER Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain l residue 138 THR Chi-restraints excluded: chain l residue 171 ILE Chi-restraints excluded: chain b residue 320 SER Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 438 LEU Chi-restraints excluded: chain b residue 457 GLU Chi-restraints excluded: chain b residue 482 CYS Chi-restraints excluded: chain b residue 505 PHE Chi-restraints excluded: chain b residue 535 HIS Chi-restraints excluded: chain b residue 559 VAL Chi-restraints excluded: chain b residue 592 ILE Chi-restraints excluded: chain b residue 653 CYS Chi-restraints excluded: chain b residue 690 GLU Chi-restraints excluded: chain b residue 844 ASN Chi-restraints excluded: chain b residue 895 LEU Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 947 LEU Chi-restraints excluded: chain b residue 987 HIS Chi-restraints excluded: chain b residue 988 VAL Chi-restraints excluded: chain a residue 2 ASN Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 95 VAL Chi-restraints excluded: chain a residue 96 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 173 ASN Chi-restraints excluded: chain a residue 278 ILE Chi-restraints excluded: chain a residue 320 SER Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 342 ILE Chi-restraints excluded: chain a residue 416 ILE Chi-restraints excluded: chain a residue 421 LEU Chi-restraints excluded: chain a residue 427 SER Chi-restraints excluded: chain a residue 452 THR Chi-restraints excluded: chain a residue 533 VAL Chi-restraints excluded: chain a residue 804 SER Chi-restraints excluded: chain a residue 816 ILE Chi-restraints excluded: chain a residue 852 LEU Chi-restraints excluded: chain a residue 882 LEU Chi-restraints excluded: chain a residue 892 ILE Chi-restraints excluded: chain a residue 917 MET Chi-restraints excluded: chain a residue 1001 ASP Chi-restraints excluded: chain a residue 1034 SER Chi-restraints excluded: chain a residue 1198 SER Chi-restraints excluded: chain a residue 1212 ASP Chi-restraints excluded: chain a residue 1236 SER Chi-restraints excluded: chain a residue 1238 THR 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: 0.5980 chunk 11 optimal weight: 40.0000 chunk 591 optimal weight: 2.9990 chunk 327 optimal weight: 0.6980 chunk 678 optimal weight: 1.9990 chunk 549 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 405 optimal weight: 0.9980 chunk 713 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 F 53 ASN H 31 ASN H 49 GLN B 362 ASN ** B 837 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 ** d 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN g 14 ASN g 37 ASN ** j 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 811 ASN ** a 167 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: 0.7359 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 66826 Z= 0.305 Angle : 0.562 7.705 90446 Z= 0.299 Chirality : 0.041 0.209 10438 Planarity : 0.004 0.060 11462 Dihedral : 4.865 57.962 8940 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.25 % Favored : 89.65 % Rotamer: Outliers : 3.88 % Allowed : 18.59 % Favored : 77.53 % 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: -1.24 (0.10), residues: 7496 helix: 1.24 (0.10), residues: 2566 sheet: -0.95 (0.13), residues: 1540 loop : -2.47 (0.10), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 649 HIS 0.008 0.001 HIS E 106 PHE 0.020 0.001 PHE C 151 TYR 0.020 0.001 TYR A 607 ARG 0.008 0.000 ARG G 11 *********************** 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 3004 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 2731 time to evaluate : 7.372 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 GLU cc_start: 0.8117 (tt0) cc_final: 0.7628 (tt0) REVERT: C 312 ARG cc_start: 0.8160 (ttm170) cc_final: 0.7582 (ttm-80) REVERT: C 417 SER cc_start: 0.9111 (p) cc_final: 0.8859 (p) REVERT: C 492 TYR cc_start: 0.8691 (m-10) cc_final: 0.8467 (m-10) REVERT: D 65 SER cc_start: 0.9614 (t) cc_final: 0.9359 (t) REVERT: D 80 LYS cc_start: 0.9075 (tttt) cc_final: 0.8845 (ttmm) REVERT: D 139 ARG cc_start: 0.8463 (ptm160) cc_final: 0.8174 (ptp-110) REVERT: D 143 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7885 (tm-30) REVERT: E 91 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7383 (mm-30) REVERT: E 113 GLU cc_start: 0.7722 (pp20) cc_final: 0.7394 (pp20) REVERT: E 166 LYS cc_start: 0.8959 (tptp) cc_final: 0.8736 (tppt) REVERT: E 185 TYR cc_start: 0.8505 (m-80) cc_final: 0.7340 (m-80) REVERT: E 252 THR cc_start: 0.8791 (t) cc_final: 0.8510 (p) REVERT: F 28 GLU cc_start: 0.8071 (pm20) cc_final: 0.7854 (pm20) REVERT: F 86 THR cc_start: 0.9465 (m) cc_final: 0.9253 (m) REVERT: F 120 ASP cc_start: 0.7920 (t0) cc_final: 0.7040 (t0) REVERT: F 121 GLU cc_start: 0.6959 (mp0) cc_final: 0.5947 (mp0) REVERT: F 136 LYS cc_start: 0.8821 (pttm) cc_final: 0.8492 (ptmm) REVERT: G 80 TYR cc_start: 0.9216 (t80) cc_final: 0.8273 (t80) REVERT: G 101 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8507 (mt0) REVERT: G 130 ASN cc_start: 0.8480 (t0) cc_final: 0.8109 (t0) REVERT: G 133 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7081 (ttp-170) REVERT: G 144 ASN cc_start: 0.8758 (m110) cc_final: 0.8260 (m110) REVERT: H 18 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8297 (tm-30) REVERT: H 100 SER cc_start: 0.7955 (p) cc_final: 0.7186 (p) REVERT: H 115 ASN cc_start: 0.9013 (p0) cc_final: 0.8731 (p0) REVERT: I 23 GLU cc_start: 0.6152 (mp0) cc_final: 0.5776 (mp0) REVERT: I 156 GLN cc_start: 0.8960 (mp10) cc_final: 0.8336 (mp10) REVERT: J 48 GLU cc_start: 0.8603 (tp30) cc_final: 0.8256 (tp30) REVERT: J 68 GLU cc_start: 0.8431 (tp30) cc_final: 0.8184 (tp30) REVERT: J 84 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8049 (mt-10) REVERT: J 255 MET cc_start: 0.8930 (mmt) cc_final: 0.8661 (mmt) REVERT: J 257 GLN cc_start: 0.9258 (pp30) cc_final: 0.9004 (pp30) REVERT: K 3 GLN cc_start: 0.9151 (mp10) cc_final: 0.8616 (mm-40) REVERT: K 22 ASN cc_start: 0.7934 (t160) cc_final: 0.7550 (t160) REVERT: K 25 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8960 (p0) REVERT: K 36 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8896 (mp) REVERT: K 113 MET cc_start: 0.8831 (tpp) cc_final: 0.8603 (tpp) REVERT: L 18 LEU cc_start: 0.8892 (tp) cc_final: 0.8681 (tp) REVERT: L 58 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8443 (mt-10) REVERT: L 59 ASN cc_start: 0.8492 (t0) cc_final: 0.7850 (t0) REVERT: L 61 LYS cc_start: 0.7830 (mmtm) cc_final: 0.7505 (mmtm) REVERT: L 63 LYS cc_start: 0.8246 (tppp) cc_final: 0.8040 (tptm) REVERT: L 101 TYR cc_start: 0.7720 (t80) cc_final: 0.6529 (t80) REVERT: L 113 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7083 (tm-30) REVERT: L 127 LYS cc_start: 0.7111 (mttm) cc_final: 0.6903 (mttm) REVERT: L 174 ILE cc_start: 0.8456 (mt) cc_final: 0.8230 (mt) REVERT: L 200 LYS cc_start: 0.8674 (tttp) cc_final: 0.8152 (ptpt) REVERT: B 276 GLN cc_start: 0.8684 (mt0) cc_final: 0.8202 (pt0) REVERT: B 349 CYS cc_start: 0.9213 (m) cc_final: 0.8885 (m) REVERT: B 355 LEU cc_start: 0.9174 (tp) cc_final: 0.8838 (mp) REVERT: B 780 ASP cc_start: 0.8729 (p0) cc_final: 0.8281 (p0) REVERT: B 911 ASN cc_start: 0.8786 (m-40) cc_final: 0.8097 (t0) REVERT: B 932 ASN cc_start: 0.8163 (m110) cc_final: 0.7732 (m110) REVERT: B 1007 ILE cc_start: 0.8408 (mt) cc_final: 0.8171 (mt) REVERT: B 1009 ASN cc_start: 0.8952 (m110) cc_final: 0.8361 (m110) REVERT: B 1047 HIS cc_start: 0.8419 (t70) cc_final: 0.8219 (t70) REVERT: B 1102 PHE cc_start: 0.7324 (t80) cc_final: 0.7116 (t80) REVERT: A 58 THR cc_start: 0.8712 (m) cc_final: 0.8452 (m) REVERT: A 99 LEU cc_start: 0.8484 (mt) cc_final: 0.8202 (mt) REVERT: A 157 ILE cc_start: 0.9443 (tp) cc_final: 0.9218 (tp) REVERT: A 317 ASP cc_start: 0.8567 (t0) cc_final: 0.8185 (t0) REVERT: A 415 CYS cc_start: 0.8883 (t) cc_final: 0.8453 (t) REVERT: A 501 GLN cc_start: 0.8796 (tp40) cc_final: 0.7980 (tm-30) REVERT: A 563 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 607 TYR cc_start: 0.7949 (m-80) cc_final: 0.7706 (m-80) REVERT: A 817 ASN cc_start: 0.6716 (m110) cc_final: 0.6235 (m110) REVERT: A 867 ASP cc_start: 0.8209 (t0) cc_final: 0.7587 (t0) REVERT: A 899 GLN cc_start: 0.8103 (tt0) cc_final: 0.7515 (tm-30) REVERT: A 913 ASP cc_start: 0.8064 (m-30) cc_final: 0.7757 (m-30) REVERT: A 933 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8351 (tptt) REVERT: A 1002 ILE cc_start: 0.8298 (mm) cc_final: 0.7734 (mm) REVERT: A 1036 ASP cc_start: 0.8157 (m-30) cc_final: 0.7687 (m-30) REVERT: A 1069 GLU cc_start: 0.7529 (pm20) cc_final: 0.7245 (pm20) REVERT: c 312 ARG cc_start: 0.8257 (ttm110) cc_final: 0.7803 (ttm-80) REVERT: c 338 GLU cc_start: 0.9192 (pm20) cc_final: 0.8917 (pm20) REVERT: c 409 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7759 (t0) REVERT: c 506 ASP cc_start: 0.6946 (m-30) cc_final: 0.6591 (m-30) REVERT: d 32 ASP cc_start: 0.8279 (m-30) cc_final: 0.7529 (m-30) REVERT: d 139 ARG cc_start: 0.8418 (ptm160) cc_final: 0.8032 (ttp80) REVERT: e 42 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8363 (tm-30) REVERT: e 185 TYR cc_start: 0.8320 (m-80) cc_final: 0.8084 (m-80) REVERT: e 206 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7596 (mm-30) REVERT: f 88 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7593 (mm-30) REVERT: f 120 ASP cc_start: 0.7941 (t70) cc_final: 0.7362 (t0) REVERT: g 66 ASP cc_start: 0.8126 (m-30) cc_final: 0.7879 (m-30) REVERT: g 118 ASN cc_start: 0.8746 (t0) cc_final: 0.8260 (t0) REVERT: g 130 ASN cc_start: 0.8593 (t0) cc_final: 0.8268 (t0) REVERT: g 144 ASN cc_start: 0.8803 (m110) cc_final: 0.8306 (m110) REVERT: h 75 MET cc_start: 0.8229 (pmm) cc_final: 0.7329 (pmm) REVERT: h 123 CYS cc_start: 0.8318 (m) cc_final: 0.7941 (m) REVERT: i 48 ASP cc_start: 0.7416 (t0) cc_final: 0.6753 (t0) REVERT: i 107 ASN cc_start: 0.8772 (m-40) cc_final: 0.8529 (m-40) REVERT: i 156 GLN cc_start: 0.9198 (mp10) cc_final: 0.8316 (mp10) REVERT: j 23 GLU cc_start: 0.8367 (tp30) cc_final: 0.7796 (tp30) REVERT: j 48 GLU cc_start: 0.8712 (tp30) cc_final: 0.8411 (tp30) REVERT: j 52 PHE cc_start: 0.8260 (t80) cc_final: 0.7990 (t80) REVERT: j 68 GLU cc_start: 0.8173 (tp30) cc_final: 0.7909 (tp30) REVERT: j 160 GLU cc_start: 0.8015 (pm20) cc_final: 0.7734 (pm20) REVERT: j 189 SER cc_start: 0.9116 (p) cc_final: 0.8820 (p) REVERT: j 228 SER cc_start: 0.9271 (t) cc_final: 0.8809 (p) REVERT: j 255 MET cc_start: 0.8872 (mmt) cc_final: 0.8317 (mmt) REVERT: j 271 ASP cc_start: 0.7874 (t0) cc_final: 0.7480 (t0) REVERT: k 3 GLN cc_start: 0.8873 (mp10) cc_final: 0.8041 (mm-40) REVERT: k 22 ASN cc_start: 0.7987 (t0) cc_final: 0.7378 (t0) REVERT: k 24 GLU cc_start: 0.6773 (pm20) cc_final: 0.6257 (mp0) REVERT: k 35 GLU cc_start: 0.8413 (tt0) cc_final: 0.8169 (tp30) REVERT: k 126 ASP cc_start: 0.8449 (t0) cc_final: 0.8120 (t0) REVERT: k 136 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7571 (tp30) REVERT: l 10 TYR cc_start: 0.9356 (p90) cc_final: 0.9125 (p90) REVERT: l 49 GLU cc_start: 0.7404 (tt0) cc_final: 0.6943 (tt0) REVERT: l 59 ASN cc_start: 0.8337 (t0) cc_final: 0.7850 (t0) REVERT: l 94 ASP cc_start: 0.7753 (t0) cc_final: 0.7539 (t0) REVERT: l 102 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7172 (tm-30) REVERT: l 106 HIS cc_start: 0.7864 (t-90) cc_final: 0.7482 (t70) REVERT: l 148 ASN cc_start: 0.8656 (m-40) cc_final: 0.7642 (m110) REVERT: b 429 ASP cc_start: 0.8631 (m-30) cc_final: 0.8306 (m-30) REVERT: b 505 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: b 551 LYS cc_start: 0.7076 (pttm) cc_final: 0.6556 (pttt) REVERT: b 615 ILE cc_start: 0.8802 (pt) cc_final: 0.8582 (pt) REVERT: b 692 GLU cc_start: 0.7488 (pt0) cc_final: 0.7223 (pt0) REVERT: b 700 MET cc_start: 0.7345 (pmm) cc_final: 0.6769 (mmm) REVERT: b 728 GLU cc_start: 0.7898 (tt0) cc_final: 0.7466 (tt0) REVERT: b 734 GLN cc_start: 0.7913 (mm110) cc_final: 0.7658 (mm-40) REVERT: b 896 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7091 (mm-30) REVERT: b 911 ASN cc_start: 0.8856 (m-40) cc_final: 0.8216 (t0) REVERT: b 926 THR cc_start: 0.9073 (m) cc_final: 0.8853 (m) REVERT: b 1102 PHE cc_start: 0.7843 (t80) cc_final: 0.7608 (t80) REVERT: a 37 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8359 (ttmm) REVERT: a 536 LEU cc_start: 0.8943 (mt) cc_final: 0.8611 (mp) REVERT: a 582 SER cc_start: 0.8939 (t) cc_final: 0.8731 (t) REVERT: a 801 LEU cc_start: 0.7304 (tp) cc_final: 0.7087 (tp) REVERT: a 867 ASP cc_start: 0.8464 (t0) cc_final: 0.8098 (t0) REVERT: a 913 ASP cc_start: 0.8408 (m-30) cc_final: 0.8087 (m-30) REVERT: a 933 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8667 (ttmm) REVERT: a 1002 ILE cc_start: 0.8399 (mm) cc_final: 0.7854 (mm) REVERT: a 1020 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8042 (tm-30) REVERT: a 1036 ASP cc_start: 0.8468 (m-30) cc_final: 0.8258 (m-30) REVERT: a 1217 ASP cc_start: 0.8486 (t70) cc_final: 0.8247 (t0) outliers start: 273 outliers final: 240 residues processed: 2801 average time/residue: 1.3228 time to fit residues: 6266.8455 Evaluate side-chains 2918 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 2672 time to evaluate : 7.