Starting phenix.real_space_refine on Fri Feb 16 18:55:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/02_2024/6toa_10542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/02_2024/6toa_10542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/02_2024/6toa_10542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/02_2024/6toa_10542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/02_2024/6toa_10542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/02_2024/6toa_10542.pdb" } resolution = 3.47 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= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 276 5.16 5 C 43152 2.51 5 N 12198 2.21 5 O 12270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H ARG 186": "NH1" <-> "NH2" Residue "H ARG 188": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "I ARG 139": "NH1" <-> "NH2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 320": "NH1" <-> "NH2" Residue "I ARG 324": "NH1" <-> "NH2" Residue "I ARG 333": "NH1" <-> "NH2" Residue "I ARG 372": "NH1" <-> "NH2" Residue "I PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J ARG 44": "NH1" <-> "NH2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J ASP 80": "OD1" <-> "OD2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J ARG 139": "NH1" <-> "NH2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J ARG 320": "NH1" <-> "NH2" Residue "J TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 324": "NH1" <-> "NH2" Residue "J ARG 333": "NH1" <-> "NH2" Residue "J ARG 372": "NH1" <-> "NH2" Residue "J PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "K ARG 131": "NH1" <-> "NH2" Residue "K ARG 186": "NH1" <-> "NH2" Residue "K ARG 188": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "M ARG 5": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 72": "NH1" <-> "NH2" Residue "M ARG 73": "NH1" <-> "NH2" Residue "M ARG 75": "NH1" <-> "NH2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "N ARG 28": "NH1" <-> "NH2" Residue "N ARG 31": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O ARG 113": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 186": "NH1" <-> "NH2" Residue "O ARG 188": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 95": "NH1" <-> "NH2" Residue "P ARG 103": "NH1" <-> "NH2" Residue "P ARG 139": "NH1" <-> "NH2" Residue "P ARG 220": "NH1" <-> "NH2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P ARG 324": "NH1" <-> "NH2" Residue "P ARG 333": "NH1" <-> "NH2" Residue "P ARG 372": "NH1" <-> "NH2" Residue "P PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 38": "NH1" <-> "NH2" Residue "Q ARG 44": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ASP 80": "OD1" <-> "OD2" Residue "Q ARG 95": "NH1" <-> "NH2" Residue "Q ARG 103": "NH1" <-> "NH