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 106 HIS Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 653 CYS Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 813 TYR Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 987 HIS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1236 SER Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 232 LEU Chi-restraints excluded: chain c residue 244 THR Chi-restraints excluded: chain c residue 263 GLU Chi-restraints excluded: chain c residue 269 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 409 ASN Chi-restraints excluded: chain c residue 500 ILE Chi-restraints excluded: chain c residue 517 THR Chi-restraints excluded: chain c residue 559 ILE Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 68 GLN Chi-restraints excluded: chain d residue 73 SER Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain e residue 238 CYS Chi-restraints excluded: chain e residue 259 SER Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain g residue 14 ASN Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 137 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 69 TYR Chi-restraints excluded: chain h residue 144 SER Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 209 GLU Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 45 ILE Chi-restraints excluded: chain j residue 88 SER Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 174 LEU Chi-restraints excluded: chain j residue 179 ILE Chi-restraints excluded: chain j residue 197 ASP Chi-restraints excluded: chain j residue 210 MET Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 25 ASN Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 105 SER Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 173 LEU Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain l residue 138 THR Chi-restraints excluded: chain l residue 143 ASN Chi-restraints excluded: chain l residue 161 ASP Chi-restraints excluded: chain l residue 171 ILE Chi-restraints excluded: chain b residue 313 ILE Chi-restraints excluded: chain b residue 320 SER Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 438 LEU Chi-restraints excluded: chain b residue 455 CYS Chi-restraints excluded: chain b residue 457 GLU Chi-restraints excluded: chain b residue 482 CYS Chi-restraints excluded: chain b residue 505 PHE Chi-restraints excluded: chain b residue 559 VAL Chi-restraints excluded: chain b residue 592 ILE Chi-restraints excluded: chain b residue 643 ASP Chi-restraints excluded: chain b residue 653 CYS Chi-restraints excluded: chain b residue 690 GLU Chi-restraints excluded: chain b residue 747 THR Chi-restraints excluded: chain b residue 801 SER Chi-restraints excluded: chain b residue 844 ASN Chi-restraints excluded: chain b residue 934 CYS Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 947 LEU Chi-restraints excluded: chain b residue 987 HIS Chi-restraints excluded: chain b residue 988 VAL Chi-restraints excluded: chain b residue 1078 VAL Chi-restraints excluded: chain b residue 1090 VAL Chi-restraints excluded: chain a residue 2 ASN Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 96 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 173 ASN Chi-restraints excluded: chain a residue 278 ILE Chi-restraints excluded: chain a residue 320 SER Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 342 ILE Chi-restraints excluded: chain a residue 416 ILE Chi-restraints excluded: chain a residue 421 LEU Chi-restraints excluded: chain a residue 427 SER Chi-restraints excluded: chain a residue 452 THR Chi-restraints excluded: chain a residue 533 VAL Chi-restraints excluded: chain a residue 804 SER Chi-restraints excluded: chain a residue 816 ILE Chi-restraints excluded: chain a residue 843 ILE Chi-restraints excluded: chain a residue 852 LEU Chi-restraints excluded: chain a residue 873 PHE Chi-restraints excluded: chain a residue 882 LEU Chi-restraints excluded: chain a residue 892 ILE Chi-restraints excluded: chain a residue 900 MET Chi-restraints excluded: chain a residue 917 MET Chi-restraints excluded: chain a residue 963 ASP Chi-restraints excluded: chain a residue 970 MET Chi-restraints excluded: chain a residue 985 ILE Chi-restraints excluded: chain a residue 1001 ASP Chi-restraints excluded: chain a residue 1003 ILE Chi-restraints excluded: chain a residue 1034 SER Chi-restraints excluded: chain a residue 1198 SER Chi-restraints excluded: chain a residue 1212 ASP Chi-restraints excluded: chain a residue 1236 SER Chi-restraints excluded: chain a residue 1238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 267 optimal weight: 1.9990 chunk 715 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 466 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 795 optimal weight: 1.9990 chunk 660 optimal weight: 1.9990 chunk 368 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 417 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 L 162 ASN B 362 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** 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 h 126 GLN ** j 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 535 HIS ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 66826 Z= 0.307 Angle : 0.560 7.570 90446 Z= 0.299 Chirality : 0.040 0.180 10438 Planarity : 0.003 0.054 11462 Dihedral : 4.863 53.009 8940 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.43 % Favored : 89.45 % Rotamer: Outliers : 3.99 % Allowed : 19.60 % Favored : 76.41 % 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: -1.26 (0.10), residues: 7496 helix: 1.25 (0.10), residues: 2558 sheet: -1.01 (0.13), residues: 1542 loop : -2.48 (0.10), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 889 HIS 0.007 0.001 HIS b 535 PHE 0.016 0.001 PHE A 731 TYR 0.020 0.001 TYR b 813 ARG 0.008 0.000 ARG L 112 *********************** 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 3016 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 2735 time to evaluate : 7.977 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 GLU cc_start: 0.8131 (tt0) cc_final: 0.7635 (tt0) REVERT: C 312 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7584 (ttm-80) REVERT: C 417 SER cc_start: 0.9124 (p) cc_final: 0.8865 (p) REVERT: C 492 TYR cc_start: 0.8692 (m-10) cc_final: 0.8466 (m-10) REVERT: D 65 SER cc_start: 0.9612 (t) cc_final: 0.9350 (t) REVERT: D 80 LYS cc_start: 0.9073 (tttt) cc_final: 0.8818 (ttmm) REVERT: D 139 ARG cc_start: 0.8459 (ptm160) cc_final: 0.8084 (ptp-110) REVERT: D 143 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7920 (tm-30) REVERT: E 91 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7380 (mm-30) REVERT: E 113 GLU cc_start: 0.7736 (pp20) cc_final: 0.7402 (pp20) REVERT: E 185 TYR cc_start: 0.8528 (m-80) cc_final: 0.7362 (m-80) REVERT: F 28 GLU cc_start: 0.8070 (pm20) cc_final: 0.7869 (pm20) REVERT: F 86 THR cc_start: 0.9482 (m) cc_final: 0.9281 (m) REVERT: F 120 ASP cc_start: 0.7935 (t0) cc_final: 0.7049 (t0) REVERT: F 121 GLU cc_start: 0.6969 (mp0) cc_final: 0.5948 (mp0) REVERT: F 126 ASP cc_start: 0.7833 (t0) cc_final: 0.7569 (t0) REVERT: F 136 LYS cc_start: 0.8807 (pttm) cc_final: 0.8506 (ptmm) REVERT: G 80 TYR cc_start: 0.9223 (t80) cc_final: 0.8253 (t80) REVERT: G 101 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8573 (mt0) REVERT: G 130 ASN cc_start: 0.8528 (t0) cc_final: 0.8166 (t0) REVERT: G 133 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7169 (ttp-170) REVERT: G 144 ASN cc_start: 0.8729 (m110) cc_final: 0.8204 (m110) REVERT: H 100 SER cc_start: 0.8211 (p) cc_final: 0.7204 (p) REVERT: H 115 ASN cc_start: 0.9048 (p0) cc_final: 0.8772 (p0) REVERT: I 23 GLU cc_start: 0.6147 (mp0) cc_final: 0.5753 (mp0) REVERT: I 156 GLN cc_start: 0.8922 (mp10) cc_final: 0.8271 (mp10) REVERT: J 48 GLU cc_start: 0.8621 (tp30) cc_final: 0.8280 (tp30) REVERT: J 68 GLU cc_start: 0.8408 (tp30) cc_final: 0.8160 (tp30) REVERT: J 255 MET cc_start: 0.8936 (mmt) cc_final: 0.8662 (mmt) REVERT: J 257 GLN cc_start: 0.9248 (pp30) cc_final: 0.8987 (pp30) REVERT: K 3 GLN cc_start: 0.9234 (mp10) cc_final: 0.8667 (mm-40) REVERT: K 22 ASN cc_start: 0.8009 (t160) cc_final: 0.7683 (t160) REVERT: K 25 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8962 (p0) REVERT: K 36 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8919 (mp) REVERT: K 113 MET cc_start: 0.8820 (tpp) cc_final: 0.8574 (tpp) REVERT: L 18 LEU cc_start: 0.8865 (tp) cc_final: 0.8651 (tp) REVERT: L 58 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8466 (mt-10) REVERT: L 59 ASN cc_start: 0.8481 (t0) cc_final: 0.7827 (t0) REVERT: L 101 TYR cc_start: 0.7718 (t80) cc_final: 0.6533 (t80) REVERT: L 113 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6976 (tm-30) REVERT: L 162 ASN cc_start: 0.7645 (t0) cc_final: 0.7201 (t0) REVERT: L 200 LYS cc_start: 0.8682 (tttp) cc_final: 0.8138 (ptpt) REVERT: B 276 GLN cc_start: 0.8685 (mt0) cc_final: 0.8209 (pt0) REVERT: B 349 CYS cc_start: 0.9197 (m) cc_final: 0.8877 (m) REVERT: B 355 LEU cc_start: 0.9171 (tp) cc_final: 0.8833 (mp) REVERT: B 654 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7612 (mmmm) REVERT: B 764 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7776 (mm-40) REVERT: B 780 ASP cc_start: 0.8731 (p0) cc_final: 0.8286 (p0) REVERT: B 911 ASN cc_start: 0.8771 (m-40) cc_final: 0.8036 (t0) REVERT: B 932 ASN cc_start: 0.8143 (m110) cc_final: 0.7706 (m110) REVERT: B 1009 ASN cc_start: 0.8948 (m110) cc_final: 0.8327 (m110) REVERT: B 1068 LEU cc_start: 0.8984 (mt) cc_final: 0.8758 (mt) REVERT: B 1102 PHE cc_start: 0.7347 (t80) cc_final: 0.7107 (t80) REVERT: A 58 THR cc_start: 0.8767 (m) cc_final: 0.8503 (m) REVERT: A 99 LEU cc_start: 0.8603 (mt) cc_final: 0.8330 (mt) REVERT: A 157 ILE cc_start: 0.9438 (tp) cc_final: 0.9224 (tp) REVERT: A 317 ASP cc_start: 0.8591 (t0) cc_final: 0.8202 (t0) REVERT: A 415 CYS cc_start: 0.8895 (t) cc_final: 0.8451 (t) REVERT: A 563 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 817 ASN cc_start: 0.6626 (m110) cc_final: 0.6124 (m110) REVERT: A 867 ASP cc_start: 0.8228 (t0) cc_final: 0.7607 (t0) REVERT: A 899 GLN cc_start: 0.8147 (tt0) cc_final: 0.7542 (tm-30) REVERT: A 913 ASP cc_start: 0.8143 (m-30) cc_final: 0.7835 (m-30) REVERT: A 933 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8351 (tptt) REVERT: A 994 THR cc_start: 0.8987 (p) cc_final: 0.8716 (p) REVERT: A 1002 ILE cc_start: 0.8291 (mm) cc_final: 0.7727 (mm) REVERT: A 1036 ASP cc_start: 0.8164 (m-30) cc_final: 0.7696 (m-30) REVERT: A 1069 GLU cc_start: 0.7480 (pm20) cc_final: 0.7238 (pm20) REVERT: c 278 ASP cc_start: 0.8612 (m-30) cc_final: 0.8339 (t0) REVERT: c 312 ARG cc_start: 0.8228 (ttm110) cc_final: 0.7781 (ttm-80) REVERT: c 338 GLU cc_start: 0.9146 (pm20) cc_final: 0.8900 (pm20) REVERT: c 409 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7777 (t0) REVERT: c 506 ASP cc_start: 0.6965 (m-30) cc_final: 0.6590 (m-30) REVERT: d 32 ASP cc_start: 0.8280 (m-30) cc_final: 0.7523 (m-30) REVERT: d 139 ARG cc_start: 0.8416 (ptm160) cc_final: 0.8030 (ttp80) REVERT: e 42 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8356 (tm-30) REVERT: e 185 TYR cc_start: 0.8349 (m-80) cc_final: 0.8118 (m-80) REVERT: e 206 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7602 (mm-30) REVERT: f 88 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7701 (mm-30) REVERT: f 120 ASP cc_start: 0.7970 (t70) cc_final: 0.7394 (t0) REVERT: g 66 ASP cc_start: 0.8109 (m-30) cc_final: 0.7898 (m-30) REVERT: g 118 ASN cc_start: 0.8729 (t0) cc_final: 0.8174 (t0) REVERT: g 130 ASN cc_start: 0.8506 (t0) cc_final: 0.8098 (t0) REVERT: g 144 ASN cc_start: 0.8771 (m110) cc_final: 0.8258 (m110) REVERT: h 75 MET cc_start: 0.8244 (pmm) cc_final: 0.7307 (pmm) REVERT: h 123 CYS cc_start: 0.8296 (m) cc_final: 0.7898 (m) REVERT: i 48 ASP cc_start: 0.7435 (t0) cc_final: 0.6767 (t0) REVERT: i 107 ASN cc_start: 0.8774 (m-40) cc_final: 0.8527 (m-40) REVERT: i 156 GLN cc_start: 0.9217 (mp10) cc_final: 0.8327 (mp10) REVERT: j 23 GLU cc_start: 0.8207 (tp30) cc_final: 0.7657 (tp30) REVERT: j 48 GLU cc_start: 0.8743 (tp30) cc_final: 0.8499 (tp30) REVERT: j 52 PHE cc_start: 0.8308 (t80) cc_final: 0.8068 (t80) REVERT: j 68 GLU cc_start: 0.8387 (tp30) cc_final: 0.8053 (tp30) REVERT: j 189 SER cc_start: 0.9117 (p) cc_final: 0.8821 (p) REVERT: j 271 ASP cc_start: 0.7896 (t0) cc_final: 0.7594 (t0) REVERT: k 3 GLN cc_start: 0.8895 (mp10) cc_final: 0.8032 (mm-40) REVERT: k 22 ASN cc_start: 0.7999 (t0) cc_final: 0.7376 (t0) REVERT: k 24 GLU cc_start: 0.6826 (pm20) cc_final: 0.6278 (mp0) REVERT: k 27 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8299 (mm-40) REVERT: k 35 GLU cc_start: 0.8414 (tt0) cc_final: 0.8184 (tp30) REVERT: k 126 ASP cc_start: 0.8472 (t0) cc_final: 0.8144 (t0) REVERT: k 136 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: l 10 TYR cc_start: 0.9365 (p90) cc_final: 0.9161 (p90) REVERT: l 49 GLU cc_start: 0.7455 (tt0) cc_final: 0.6972 (tt0) REVERT: l 59 ASN cc_start: 0.8335 (t0) cc_final: 0.7851 (t0) REVERT: l 94 ASP cc_start: 0.7792 (t0) cc_final: 0.7591 (t0) REVERT: l 102 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7170 (tm-30) REVERT: l 106 HIS cc_start: 0.7821 (t-90) cc_final: 0.7437 (t70) REVERT: l 147 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7144 (mm-30) REVERT: l 148 ASN cc_start: 0.8640 (m-40) cc_final: 0.7620 (m110) REVERT: b 354 GLU cc_start: 0.8726 (tp30) cc_final: 0.8477 (tp30) REVERT: b 363 TRP cc_start: 0.9460 (t60) cc_final: 0.8987 (t60) REVERT: b 429 ASP cc_start: 0.8597 (m-30) cc_final: 0.8274 (m-30) REVERT: b 506 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8465 (tt) REVERT: b 510 LYS cc_start: 0.9238 (pttp) cc_final: 0.9034 (pttp) REVERT: b 615 ILE cc_start: 0.8732 (pt) cc_final: 0.8515 (pt) REVERT: b 692 GLU cc_start: 0.7587 (pt0) cc_final: 0.7313 (pt0) REVERT: b 728 GLU cc_start: 0.7872 (tt0) cc_final: 0.7603 (tt0) REVERT: b 734 GLN cc_start: 0.7944 (mm110) cc_final: 0.7681 (mm-40) REVERT: b 746 PHE cc_start: 0.9249 (p90) cc_final: 0.8951 (p90) REVERT: b 891 THR cc_start: 0.8842 (t) cc_final: 0.8486 (p) REVERT: b 896 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7132 (mm-30) REVERT: b 911 ASN cc_start: 0.8870 (m-40) cc_final: 0.8229 (t0) REVERT: b 926 THR cc_start: 0.9079 (m) cc_final: 0.8856 (m) REVERT: b 1102 PHE cc_start: 0.7837 (t80) cc_final: 0.7580 (t80) REVERT: a 37 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8339 (ttmm) REVERT: a 124 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8556 (p0) REVERT: a 536 LEU cc_start: 0.8940 (mt) cc_final: 0.8612 (mp) REVERT: a 629 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: a 801 LEU cc_start: 0.7233 (tp) cc_final: 0.7025 (tp) REVERT: a 867 ASP cc_start: 0.8531 (t0) cc_final: 0.8173 (t0) REVERT: a 879 ASN cc_start: 0.8618 (t0) cc_final: 0.8329 (t0) REVERT: a 913 ASP cc_start: 0.8410 (m-30) cc_final: 0.8102 (m-30) REVERT: a 933 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8670 (ttmm) REVERT: a 1002 ILE cc_start: 0.8420 (mm) cc_final: 0.7884 (mm) REVERT: a 1020 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8055 (tm-30) REVERT: a 1036 ASP cc_start: 0.8480 (m-30) cc_final: 0.8262 (m-30) REVERT: a 1217 ASP cc_start: 0.8484 (t70) cc_final: 0.8243 (t0) outliers start: 281 outliers final: 254 residues processed: 2815 average time/residue: 1.4263 time to fit residues: 6844.2169 Evaluate side-chains 2926 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 2664 time to evaluate : 7.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 TYR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 653 CYS Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 813 TYR Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 987 HIS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1236 SER Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 232 LEU Chi-restraints excluded: chain c residue 244 THR Chi-restraints excluded: chain c residue 263 GLU Chi-restraints excluded: chain c residue 269 ILE Chi-restraints excluded: chain c residue 337 THR Chi-restraints excluded: chain c residue 409 ASN Chi-restraints excluded: chain c residue 417 SER Chi-restraints excluded: chain c residue 517 THR Chi-restraints excluded: chain c residue 559 ILE Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 68 GLN Chi-restraints excluded: chain d residue 73 SER Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain e residue 199 LEU Chi-restraints excluded: chain e residue 259 SER Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 91 SER Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 137 THR Chi-restraints excluded: chain g residue 140 ILE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 48 SER Chi-restraints excluded: chain h residue 69 TYR Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain h residue 195 SER Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 209 GLU Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 165 SER Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 45 ILE Chi-restraints excluded: chain j residue 88 SER Chi-restraints excluded: chain j residue 174 LEU Chi-restraints excluded: chain j residue 179 ILE Chi-restraints excluded: chain j residue 210 MET Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 19 GLU Chi-restraints excluded: chain k residue 25 ASN Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 105 SER Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 173 LEU Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain l residue 138 THR Chi-restraints excluded: chain l residue 143 ASN Chi-restraints excluded: chain l residue 161 ASP Chi-restraints excluded: chain l residue 171 ILE Chi-restraints excluded: chain b residue 313 ILE Chi-restraints excluded: chain b residue 320 SER Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 361 ASP Chi-restraints excluded: chain b residue 438 LEU Chi-restraints excluded: chain b residue 455 CYS Chi-restraints excluded: chain b residue 457 GLU Chi-restraints excluded: chain b residue 482 CYS Chi-restraints excluded: chain b residue 506 LEU Chi-restraints excluded: chain b residue 535 HIS Chi-restraints excluded: chain b residue 559 VAL Chi-restraints excluded: chain b residue 592 ILE Chi-restraints excluded: chain b residue 643 ASP Chi-restraints excluded: chain b residue 653 CYS Chi-restraints excluded: chain b residue 690 GLU Chi-restraints excluded: chain b residue 747 THR Chi-restraints excluded: chain b residue 801 SER Chi-restraints excluded: chain b residue 844 ASN Chi-restraints excluded: chain b residue 934 CYS Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 947 LEU Chi-restraints excluded: chain b residue 987 HIS Chi-restraints excluded: chain b residue 988 VAL Chi-restraints excluded: chain b residue 1078 VAL Chi-restraints excluded: chain b residue 1090 VAL Chi-restraints excluded: chain a residue 2 ASN Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 96 ILE Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 173 ASN Chi-restraints excluded: chain a residue 278 ILE Chi-restraints excluded: chain a residue 320 SER Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 342 ILE Chi-restraints excluded: chain a residue 421 LEU Chi-restraints excluded: chain a residue 427 SER Chi-restraints excluded: chain a residue 452 THR Chi-restraints excluded: chain a residue 500 LEU Chi-restraints excluded: chain a residue 533 VAL Chi-restraints excluded: chain a residue 629 ASP Chi-restraints excluded: chain a residue 804 SER Chi-restraints excluded: chain a residue 816 ILE Chi-restraints excluded: chain a residue 852 LEU Chi-restraints excluded: chain a residue 873 PHE Chi-restraints excluded: chain a residue 882 LEU Chi-restraints excluded: chain a residue 892 ILE Chi-restraints excluded: chain a residue 900 MET Chi-restraints excluded: chain a residue 917 MET Chi-restraints excluded: chain a residue 963 ASP Chi-restraints excluded: chain a residue 985 ILE Chi-restraints excluded: chain a residue 1001 ASP Chi-restraints excluded: chain a residue 1034 SER Chi-restraints excluded: chain a residue 1078 VAL Chi-restraints excluded: chain a residue 1092 ASN Chi-restraints excluded: chain a residue 1198 SER Chi-restraints excluded: chain a residue 1212 ASP Chi-restraints excluded: chain a residue 1236 SER Chi-restraints excluded: chain a residue 1238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 766 optimal weight: 0.0770 chunk 89 optimal weight: 1.9990 chunk 453 optimal weight: 0.5980 chunk 580 optimal weight: 3.9990 chunk 449 optimal weight: 0.9990 chunk 669 optimal weight: 0.0050 chunk 444 optimal weight: 0.4980 chunk 792 optimal weight: 0.7980 chunk 495 optimal weight: 0.9990 chunk 483 optimal weight: 1.9990 chunk 365 optimal weight: 1.9990 overall best weight: 0.3952 ------------------------------------------------------------------------------- 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 K 54 GLN B 362 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** B1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN ** j 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 362 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 66826 Z= 0.159 Angle : 0.528 7.401 90446 Z= 0.277 Chirality : 0.040 0.178 10438 Planarity : 0.003 0.049 11462 Dihedral : 4.733 50.381 8940 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.12 % Favored : 90.77 % Rotamer: Outliers : 3.41 % Allowed : 20.58 % Favored : 76.02 % 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: -1.05 (0.10), residues: 7496 helix: 1.42 (0.11), residues: 2548 sheet: -0.88 (0.13), residues: 1540 loop : -2.34 (0.10), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 21 HIS 0.011 0.001 HIS b 535 PHE 0.015 0.001 PHE C 247 TYR 0.019 0.001 TYR b 813 ARG 0.006 0.000 ARG A 307 *********************** 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 3018 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 2778 time to evaluate : 7.440 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 GLU cc_start: 0.8114 (tt0) cc_final: 0.7602 (tt0) REVERT: C 312 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7586 (ttm-80) REVERT: C 417 SER cc_start: 0.9119 (p) cc_final: 0.8856 (p) REVERT: C 492 TYR cc_start: 0.8661 (m-10) cc_final: 0.8450 (m-10) REVERT: D 64 LYS cc_start: 0.9086 (mmtp) cc_final: 0.8718 (mmtp) REVERT: D 65 SER cc_start: 0.9580 (t) cc_final: 0.9298 (t) REVERT: D 80 LYS cc_start: 0.9055 (tttt) cc_final: 0.8840 (ttmm) REVERT: D 139 ARG cc_start: 0.8414 (ptm160) cc_final: 0.8122 (ptp-110) REVERT: D 143 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 42 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8416 (tm-30) REVERT: E 91 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7386 (mm-30) REVERT: E 113 GLU cc_start: 0.7719 (pp20) cc_final: 0.7387 (pp20) REVERT: E 114 GLU cc_start: 0.8411 (pp20) cc_final: 0.8152 (pp20) REVERT: E 157 MET cc_start: 0.9338 (mmt) cc_final: 0.9121 (mmt) REVERT: E 185 TYR cc_start: 0.8519 (m-80) cc_final: 0.7373 (m-80) REVERT: F 120 ASP cc_start: 0.7892 (t0) cc_final: 0.7004 (t0) REVERT: F 121 GLU cc_start: 0.6956 (mp0) cc_final: 0.5910 (mp0) REVERT: F 136 LYS cc_start: 0.8781 (pttm) cc_final: 0.8456 (ptmm) REVERT: G 80 TYR cc_start: 0.9201 (t80) cc_final: 0.8161 (t80) REVERT: G 101 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8510 (mt0) REVERT: G 130 ASN cc_start: 0.8495 (t0) cc_final: 0.8092 (t0) REVERT: G 144 ASN cc_start: 0.8676 (m110) cc_final: 0.8181 (m110) REVERT: H 100 SER cc_start: 0.8284 (p) cc_final: 0.7507 (p) REVERT: H 115 ASN cc_start: 0.9016 (p0) cc_final: 0.8704 (p0) REVERT: I 23 GLU cc_start: 0.6145 (mp0) cc_final: 0.5755 (mp0) REVERT: I 43 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: I 156 GLN cc_start: 0.8836 (mp10) cc_final: 0.8306 (mp10) REVERT: J 48 GLU cc_start: 0.8590 (tp30) cc_final: 0.8247 (tp30) REVERT: J 255 MET cc_start: 0.8944 (mmt) cc_final: 0.8674 (mmt) REVERT: J 257 GLN cc_start: 0.9254 (pp30) cc_final: 0.8858 (pp30) REVERT: K 3 GLN cc_start: 0.9205 (mp10) cc_final: 0.8655 (mm-40) REVERT: K 22 ASN cc_start: 0.7995 (t160) cc_final: 0.7531 (t160) REVERT: K 113 MET cc_start: 0.8643 (tpp) cc_final: 0.8379 (tpp) REVERT: L 58 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8439 (mt-10) REVERT: L 59 ASN cc_start: 0.8480 (t0) cc_final: 0.7805 (t0) REVERT: L 101 TYR cc_start: 0.7697 (t80) cc_final: 0.6453 (t80) REVERT: L 113 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6883 (tm-30) REVERT: L 162 ASN cc_start: 0.7741 (t0) cc_final: 0.7343 (t0) REVERT: L 200 LYS cc_start: 0.8666 (tttp) cc_final: 0.8131 (ptpt) REVERT: B 276 GLN cc_start: 0.8667 (mt0) cc_final: 0.8191 (pt0) REVERT: B 349 CYS cc_start: 0.9176 (m) cc_final: 0.8849 (m) REVERT: B 355 LEU cc_start: 0.9125 (tp) cc_final: 0.8791 (mp) REVERT: B 654 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7586 (mmmm) REVERT: B 780 ASP cc_start: 0.8732 (p0) cc_final: 0.8289 (p0) REVERT: B 802 SER cc_start: 0.8283 (p) cc_final: 0.7801 (p) REVERT: B 911 ASN cc_start: 0.8785 (m-40) cc_final: 0.8101 (t0) REVERT: B 932 ASN cc_start: 0.7942 (m110) cc_final: 0.7505 (m110) REVERT: B 1009 ASN cc_start: 0.8948 (m110) cc_final: 0.8307 (m110) REVERT: A 58 THR cc_start: 0.8674 (m) cc_final: 0.8430 (m) REVERT: A 99 LEU cc_start: 0.8529 (mt) cc_final: 0.8257 (mt) REVERT: A 317 ASP cc_start: 0.8565 (t0) cc_final: 0.8178 (t0) REVERT: A 415 CYS cc_start: 0.8866 (t) cc_final: 0.8417 (t) REVERT: A 563 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 656 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7409 (mt-10) REVERT: A 817 ASN cc_start: 0.6637 (m110) cc_final: 0.6136 (m110) REVERT: A 867 ASP cc_start: 0.8171 (t0) cc_final: 0.7556 (t0) REVERT: A 899 GLN cc_start: 0.8126 (tt0) cc_final: 0.7494 (tm-30) REVERT: A 913 ASP cc_start: 0.8147 (m-30) cc_final: 0.7792 (m-30) REVERT: A 933 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8321 (tptt) REVERT: A 966 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8727 (pt) REVERT: A 994 THR cc_start: 0.8918 (p) cc_final: 0.8668 (p) REVERT: A 1020 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 1036 ASP cc_start: 0.8142 (m-30) cc_final: 0.7666 (m-30) REVERT: A 1069 GLU cc_start: 0.7465 (pm20) cc_final: 0.7232 (pm20) REVERT: c 278 ASP cc_start: 0.8585 (m-30) cc_final: 0.8318 (t0) REVERT: c 312 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7783 (ttm-80) REVERT: c 338 GLU cc_start: 0.9099 (pm20) cc_final: 0.8875 (pm20) REVERT: c 409 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7802 (t0) REVERT: c 506 ASP cc_start: 0.6937 (m-30) cc_final: 0.6553 (m-30) REVERT: d 32 ASP cc_start: 0.8224 (m-30) cc_final: 0.7460 (m-30) REVERT: d 139 ARG cc_start: 0.8391 (ptm160) cc_final: 0.7998 (ttp80) REVERT: e 42 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8284 (tm-30) REVERT: e 165 TRP cc_start: 0.8383 (m100) cc_final: 0.7567 (m100) REVERT: e 185 TYR cc_start: 0.8290 (m-80) cc_final: 0.8051 (m-80) REVERT: e 206 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7576 (mm-30) REVERT: f 88 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7664 (mm-30) REVERT: f 120 ASP cc_start: 0.7877 (t70) cc_final: 0.7279 (t0) REVERT: g 66 ASP cc_start: 0.8072 (m-30) cc_final: 0.7871 (m-30) REVERT: g 118 ASN cc_start: 0.8615 (t0) cc_final: 0.8089 (t0) REVERT: g 130 ASN cc_start: 0.8578 (t0) cc_final: 0.8255 (t0) REVERT: g 144 ASN cc_start: 0.8683 (m110) cc_final: 0.8214 (m110) REVERT: h 75 MET cc_start: 0.8220 (pmm) cc_final: 0.7405 (pmm) REVERT: h 123 CYS cc_start: 0.8235 (m) cc_final: 0.7851 (m) REVERT: i 107 ASN cc_start: 0.8745 (m-40) cc_final: 0.8506 (m-40) REVERT: i 155 VAL cc_start: 0.8967 (m) cc_final: 0.8585 (m) REVERT: i 156 GLN cc_start: 0.9206 (mp10) cc_final: 0.8335 (mp10) REVERT: j 23 GLU cc_start: 0.8299 (tp30) cc_final: 0.7704 (tp30) REVERT: j 48 GLU cc_start: 0.8691 (tp30) cc_final: 0.8365 (tp30) REVERT: j 68 GLU cc_start: 0.8407 (tp30) cc_final: 0.8048 (tp30) REVERT: j 189 SER cc_start: 0.9091 (p) cc_final: 0.8785 (p) REVERT: j 271 ASP cc_start: 0.8031 (t0) cc_final: 0.7610 (t0) REVERT: k 3 GLN cc_start: 0.8892 (mp10) cc_final: 0.8037 (mm-40) REVERT: k 22 ASN cc_start: 0.7992 (t0) cc_final: 0.7353 (t0) REVERT: k 24 GLU cc_start: 0.6809 (pm20) cc_final: 0.6250 (mp0) REVERT: k 27 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8263 (mm-40) REVERT: k 35 GLU cc_start: 0.8381 (tt0) cc_final: 0.8119 (tp30) REVERT: k 126 ASP cc_start: 0.8415 (t0) cc_final: 0.8073 (t0) REVERT: k 136 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: l 49 GLU cc_start: 0.7418 (tt0) cc_final: 0.6738 (tt0) REVERT: l 59 ASN cc_start: 0.8361 (t0) cc_final: 0.7797 (t0) REVERT: l 102 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7135 (tm-30) REVERT: l 106 HIS cc_start: 0.7809 (t-90) cc_final: 0.7430 (t70) REVERT: l 147 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7041 (mm-30) REVERT: l 148 ASN cc_start: 0.8598 (m-40) cc_final: 0.7553 (m110) REVERT: b 354 GLU cc_start: 0.8719 (tp30) cc_final: 0.8433 (tp30) REVERT: b 363 TRP cc_start: 0.9449 (t60) cc_final: 0.8937 (t60) REVERT: b 429 ASP cc_start: 0.8554 (m-30) cc_final: 0.8216 (m-30) REVERT: b 458 TYR cc_start: 0.8308 (t80) cc_final: 0.7901 (t80) REVERT: b 506 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8409 (tt) REVERT: b 535 HIS cc_start: 0.7810 (t-90) cc_final: 0.7537 (t-90) REVERT: b 551 LYS cc_start: 0.6920 (pttm) cc_final: 0.6449 (pttt) REVERT: b 615 ILE cc_start: 0.8723 (pt) cc_final: 0.8483 (pt) REVERT: b 663 GLN cc_start: 0.8316 (tp40) cc_final: 0.8107 (tt0) REVERT: b 692 GLU cc_start: 0.7498 (pt0) cc_final: 0.7291 (pt0) REVERT: b 728 GLU cc_start: 0.7906 (tt0) cc_final: 0.7580 (tt0) REVERT: b 734 GLN cc_start: 0.7880 (mm110) cc_final: 0.7612 (mm-40) REVERT: b 746 PHE cc_start: 0.9197 (p90) cc_final: 0.8889 (p90) REVERT: b 891 THR cc_start: 0.8810 (t) cc_final: 0.8442 (p) REVERT: b 896 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7136 (mm-30) REVERT: b 911 ASN cc_start: 0.8850 (m-40) cc_final: 0.8222 (t0) REVERT: b 926 THR cc_start: 0.9086 (m) cc_final: 0.8863 (m) REVERT: a 37 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8304 (ttmm) REVERT: a 536 LEU cc_start: 0.8987 (mt) cc_final: 0.8664 (mp) REVERT: a 629 ASP cc_start: 0.8568 (t0) cc_final: 0.8352 (m-30) REVERT: a 752 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8169 (pp20) REVERT: a 867 ASP cc_start: 0.8331 (t0) cc_final: 0.7983 (t0) REVERT: a 913 ASP cc_start: 0.8393 (m-30) cc_final: 0.8075 (m-30) REVERT: a 933 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8647 (ttmm) REVERT: a 1002 ILE cc_start: 0.8313 (mm) cc_final: 0.7726 (mm) REVERT: a 1020 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8041 (tm-30) REVERT: a 1036 ASP cc_start: 0.8453 (m-30) cc_final: 0.8250 (m-30) REVERT: a 1217 ASP cc_start: 0.8515 (t70) cc_final: 0.8279 (t0) outliers start: 240 outliers final: 210 residues processed: 2841 average time/residue: 1.3101 time to fit residues: 6298.6453 Evaluate side-chains 2933 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 2718 time to evaluate : 7.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 106 HIS Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 653 CYS Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 813 TYR Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 987 HIS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 232 LEU Chi-restraints excluded: chain c residue 244 THR Chi-restraints excluded: chain c residue 263 GLU Chi-restraints excluded: chain c residue 409 ASN Chi-restraints excluded: chain c residue 517 THR Chi-restraints excluded: chain c residue 559 ILE Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain e residue 199 LEU Chi-restraints excluded: chain e residue 259 SER Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 118 ILE Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 137 THR Chi-restraints excluded: chain g residue 140 ILE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 69 TYR Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 174 LEU Chi-restraints excluded: chain j residue 179 ILE Chi-restraints excluded: chain j residue 197 ASP Chi-restraints excluded: chain j residue 210 MET Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 25 ASN Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain k residue 105 SER Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 173 LEU Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain l residue 138 THR Chi-restraints excluded: chain l residue 143 ASN Chi-restraints excluded: chain l residue 171 ILE Chi-restraints excluded: chain b residue 313 ILE Chi-restraints excluded: chain b residue 320 SER Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 438 LEU Chi-restraints excluded: chain b residue 457 GLU Chi-restraints excluded: chain b residue 482 CYS Chi-restraints excluded: chain b residue 506 LEU Chi-restraints excluded: chain b residue 559 VAL Chi-restraints excluded: chain b residue 592 ILE Chi-restraints excluded: chain b residue 653 CYS Chi-restraints excluded: chain b residue 690 GLU Chi-restraints excluded: chain b residue 747 THR Chi-restraints excluded: chain b residue 844 ASN Chi-restraints excluded: chain b residue 934 CYS Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 947 LEU Chi-restraints excluded: chain b residue 987 HIS Chi-restraints excluded: chain b residue 988 VAL Chi-restraints excluded: chain b residue 1078 VAL Chi-restraints excluded: chain b residue 1090 VAL Chi-restraints excluded: chain a residue 2 ASN Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 96 ILE Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 173 ASN Chi-restraints excluded: chain a residue 278 ILE Chi-restraints excluded: chain a residue 320 SER Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 342 ILE Chi-restraints excluded: chain a residue 416 ILE Chi-restraints excluded: chain a residue 421 LEU Chi-restraints excluded: chain a residue 427 SER Chi-restraints excluded: chain a residue 447 THR Chi-restraints excluded: chain a residue 495 ASN Chi-restraints excluded: chain a residue 500 LEU Chi-restraints excluded: chain a residue 533 VAL Chi-restraints excluded: chain a residue 804 SER Chi-restraints excluded: chain a residue 816 ILE Chi-restraints excluded: chain a residue 843 ILE Chi-restraints excluded: chain a residue 852 LEU Chi-restraints excluded: chain a residue 873 PHE Chi-restraints excluded: chain a residue 882 LEU Chi-restraints excluded: chain a residue 900 MET Chi-restraints excluded: chain a residue 917 MET Chi-restraints excluded: chain a residue 963 ASP Chi-restraints excluded: chain a residue 985 ILE Chi-restraints excluded: chain a residue 1034 SER Chi-restraints excluded: chain a residue 1078 VAL Chi-restraints excluded: chain a residue 1092 ASN Chi-restraints excluded: chain a residue 1173 VAL Chi-restraints excluded: chain a residue 1236 SER 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: 1.9990 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: 0.5980 chunk 539 optimal weight: 0.8980 chunk 391 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 622 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 133 GLN K 25 ASN B 362 ASN B 481 HIS ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 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 129 GLN e 145 ASN f 50 ASN g 33 ASN ** j 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 535 HIS ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 66826 Z= 0.292 Angle : 0.556 7.552 90446 Z= 0.295 Chirality : 0.040 0.158 10438 Planarity : 0.003 0.064 11462 Dihedral : 4.756 48.777 8938 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.63 % Favored : 89.27 % Rotamer: Outliers : 3.76 % Allowed : 21.06 % Favored : 75.18 % 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: -1.16 (0.10), residues: 7496 helix: 1.34 (0.10), residues: 2570 sheet: -0.93 (0.13), residues: 1568 loop : -2.47 (0.10), residues: 3358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 649 HIS 0.006 0.001 HIS b 535 PHE 0.027 0.001 PHE C 151 TYR 0.031 0.001 TYR a 434 ARG 0.012 0.000 ARG b 287 *********************** 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 2984 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 2719 time to evaluate : 7.465 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 GLU cc_start: 0.8116 (tt0) cc_final: 0.7646 (tt0) REVERT: C 312 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7590 (ttm-80) REVERT: C 417 SER cc_start: 0.9119 (p) cc_final: 0.8852 (p) REVERT: C 492 TYR cc_start: 0.8681 (m-10) cc_final: 0.8457 (m-10) REVERT: D 65 SER cc_start: 0.9599 (t) cc_final: 0.9335 (t) REVERT: D 80 LYS cc_start: 0.9122 (tttt) cc_final: 0.8868 (ttmm) REVERT: D 139 ARG cc_start: 0.8421 (ptm160) cc_final: 0.8123 (ptp-110) REVERT: D 143 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7890 (tm-30) REVERT: E 91 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7231 (mm-30) REVERT: E 157 MET cc_start: 0.9362 (mmt) cc_final: 0.9115 (mmt) REVERT: E 185 TYR cc_start: 0.8625 (m-80) cc_final: 0.7441 (m-80) REVERT: F 120 ASP cc_start: 0.7931 (t0) cc_final: 0.7376 (t0) REVERT: F 126 ASP cc_start: 0.8083 (t0) cc_final: 0.7736 (t0) REVERT: F 136 LYS cc_start: 0.8813 (pttm) cc_final: 0.8515 (ptmm) REVERT: G 80 TYR cc_start: 0.9146 (t80) cc_final: 0.8201 (t80) REVERT: G 118 ASN cc_start: 0.8874 (t0) cc_final: 0.8506 (t0) REVERT: G 130 ASN cc_start: 0.8582 (t0) cc_final: 0.8196 (t0) REVERT: G 144 ASN cc_start: 0.8698 (m110) cc_final: 0.8224 (m110) REVERT: H 100 SER cc_start: 0.8176 (p) cc_final: 0.7156 (p) REVERT: H 115 ASN cc_start: 0.9022 (p0) cc_final: 0.8740 (p0) REVERT: I 23 GLU cc_start: 0.6144 (mp0) cc_final: 0.5740 (mp0) REVERT: I 156 GLN cc_start: 0.8899 (mp10) cc_final: 0.8244 (mp10) REVERT: J 48 GLU cc_start: 0.8631 (tp30) cc_final: 0.8287 (tp30) REVERT: J 84 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8060 (mt-10) REVERT: J 255 MET cc_start: 0.8970 (mmt) cc_final: 0.8706 (mmt) REVERT: J 257 GLN cc_start: 0.9256 (pp30) cc_final: 0.8157 (pp30) REVERT: K 3 GLN cc_start: 0.9235 (mp10) cc_final: 0.8679 (mm-40) REVERT: K 22 ASN cc_start: 0.7976 (t160) cc_final: 0.7569 (t160) REVERT: K 36 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8920 (mp) REVERT: K 53 TRP cc_start: 0.7817 (m-10) cc_final: 0.7222 (m-10) REVERT: K 91 LYS cc_start: 0.9258 (tttt) cc_final: 0.9056 (tttt) REVERT: K 113 MET cc_start: 0.8787 (tpp) cc_final: 0.8514 (tpp) REVERT: L 58 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8380 (mt-10) REVERT: L 59 ASN cc_start: 0.8490 (t0) cc_final: 0.7825 (t0) REVERT: L 101 TYR cc_start: 0.7712 (t80) cc_final: 0.6452 (t80) REVERT: L 113 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6977 (tm-30) REVERT: L 162 ASN cc_start: 0.7710 (t0) cc_final: 0.7347 (t0) REVERT: L 200 LYS cc_start: 0.8688 (tttp) cc_final: 0.8140 (ptpt) REVERT: B 276 GLN cc_start: 0.8682 (mt0) cc_final: 0.8215 (pt0) REVERT: B 349 CYS cc_start: 0.9193 (m) cc_final: 0.8863 (m) REVERT: B 355 LEU cc_start: 0.9154 (tp) cc_final: 0.8815 (mp) REVERT: B 538 TYR cc_start: 0.8590 (t80) cc_final: 0.8181 (t80) REVERT: B 654 LYS cc_start: 0.8092 (ttmm) cc_final: 0.7616 (mmmm) REVERT: B 780 ASP cc_start: 0.8731 (p0) cc_final: 0.8291 (p0) REVERT: B 802 SER cc_start: 0.8446 (p) cc_final: 0.7988 (p) REVERT: B 911 ASN cc_start: 0.8775 (m-40) cc_final: 0.8046 (t0) REVERT: B 932 ASN cc_start: 0.7990 (m110) cc_final: 0.7557 (m110) REVERT: A 58 THR cc_start: 0.8740 (m) cc_final: 0.8482 (m) REVERT: A 317 ASP cc_start: 0.8584 (t0) cc_final: 0.8190 (t0) REVERT: A 415 CYS cc_start: 0.8900 (t) cc_final: 0.8464 (t) REVERT: A 467 ASN cc_start: 0.7659 (m-40) cc_final: 0.7306 (m-40) REVERT: A 563 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 817 ASN cc_start: 0.6730 (m110) cc_final: 0.6219 (m110) REVERT: A 867 ASP cc_start: 0.8239 (t0) cc_final: 0.7634 (t0) REVERT: A 899 GLN cc_start: 0.8168 (tt0) cc_final: 0.7527 (tm-30) REVERT: A 913 ASP cc_start: 0.8201 (m-30) cc_final: 0.7846 (m-30) REVERT: A 933 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8345 (tptt) REVERT: A 966 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8805 (pt) REVERT: A 994 THR cc_start: 0.8989 (p) cc_final: 0.8748 (p) REVERT: A 1020 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 1036 ASP cc_start: 0.8148 (m-30) cc_final: 0.7690 (m-30) REVERT: A 1069 GLU cc_start: 0.7475 (pm20) cc_final: 0.7231 (pm20) REVERT: c 278 ASP cc_start: 0.8613 (m-30) cc_final: 0.8343 (t0) REVERT: c 312 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7750 (ttm-80) REVERT: c 338 GLU cc_start: 0.9193 (pm20) cc_final: 0.8973 (pm20) REVERT: c 409 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7864 (t0) REVERT: c 506 ASP cc_start: 0.6956 (m-30) cc_final: 0.6561 (m-30) REVERT: d 32 ASP cc_start: 0.8246 (m-30) cc_final: 0.7480 (m-30) REVERT: d 139 ARG cc_start: 0.8409 (ptm160) cc_final: 0.8030 (ttp80) REVERT: e 42 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8341 (tm-30) REVERT: e 107 GLU cc_start: 0.8280 (tp30) cc_final: 0.7941 (tp30) REVERT: e 185 TYR cc_start: 0.8339 (m-80) cc_final: 0.8036 (m-80) REVERT: e 206 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7570 (mm-30) REVERT: f 88 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7685 (mm-30) REVERT: f 120 ASP cc_start: 0.7895 (t70) cc_final: 0.7344 (t0) REVERT: g 118 ASN cc_start: 0.8706 (t0) cc_final: 0.8177 (t0) REVERT: g 130 ASN cc_start: 0.8526 (t0) cc_final: 0.8130 (t0) REVERT: g 144 ASN cc_start: 0.8730 (m110) cc_final: 0.8232 (m110) REVERT: h 75 MET cc_start: 0.8218 (pmm) cc_final: 0.7320 (pmm) REVERT: h 123 CYS cc_start: 0.8234 (m) cc_final: 0.7842 (m) REVERT: i 48 ASP cc_start: 0.7384 (t0) cc_final: 0.6695 (t0) REVERT: i 107 ASN cc_start: 0.8778 (m-40) cc_final: 0.8523 (m-40) REVERT: i 156 GLN cc_start: 0.9215 (mp10) cc_final: 0.8320 (mp10) REVERT: j 23 GLU cc_start: 0.8327 (tp30) cc_final: 0.7731 (tp30) REVERT: j 48 GLU cc_start: 0.8732 (tp30) cc_final: 0.8507 (tp30) REVERT: j 68 GLU cc_start: 0.8402 (tp30) cc_final: 0.8082 (tp30) REVERT: j 189 SER cc_start: 0.9112 (p) cc_final: 0.8815 (p) REVERT: j 271 ASP cc_start: 0.7973 (t0) cc_final: 0.7588 (t0) REVERT: k 3 GLN cc_start: 0.8917 (mp10) cc_final: 0.8036 (mm-40) REVERT: k 22 ASN cc_start: 0.8020 (t0) cc_final: 0.7371 (t0) REVERT: k 24 GLU cc_start: 0.6814 (pm20) cc_final: 0.6224 (mp0) REVERT: k 27 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8277 (mm-40) REVERT: k 35 GLU cc_start: 0.8408 (tt0) cc_final: 0.8146 (tp30) REVERT: k 126 ASP cc_start: 0.8504 (t0) cc_final: 0.8159 (t0) REVERT: k 136 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: k 163 SER cc_start: 0.9036 (t) cc_final: 0.8760 (p) REVERT: l 49 GLU cc_start: 0.7452 (tt0) cc_final: 0.6825 (tt0) REVERT: l 59 ASN cc_start: 0.8372 (t0) cc_final: 0.7851 (t0) REVERT: l 102 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7156 (tm-30) REVERT: l 106 HIS cc_start: 0.7790 (t-90) cc_final: 0.7424 (t70) REVERT: l 143 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7840 (m110) REVERT: l 147 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6999 (mm-30) REVERT: l 148 ASN cc_start: 0.8507 (m-40) cc_final: 0.7307 (m110) REVERT: b 354 GLU cc_start: 0.8688 (tp30) cc_final: 0.8417 (tp30) REVERT: b 363 TRP cc_start: 0.9468 (t60) cc_final: 0.8988 (t60) REVERT: b 429 ASP cc_start: 0.8584 (m-30) cc_final: 0.8267 (m-30) REVERT: b 506 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8392 (tt) REVERT: b 535 HIS cc_start: 0.7669 (t70) cc_final: 0.7382 (t70) REVERT: b 538 TYR cc_start: 0.8473 (t80) cc_final: 0.8199 (t80) REVERT: b 615 ILE cc_start: 0.8682 (pt) cc_final: 0.8478 (pt) REVERT: b 692 GLU cc_start: 0.7535 (pt0) cc_final: 0.7305 (pt0) REVERT: b 728 GLU cc_start: 0.7793 (tt0) cc_final: 0.7473 (tt0) REVERT: b 734 GLN cc_start: 0.7925 (mm110) cc_final: 0.7657 (mm-40) REVERT: b 896 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7163 (mm-30) REVERT: b 911 ASN cc_start: 0.8872 (m-40) cc_final: 0.8236 (t0) REVERT: b 926 THR cc_start: 0.9089 (m) cc_final: 0.8874 (m) REVERT: b 1102 PHE cc_start: 0.7892 (t80) cc_final: 0.7690 (t80) REVERT: a 37 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8297 (ttmm) REVERT: a 124 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8603 (p0) REVERT: a 536 LEU cc_start: 0.8943 (mt) cc_final: 0.8627 (mp) REVERT: a 629 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: a 752 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8181 (pp20) REVERT: a 867 ASP cc_start: 0.8524 (t0) cc_final: 0.8209 (t0) REVERT: a 913 ASP cc_start: 0.8462 (m-30) cc_final: 0.8155 (m-30) REVERT: a 933 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8682 (ttmm) REVERT: a 1002 ILE cc_start: 0.8365 (mm) cc_final: 0.7839 (mm) REVERT: a 1020 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8058 (tm-30) REVERT: a 1217 ASP cc_start: 0.8479 (t70) cc_final: 0.8263 (t0) REVERT: a 1272 ASN cc_start: 0.8141 (m-40) cc_final: 0.7940 (p0) outliers start: 265 outliers final: 237 residues processed: 2792 average time/residue: 1.3019 time to fit residues: 6148.9406 Evaluate side-chains 2929 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 2684 time to evaluate : 7.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 106 HIS Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 653 CYS Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 813 TYR Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 894 GLU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 987 HIS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 963 ASP Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1236 SER Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 232 LEU Chi-restraints excluded: chain c residue 244 THR Chi-restraints excluded: chain c residue 263 GLU Chi-restraints excluded: chain c residue 409 ASN Chi-restraints excluded: chain c residue 517 THR Chi-restraints excluded: chain c residue 559 ILE Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 63 LEU Chi-restraints excluded: chain d residue 68 GLN Chi-restraints excluded: chain d residue 73 SER Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 106 HIS Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain e residue 199 LEU Chi-restraints excluded: chain e residue 259 SER Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 118 ILE Chi-restraints excluded: chain f residue 148 LEU Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 137 THR Chi-restraints excluded: chain g residue 140 ILE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 48 SER Chi-restraints excluded: chain h residue 69 TYR Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 209 GLU Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 44 ASP Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 165 SER Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 45 ILE Chi-restraints excluded: chain j residue 88 SER Chi-restraints excluded: chain j residue 174 LEU Chi-restraints excluded: chain j residue 179 ILE Chi-restraints excluded: chain j residue 210 MET Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 25 ASN Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 105 SER Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 173 LEU Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain l residue 138 THR Chi-restraints excluded: chain l residue 143 ASN Chi-restraints excluded: chain l residue 161 ASP Chi-restraints excluded: chain l residue 171 ILE Chi-restraints excluded: chain b residue 313 ILE Chi-restraints excluded: chain b residue 320 SER Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 438 LEU Chi-restraints excluded: chain b residue 457 GLU Chi-restraints excluded: chain b residue 482 CYS Chi-restraints excluded: chain b residue 506 LEU Chi-restraints excluded: chain b residue 559 VAL Chi-restraints excluded: chain b residue 592 ILE Chi-restraints excluded: chain b residue 653 CYS Chi-restraints excluded: chain b residue 690 GLU Chi-restraints excluded: chain b residue 747 THR Chi-restraints excluded: chain b residue 813 TYR Chi-restraints excluded: chain b residue 844 ASN Chi-restraints excluded: chain b residue 934 CYS Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 947 LEU Chi-restraints excluded: chain b residue 987 HIS Chi-restraints excluded: chain b residue 988 VAL Chi-restraints excluded: chain b residue 1078 VAL Chi-restraints excluded: chain b residue 1090 VAL Chi-restraints excluded: chain a residue 2 ASN Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 96 ILE Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 173 ASN Chi-restraints excluded: chain a residue 278 ILE Chi-restraints excluded: chain a residue 320 SER Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 342 ILE Chi-restraints excluded: chain a residue 421 LEU Chi-restraints excluded: chain a residue 427 SER Chi-restraints excluded: chain a residue 447 THR Chi-restraints excluded: chain a residue 500 LEU Chi-restraints excluded: chain a residue 533 VAL Chi-restraints excluded: chain a residue 629 ASP Chi-restraints excluded: chain a residue 804 SER Chi-restraints excluded: chain a residue 816 ILE Chi-restraints excluded: chain a residue 843 ILE Chi-restraints excluded: chain a residue 852 LEU Chi-restraints excluded: chain a residue 873 PHE Chi-restraints excluded: chain a residue 882 LEU Chi-restraints excluded: chain a residue 892 ILE Chi-restraints excluded: chain a residue 900 MET Chi-restraints excluded: chain a residue 917 MET Chi-restraints excluded: chain a residue 985 ILE Chi-restraints excluded: chain a residue 1034 SER Chi-restraints excluded: chain a residue 1078 VAL Chi-restraints excluded: chain a residue 1212 ASP Chi-restraints excluded: chain a residue 1236 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 720 optimal weight: 1.9990 chunk 759 optimal weight: 1.9990 chunk 692 optimal weight: 1.9990 chunk 738 optimal weight: 0.0770 chunk 758 optimal weight: 0.7980 chunk 444 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 579 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 667 optimal weight: 3.9990 chunk 698 optimal weight: 0.5980 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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 H 133 GLN K 25 ASN B 362 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 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 e 145 ASN f 50 ASN g 33 ASN ** j 243 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 66826 Z= 0.236 Angle : 0.547 7.452 90446 Z= 0.289 Chirality : 0.040 0.172 10438 Planarity : 0.003 0.050 11462 Dihedral : 4.740 49.431 8938 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.17 % Favored : 89.71 % Rotamer: Outliers : 3.52 % Allowed : 21.61 % Favored : 74.87 % 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: -1.12 (0.10), residues: 7496 helix: 1.38 (0.10), residues: 2558 sheet: -0.93 (0.13), residues: 1540 loop : -2.41 (0.10), residues: 3398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 649 HIS 0.006 0.001 HIS B 987 PHE 0.025 0.001 PHE j 52 TYR 0.023 0.001 TYR a 434 ARG 0.009 0.000 ARG J 172 *********************** 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 2980 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 2732 time to evaluate : 9.004 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 GLU cc_start: 0.8116 (tt0) cc_final: 0.7630 (tt0) REVERT: C 312 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7592 (ttm-80) REVERT: C 417 SER cc_start: 0.9116 (p) cc_final: 0.8852 (p) REVERT: C 492 TYR cc_start: 0.8672 (m-10) cc_final: 0.8467 (m-10) REVERT: D 65 SER cc_start: 0.9582 (t) cc_final: 0.9309 (t) REVERT: D 80 LYS cc_start: 0.9068 (tttt) cc_final: 0.8851 (ttmm) REVERT: D 139 ARG cc_start: 0.8419 (ptm160) cc_final: 0.8120 (ptp-110) REVERT: D 143 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7890 (tm-30) REVERT: E 91 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7245 (mm-30) REVERT: E 114 GLU cc_start: 0.8172 (pp20) cc_final: 0.7898 (pp20) REVERT: E 157 MET cc_start: 0.9353 (mmt) cc_final: 0.9122 (mmt) REVERT: E 185 TYR cc_start: 0.8637 (m-80) cc_final: 0.7457 (m-80) REVERT: E 252 THR cc_start: 0.8598 (t) cc_final: 0.8190 (p) REVERT: F 120 ASP cc_start: 0.7868 (t0) cc_final: 0.7300 (t0) REVERT: F 126 ASP cc_start: 0.8050 (t0) cc_final: 0.7694 (t0) REVERT: F 136 LYS cc_start: 0.8791 (pttm) cc_final: 0.8501 (ptmm) REVERT: G 80 TYR cc_start: 0.9145 (t80) cc_final: 0.8209 (t80) REVERT: G 130 ASN cc_start: 0.8614 (t0) cc_final: 0.8214 (t0) REVERT: G 144 ASN cc_start: 0.8681 (m110) cc_final: 0.8213 (m110) REVERT: H 100 SER cc_start: 0.8135 (p) cc_final: 0.7219 (p) REVERT: H 115 ASN cc_start: 0.9010 (p0) cc_final: 0.8738 (p0) REVERT: I 23 GLU cc_start: 0.6147 (mp0) cc_final: 0.5745 (mp0) REVERT: I 156 GLN cc_start: 0.8877 (mp10) cc_final: 0.8227 (mp10) REVERT: J 48 GLU cc_start: 0.8619 (tp30) cc_final: 0.8279 (tp30) REVERT: J 255 MET cc_start: 0.8973 (mmt) cc_final: 0.8701 (mmt) REVERT: J 257 GLN cc_start: 0.9256 (pp30) cc_final: 0.8162 (pp30) REVERT: J 277 ARG cc_start: 0.6359 (tmm-80) cc_final: 0.6091 (tmm-80) REVERT: K 3 GLN cc_start: 0.9256 (mp10) cc_final: 0.8711 (mm-40) REVERT: K 22 ASN cc_start: 0.7911 (t160) cc_final: 0.7493 (t160) REVERT: K 25 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8210 (t0) REVERT: K 36 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8904 (mp) REVERT: K 53 TRP cc_start: 0.7858 (m-10) cc_final: 0.7262 (m-10) REVERT: K 91 LYS cc_start: 0.9261 (tttt) cc_final: 0.9059 (tttt) REVERT: K 113 MET cc_start: 0.8757 (tpp) cc_final: 0.8474 (tpp) REVERT: L 58 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8376 (mt-10) REVERT: L 59 ASN cc_start: 0.8480 (t0) cc_final: 0.7810 (t0) REVERT: L 101 TYR cc_start: 0.7704 (t80) cc_final: 0.6452 (t80) REVERT: L 113 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6963 (tm-30) REVERT: L 162 ASN cc_start: 0.7699 (t0) cc_final: 0.7303 (t0) REVERT: L 200 LYS cc_start: 0.8690 (tttp) cc_final: 0.8100 (ptpt) REVERT: B 276 GLN cc_start: 0.8675 (mt0) cc_final: 0.8211 (pt0) REVERT: B 349 CYS cc_start: 0.9182 (m) cc_final: 0.8854 (m) REVERT: B 355 LEU cc_start: 0.9141 (tp) cc_final: 0.8805 (mp) REVERT: B 538 TYR cc_start: 0.8591 (t80) cc_final: 0.8161 (t80) REVERT: B 654 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7613 (mmmm) REVERT: B 780 ASP cc_start: 0.8728 (p0) cc_final: 0.8291 (p0) REVERT: B 802 SER cc_start: 0.8380 (p) cc_final: 0.7914 (p) REVERT: B 911 ASN cc_start: 0.8774 (m-40) cc_final: 0.8044 (t0) REVERT: B 932 ASN cc_start: 0.7968 (m110) cc_final: 0.7538 (m110) REVERT: A 58 THR cc_start: 0.8740 (m) cc_final: 0.8480 (m) REVERT: A 99 LEU cc_start: 0.8352 (mt) cc_final: 0.8112 (mt) REVERT: A 154 GLN cc_start: 0.7570 (mm110) cc_final: 0.6954 (mp10) REVERT: A 317 ASP cc_start: 0.8587 (t0) cc_final: 0.8189 (t0) REVERT: A 415 CYS cc_start: 0.8889 (t) cc_final: 0.8445 (t) REVERT: A 467 ASN cc_start: 0.7651 (m-40) cc_final: 0.7300 (m-40) REVERT: A 563 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 817 ASN cc_start: 0.6731 (m110) cc_final: 0.6221 (m110) REVERT: A 867 ASP cc_start: 0.8216 (t0) cc_final: 0.7628 (t0) REVERT: A 899 GLN cc_start: 0.8161 (tt0) cc_final: 0.7464 (tm-30) REVERT: A 913 ASP cc_start: 0.8199 (m-30) cc_final: 0.7840 (m-30) REVERT: A 933 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8337 (tptt) REVERT: A 966 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8773 (pt) REVERT: A 994 THR cc_start: 0.8995 (p) cc_final: 0.8770 (p) REVERT: A 1020 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 1036 ASP cc_start: 0.8156 (m-30) cc_final: 0.7682 (m-30) REVERT: A 1069 GLU cc_start: 0.7477 (pm20) cc_final: 0.7234 (pm20) REVERT: c 278 ASP cc_start: 0.8604 (m-30) cc_final: 0.8332 (t0) REVERT: c 312 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7806 (ttm-80) REVERT: c 338 GLU cc_start: 0.9146 (pm20) cc_final: 0.8928 (pm20) REVERT: c 409 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7868 (t0) REVERT: c 506 ASP cc_start: 0.6962 (m-30) cc_final: 0.6552 (m-30) REVERT: d 32 ASP cc_start: 0.8250 (m-30) cc_final: 0.7576 (m-30) REVERT: d 139 ARG cc_start: 0.8400 (ptm160) cc_final: 0.8020 (ttp80) REVERT: e 42 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8321 (tm-30) REVERT: e 107 GLU cc_start: 0.8271 (tp30) cc_final: 0.8043 (tp30) REVERT: e 165 TRP cc_start: 0.8411 (m100) cc_final: 0.8067 (m100) REVERT: e 185 TYR cc_start: 0.8347 (m-80) cc_final: 0.8042 (m-80) REVERT: e 206 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7562 (mm-30) REVERT: f 88 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7674 (mm-30) REVERT: f 120 ASP cc_start: 0.7897 (t70) cc_final: 0.7341 (t0) REVERT: g 118 ASN cc_start: 0.8675 (t0) cc_final: 0.8121 (t0) REVERT: g 130 ASN cc_start: 0.8495 (t0) cc_final: 0.8109 (t0) REVERT: g 144 ASN cc_start: 0.8699 (m110) cc_final: 0.8224 (m110) REVERT: h 123 CYS cc_start: 0.8220 (m) cc_final: 0.7819 (m) REVERT: i 48 ASP cc_start: 0.7354 (t0) cc_final: 0.6676 (t0) REVERT: i 107 ASN cc_start: 0.8771 (m-40) cc_final: 0.8517 (m-40) REVERT: i 155 VAL cc_start: 0.8968 (m) cc_final: 0.8593 (m) REVERT: i 156 GLN cc_start: 0.9223 (mp10) cc_final: 0.8310 (mp10) REVERT: j 23 GLU cc_start: 0.8321 (tp30) cc_final: 0.7699 (tp30) REVERT: j 48 GLU cc_start: 0.8722 (tp30) cc_final: 0.8501 (tp30) REVERT: j 68 GLU cc_start: 0.8397 (tp30) cc_final: 0.8092 (tp30) REVERT: j 189 SER cc_start: 0.9106 (p) cc_final: 0.8806 (p) REVERT: j 271 ASP cc_start: 0.7969 (t0) cc_final: 0.7580 (t0) REVERT: k 3 GLN cc_start: 0.8924 (mp10) cc_final: 0.8019 (mm-40) REVERT: k 22 ASN cc_start: 0.8023 (t0) cc_final: 0.7363 (t0) REVERT: k 24 GLU cc_start: 0.6817 (pm20) cc_final: 0.6218 (mp0) REVERT: k 35 GLU cc_start: 0.8399 (tt0) cc_final: 0.8132 (tp30) REVERT: k 126 ASP cc_start: 0.8515 (t0) cc_final: 0.8167 (t0) REVERT: k 136 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: k 163 SER cc_start: 0.9028 (t) cc_final: 0.8753 (p) REVERT: l 49 GLU cc_start: 0.7459 (tt0) cc_final: 0.6782 (tt0) REVERT: l 59 ASN cc_start: 0.8365 (t0) cc_final: 0.7842 (t0) REVERT: l 102 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7148 (tm-30) REVERT: l 106 HIS cc_start: 0.7786 (t-90) cc_final: 0.7421 (t70) REVERT: l 143 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7825 (m110) REVERT: l 148 ASN cc_start: 0.8481 (m-40) cc_final: 0.7856 (m110) REVERT: b 354 GLU cc_start: 0.8669 (tp30) cc_final: 0.8449 (tp30) REVERT: b 363 TRP cc_start: 0.9462 (t60) cc_final: 0.8978 (t60) REVERT: b 429 ASP cc_start: 0.8607 (m-30) cc_final: 0.8178 (m-30) REVERT: b 506 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8384 (tt) REVERT: b 535 HIS cc_start: 0.7717 (t70) cc_final: 0.7449 (t70) REVERT: b 538 TYR cc_start: 0.8537 (t80) cc_final: 0.8284 (t80) REVERT: b 692 GLU cc_start: 0.7527 (pt0) cc_final: 0.7308 (pt0) REVERT: b 728 GLU cc_start: 0.7862 (tt0) cc_final: 0.7380 (tt0) REVERT: b 734 GLN cc_start: 0.7911 (mm110) cc_final: 0.7648 (mm-40) REVERT: b 896 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7163 (mm-30) REVERT: b 911 ASN cc_start: 0.8871 (m-40) cc_final: 0.8237 (t0) REVERT: a 37 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8268 (ttmm) REVERT: a 124 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8609 (p0) REVERT: a 536 LEU cc_start: 0.8981 (mt) cc_final: 0.8665 (mp) REVERT: a 629 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: a 752 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8173 (pp20) REVERT: a 867 ASP cc_start: 0.8437 (t0) cc_final: 0.8112 (t0) REVERT: a 913 ASP cc_start: 0.8456 (m-30) cc_final: 0.8143 (m-30) REVERT: a 933 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8674 (ttmm) REVERT: a 1002 ILE cc_start: 0.8329 (mm) cc_final: 0.7801 (mm) REVERT: a 1020 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8058 (tm-30) REVERT: a 1217 ASP cc_start: 0.8473 (t70) cc_final: 0.8266 (t0) outliers start: 248 outliers final: 229 residues processed: 2801 average time/residue: 1.3984 time to fit residues: 6677.2298 Evaluate side-chains 2953 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 2715 time to evaluate : 6.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 106 HIS Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 653 CYS Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 813 TYR Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 894 GLU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 987 HIS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1236 SER Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 232 LEU Chi-restraints excluded: chain c residue 244 THR Chi-restraints excluded: chain c residue 263 GLU Chi-restraints excluded: chain c residue 409 ASN Chi-restraints excluded: chain c residue 517 THR Chi-restraints excluded: chain c residue 559 ILE Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 68 GLN Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 106 HIS Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain e residue 199 LEU Chi-restraints excluded: chain e residue 259 SER Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 118 ILE Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 137 THR Chi-restraints excluded: chain g residue 140 ILE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 69 TYR Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 209 GLU Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 165 SER Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 45 ILE Chi-restraints excluded: chain j residue 88 SER Chi-restraints excluded: chain j residue 174 LEU Chi-restraints excluded: chain j residue 179 ILE Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain j residue 210 MET Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 25 ASN Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 105 SER Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 173 LEU Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain l residue 138 THR Chi-restraints excluded: chain l residue 143 ASN Chi-restraints excluded: chain l residue 171 ILE Chi-restraints excluded: chain b residue 313 ILE Chi-restraints excluded: chain b residue 320 SER Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 438 LEU Chi-restraints excluded: chain b residue 457 GLU Chi-restraints excluded: chain b residue 482 CYS Chi-restraints excluded: chain b residue 506 LEU Chi-restraints excluded: chain b residue 559 VAL Chi-restraints excluded: chain b residue 592 ILE Chi-restraints excluded: chain b residue 653 CYS Chi-restraints excluded: chain b residue 690 GLU Chi-restraints excluded: chain b residue 747 THR Chi-restraints excluded: chain b residue 813 TYR Chi-restraints excluded: chain b residue 844 ASN Chi-restraints excluded: chain b residue 934 CYS Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 947 LEU Chi-restraints excluded: chain b residue 987 HIS Chi-restraints excluded: chain b residue 988 VAL Chi-restraints excluded: chain b residue 1078 VAL Chi-restraints excluded: chain b residue 1090 VAL Chi-restraints excluded: chain a residue 2 ASN Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 96 ILE Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 173 ASN Chi-restraints excluded: chain a residue 278 ILE Chi-restraints excluded: chain a residue 320 SER Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 342 ILE Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 421 LEU Chi-restraints excluded: chain a residue 427 SER Chi-restraints excluded: chain a residue 447 THR Chi-restraints excluded: chain a residue 452 THR Chi-restraints excluded: chain a residue 500 LEU Chi-restraints excluded: chain a residue 533 VAL Chi-restraints excluded: chain a residue 629 ASP Chi-restraints excluded: chain a residue 804 SER Chi-restraints excluded: chain a residue 816 ILE Chi-restraints excluded: chain a residue 843 ILE Chi-restraints excluded: chain a residue 852 LEU Chi-restraints excluded: chain a residue 873 PHE Chi-restraints excluded: chain a residue 882 LEU Chi-restraints excluded: chain a residue 900 MET Chi-restraints excluded: chain a residue 917 MET Chi-restraints excluded: chain a residue 985 ILE Chi-restraints excluded: chain a residue 1034 SER Chi-restraints excluded: chain a residue 1078 VAL Chi-restraints excluded: chain a residue 1092 ASN Chi-restraints excluded: chain a residue 1212 ASP Chi-restraints excluded: chain a residue 1236 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 735 optimal weight: 0.9990 chunk 484 optimal weight: 0.9980 chunk 780 optimal weight: 1.9990 chunk 476 optimal weight: 1.9990 chunk 370 optimal weight: 0.9990 chunk 542 optimal weight: 1.9990 chunk 818 optimal weight: 9.9990 chunk 753 optimal weight: 2.9990 chunk 652 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 503 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 H 133 GLN K 25 ASN B 362 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 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 129 GLN e 145 ASN f 50 ASN g 33 ASN ** j 243 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 66826 Z= 0.236 Angle : 0.549 8.021 90446 Z= 0.290 Chirality : 0.040 0.177 10438 Planarity : 0.003 0.049 11462 Dihedral : 4.729 50.451 8938 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.34 % Favored : 89.55 % Rotamer: Outliers : 3.54 % Allowed : 21.80 % Favored : 74.67 % 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: -1.11 (0.10), residues: 7496 helix: 1.38 (0.11), residues: 2558 sheet: -0.93 (0.13), residues: 1544 loop : -2.40 (0.10), residues: 3394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 649 HIS 0.006 0.001 HIS B 987 PHE 0.029 0.001 PHE j 52 TYR 0.024 0.001 TYR B 440 ARG 0.009 0.000 ARG g 133 ********************** 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 2987 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 2738 time to evaluate : 7.744 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 GLU cc_start: 0.8115 (tt0) cc_final: 0.7632 (tt0) REVERT: C 312 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7595 (ttm-80) REVERT: C 417 SER cc_start: 0.9122 (p) cc_final: 0.8855 (p) REVERT: C 492 TYR cc_start: 0.8670 (m-10) cc_final: 0.8443 (m-10) REVERT: D 65 SER cc_start: 0.9581 (t) cc_final: 0.9303 (t) REVERT: D 80 LYS cc_start: 0.9059 (tttt) cc_final: 0.8848 (ttmm) REVERT: D 139 ARG cc_start: 0.8422 (ptm160) cc_final: 0.8122 (ptp-110) REVERT: D 143 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7892 (tm-30) REVERT: E 114 GLU cc_start: 0.8181 (pp20) cc_final: 0.7884 (pp20) REVERT: E 157 MET cc_start: 0.9357 (mmt) cc_final: 0.9138 (mmt) REVERT: E 185 TYR cc_start: 0.8648 (m-80) cc_final: 0.7475 (m-80) REVERT: E 252 THR cc_start: 0.8764 (t) cc_final: 0.8472 (p) REVERT: F 120 ASP cc_start: 0.7867 (t0) cc_final: 0.7304 (t0) REVERT: F 126 ASP cc_start: 0.8057 (t0) cc_final: 0.7695 (t0) REVERT: F 136 LYS cc_start: 0.8798 (pttm) cc_final: 0.8503 (ptmm) REVERT: G 80 TYR cc_start: 0.9152 (t80) cc_final: 0.8233 (t80) REVERT: G 130 ASN cc_start: 0.8605 (t0) cc_final: 0.8220 (t0) REVERT: G 144 ASN cc_start: 0.8677 (m110) cc_final: 0.8226 (m110) REVERT: H 100 SER cc_start: 0.8051 (p) cc_final: 0.7177 (p) REVERT: H 115 ASN cc_start: 0.9002 (p0) cc_final: 0.8748 (p0) REVERT: I 23 GLU cc_start: 0.6144 (mp0) cc_final: 0.5742 (mp0) REVERT: I 156 GLN cc_start: 0.8861 (mp10) cc_final: 0.8217 (mp10) REVERT: J 48 GLU cc_start: 0.8618 (tp30) cc_final: 0.8284 (tp30) REVERT: J 255 MET cc_start: 0.8972 (mmt) cc_final: 0.8705 (mmt) REVERT: J 257 GLN cc_start: 0.9253 (pp30) cc_final: 0.8170 (pp30) REVERT: J 277 ARG cc_start: 0.6352 (tmm-80) cc_final: 0.6093 (tmm-80) REVERT: K 3 GLN cc_start: 0.9260 (mp10) cc_final: 0.8718 (mm-40) REVERT: K 22 ASN cc_start: 0.7988 (t160) cc_final: 0.7644 (t160) REVERT: K 24 GLU cc_start: 0.7074 (mp0) cc_final: 0.6607 (mp0) REVERT: K 36 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8903 (mp) REVERT: K 53 TRP cc_start: 0.7908 (m-10) cc_final: 0.7396 (m-10) REVERT: K 91 LYS cc_start: 0.9263 (tttt) cc_final: 0.9058 (tttt) REVERT: K 113 MET cc_start: 0.8736 (tpp) cc_final: 0.8429 (tpp) REVERT: L 58 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8372 (mt-10) REVERT: L 59 ASN cc_start: 0.8476 (t0) cc_final: 0.7806 (t0) REVERT: L 101 TYR cc_start: 0.7705 (t80) cc_final: 0.6385 (t80) REVERT: L 113 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6988 (tm-30) REVERT: L 162 ASN cc_start: 0.7686 (t0) cc_final: 0.7288 (t0) REVERT: L 177 MET cc_start: 0.8482 (ttt) cc_final: 0.8278 (ttt) REVERT: L 200 LYS cc_start: 0.8693 (tttp) cc_final: 0.8102 (ptpt) REVERT: B 276 GLN cc_start: 0.8672 (mt0) cc_final: 0.8212 (pt0) REVERT: B 349 CYS cc_start: 0.9184 (m) cc_final: 0.8855 (m) REVERT: B 355 LEU cc_start: 0.9136 (tp) cc_final: 0.8785 (mp) REVERT: B 538 TYR cc_start: 0.8598 (t80) cc_final: 0.8211 (t80) REVERT: B 780 ASP cc_start: 0.8726 (p0) cc_final: 0.8287 (p0) REVERT: B 802 SER cc_start: 0.8394 (p) cc_final: 0.7934 (p) REVERT: B 911 ASN cc_start: 0.8776 (m-40) cc_final: 0.8047 (t0) REVERT: B 932 ASN cc_start: 0.7962 (m110) cc_final: 0.7532 (m110) REVERT: A 58 THR cc_start: 0.8741 (m) cc_final: 0.8481 (m) REVERT: A 99 LEU cc_start: 0.8306 (mt) cc_final: 0.8006 (mt) REVERT: A 317 ASP cc_start: 0.8589 (t0) cc_final: 0.8191 (t0) REVERT: A 415 CYS cc_start: 0.8886 (t) cc_final: 0.8440 (t) REVERT: A 467 ASN cc_start: 0.7656 (m-40) cc_final: 0.7299 (m-40) REVERT: A 563 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 817 ASN cc_start: 0.6748 (m110) cc_final: 0.6237 (m110) REVERT: A 867 ASP cc_start: 0.8226 (t0) cc_final: 0.7649 (t0) REVERT: A 899 GLN cc_start: 0.8182 (tt0) cc_final: 0.7532 (tm-30) REVERT: A 913 ASP cc_start: 0.8209 (m-30) cc_final: 0.7857 (m-30) REVERT: A 933 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8336 (tptt) REVERT: A 966 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8773 (pt) REVERT: A 994 THR cc_start: 0.8994 (p) cc_final: 0.8779 (p) REVERT: A 1020 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 1036 ASP cc_start: 0.8245 (m-30) cc_final: 0.7739 (m-30) REVERT: A 1069 GLU cc_start: 0.7483 (pm20) cc_final: 0.7240 (pm20) REVERT: c 278 ASP cc_start: 0.8600 (m-30) cc_final: 0.8330 (t0) REVERT: c 312 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7806 (ttm-80) REVERT: c 338 GLU cc_start: 0.9094 (pm20) cc_final: 0.8875 (pm20) REVERT: c 409 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7872 (t0) REVERT: c 506 ASP cc_start: 0.6964 (m-30) cc_final: 0.6554 (m-30) REVERT: d 32 ASP cc_start: 0.8242 (m-30) cc_final: 0.7561 (m-30) REVERT: d 139 ARG cc_start: 0.8398 (ptm160) cc_final: 0.8022 (ttp80) REVERT: e 42 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8322 (tm-30) REVERT: e 107 GLU cc_start: 0.8278 (tp30) cc_final: 0.8037 (tp30) REVERT: e 165 TRP cc_start: 0.8406 (m100) cc_final: 0.8050 (m100) REVERT: e 185 TYR cc_start: 0.8364 (m-80) cc_final: 0.8066 (m-80) REVERT: e 206 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7684 (mm-30) REVERT: f 88 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7674 (mm-30) REVERT: f 120 ASP cc_start: 0.7898 (t70) cc_final: 0.7340 (t0) REVERT: g 118 ASN cc_start: 0.8693 (t0) cc_final: 0.8134 (t0) REVERT: g 130 ASN cc_start: 0.8501 (t0) cc_final: 0.8121 (t0) REVERT: g 144 ASN cc_start: 0.8696 (m110) cc_final: 0.8222 (m110) REVERT: h 75 MET cc_start: 0.8216 (pmm) cc_final: 0.7243 (pmm) REVERT: h 123 CYS cc_start: 0.8170 (m) cc_final: 0.7800 (m) REVERT: i 48 ASP cc_start: 0.7345 (t0) cc_final: 0.6667 (t0) REVERT: i 107 ASN cc_start: 0.8775 (m-40) cc_final: 0.8522 (m-40) REVERT: i 155 VAL cc_start: 0.8966 (m) cc_final: 0.8589 (m) REVERT: i 156 GLN cc_start: 0.9217 (mp10) cc_final: 0.8302 (mp10) REVERT: j 23 GLU cc_start: 0.8327 (tp30) cc_final: 0.7707 (tp30) REVERT: j 48 GLU cc_start: 0.8722 (tp30) cc_final: 0.8509 (tp30) REVERT: j 68 GLU cc_start: 0.8461 (tp30) cc_final: 0.8193 (tp30) REVERT: j 189 SER cc_start: 0.9100 (p) cc_final: 0.8799 (p) REVERT: j 271 ASP cc_start: 0.7969 (t0) cc_final: 0.7582 (t0) REVERT: k 3 GLN cc_start: 0.8944 (mp10) cc_final: 0.7999 (mm-40) REVERT: k 22 ASN cc_start: 0.8027 (t0) cc_final: 0.7475 (t0) REVERT: k 27 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8296 (mm-40) REVERT: k 35 GLU cc_start: 0.8400 (tt0) cc_final: 0.8123 (tp30) REVERT: k 126 ASP cc_start: 0.8569 (t0) cc_final: 0.8240 (t0) REVERT: k 136 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7441 (tp30) REVERT: k 163 SER cc_start: 0.9032 (t) cc_final: 0.8757 (p) REVERT: l 49 GLU cc_start: 0.7368 (tt0) cc_final: 0.6726 (tt0) REVERT: l 59 ASN cc_start: 0.8365 (t0) cc_final: 0.7843 (t0) REVERT: l 102 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7148 (tm-30) REVERT: l 106 HIS cc_start: 0.7779 (t-90) cc_final: 0.7415 (t70) REVERT: l 113 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6935 (tm-30) REVERT: l 143 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7643 (m110) REVERT: l 147 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6889 (mm-30) REVERT: l 148 ASN cc_start: 0.8454 (m-40) cc_final: 0.7829 (m110) REVERT: b 354 GLU cc_start: 0.8689 (tp30) cc_final: 0.8450 (tp30) REVERT: b 363 TRP cc_start: 0.9463 (t60) cc_final: 0.8989 (t60) REVERT: b 429 ASP cc_start: 0.8601 (m-30) cc_final: 0.8179 (m-30) REVERT: b 506 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8368 (tt) REVERT: b 535 HIS cc_start: 0.7770 (t70) cc_final: 0.7566 (t-90) REVERT: b 538 TYR cc_start: 0.8556 (t80) cc_final: 0.8291 (t80) REVERT: b 663 GLN cc_start: 0.8322 (tp40) cc_final: 0.8104 (tt0) REVERT: b 692 GLU cc_start: 0.7526 (pt0) cc_final: 0.7291 (pt0) REVERT: b 728 GLU cc_start: 0.7866 (tt0) cc_final: 0.7461 (tt0) REVERT: b 734 GLN cc_start: 0.7902 (mm110) cc_final: 0.7646 (mm-40) REVERT: b 896 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7165 (mm-30) REVERT: b 911 ASN cc_start: 0.8866 (m-40) cc_final: 0.8232 (t0) REVERT: a 37 LYS cc_start: 0.8986 (ttmt) cc_final: 0.8255 (ttmm) REVERT: a 124 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8540 (p0) REVERT: a 536 LEU cc_start: 0.8980 (mt) cc_final: 0.8665 (mp) REVERT: a 629 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: a 752 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8077 (pp20) REVERT: a 867 ASP cc_start: 0.8417 (t0) cc_final: 0.8090 (t0) REVERT: a 913 ASP cc_start: 0.8457 (m-30) cc_final: 0.8159 (m-30) REVERT: a 933 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8677 (ttmm) REVERT: a 1002 ILE cc_start: 0.8379 (mm) cc_final: 0.7864 (mm) REVERT: a 1020 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8061 (tm-30) REVERT: a 1116 GLU cc_start: 0.8512 (tt0) cc_final: 0.8113 (tt0) REVERT: a 1217 ASP cc_start: 0.8479 (t70) cc_final: 0.8273 (t0) outliers start: 249 outliers final: 237 residues processed: 2808 average time/residue: 1.3197 time to fit residues: 6281.4944 Evaluate side-chains 2957 residues out of total 7054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 2712 time to evaluate : 7.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 106 HIS Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 TYR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 173 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 653 CYS Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 813 TYR Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 894 GLU Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain B residue 987 HIS Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1090 VAL Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 966 ILE Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1236 SER Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 232 LEU Chi-restraints excluded: chain c residue 244 THR Chi-restraints excluded: chain c residue 263 GLU Chi-restraints excluded: chain c residue 409 ASN Chi-restraints excluded: chain c residue 517 THR Chi-restraints excluded: chain c residue 559 ILE Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 40 SER Chi-restraints excluded: chain d residue 68 GLN Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 106 HIS Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 141 SER Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain e residue 199 LEU Chi-restraints excluded: chain e residue 259 SER Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 118 ILE Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 40 ASP Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 137 THR Chi-restraints excluded: chain g residue 140 ILE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 48 SER Chi-restraints excluded: chain h residue 69 TYR Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain h residue 204 SER Chi-restraints excluded: chain h residue 209 GLU Chi-restraints excluded: chain h residue 215 VAL Chi-restraints excluded: chain i residue 15 GLU Chi-restraints excluded: chain i residue 77 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 165 SER Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 45 ILE Chi-restraints excluded: chain j residue 88 SER Chi-restraints excluded: chain j residue 174 LEU Chi-restraints excluded: chain j residue 179 ILE Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain j residue 210 MET Chi-restraints excluded: chain j residue 226 ASN Chi-restraints excluded: chain k residue 25 ASN Chi-restraints excluded: chain k residue 44 SER Chi-restraints excluded: chain k residue 105 SER Chi-restraints excluded: chain k residue 136 GLU Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 173 LEU Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain l residue 111 LEU Chi-restraints excluded: chain l residue 138 THR Chi-restraints excluded: chain l residue 143 ASN Chi-restraints excluded: chain l residue 171 ILE Chi-restraints excluded: chain b residue 320 SER Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 438 LEU Chi-restraints excluded: chain b residue 457 GLU Chi-restraints excluded: chain b residue 482 CYS Chi-restraints excluded: chain b residue 506 LEU Chi-restraints excluded: chain b residue 559 VAL Chi-restraints excluded: chain b residue 592 ILE Chi-restraints excluded: chain b residue 653 CYS Chi-restraints excluded: chain b residue 690 GLU Chi-restraints excluded: chain b residue 747 THR Chi-restraints excluded: chain b residue 813 TYR Chi-restraints excluded: chain b residue 844 ASN Chi-restraints excluded: chain b residue 934 CYS Chi-restraints excluded: chain b residue 945 ILE Chi-restraints excluded: chain b residue 947 LEU Chi-restraints excluded: chain b residue 987 HIS Chi-restraints excluded: chain b residue 988 VAL Chi-restraints excluded: chain b residue 1078 VAL Chi-restraints excluded: chain b residue 1090 VAL Chi-restraints excluded: chain a residue 2 ASN Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 96 ILE Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain a residue 160 ILE Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 173 ASN Chi-restraints excluded: chain a residue 278 ILE Chi-restraints excluded: chain a residue 320 SER Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 342 ILE Chi-restraints excluded: chain a residue 416 ILE Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 421 LEU Chi-restraints excluded: chain a residue 427 SER Chi-restraints excluded: chain a residue 447 THR Chi-restraints excluded: chain a residue 452 THR Chi-restraints excluded: chain a residue 500 LEU Chi-restraints excluded: chain a residue 533 VAL Chi-restraints excluded: chain a residue 629 ASP Chi-restraints excluded: chain a residue 720 ILE Chi-restraints excluded: chain a residue 804 SER Chi-restraints excluded: chain a residue 816 ILE Chi-restraints excluded: chain a residue 843 ILE Chi-restraints excluded: chain a residue 852 LEU Chi-restraints excluded: chain a residue 873 PHE Chi-restraints excluded: chain a residue 882 LEU Chi-restraints excluded: chain a residue 900 MET Chi-restraints excluded: chain a residue 917 MET Chi-restraints excluded: chain a residue 985 ILE Chi-restraints excluded: chain a residue 1034 SER Chi-restraints excluded: chain a residue 1061 PHE Chi-restraints excluded: chain a residue 1078 VAL Chi-restraints excluded: chain a residue 1092 ASN Chi-restraints excluded: chain a residue 1198 SER Chi-restraints excluded: chain a residue 1212 ASP Chi-restraints excluded: chain a residue 1236 SER Chi-restraints excluded: chain a residue 1238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 822 random chunks: chunk 399 optimal weight: 0.7980 chunk 517 optimal weight: 2.9990 chunk 694 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 601 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 653 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 670 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 133 GLN B 362 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 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 e 145 ASN f 50 ASN g 33 ASN h 126 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.130724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.099814 restraints weight = 304285.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.104544 restraints weight = 128874.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.107675 restraints weight = 76375.111| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 66826 Z= 0.203 Angle : 0.544 7.846 90446 Z= 0.286 Chirality : 0.040 0.179 10438 Planarity : 0.003 0.064 11462 Dihedral : 4.695 51.847 8938 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.87 % Favored : 90.01 % Rotamer: Outliers : 3.51 % Allowed : 21.97 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.06 (0.10), residues: 7496 helix: 1.42 (0.11), residues: 2560 sheet: -0.92 (0.13), residues: 1546 loop : -2.36 (0.10), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 649 HIS 0.006 0.001 HIS B 987 PHE 0.029 0.001 PHE j 52 TYR 0.028 0.001 TYR b1034 ARG 0.008 0.000 ARG g 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 73101.19 seconds wall clock time: 1242 minutes 25.70 seconds (74545.70 seconds total)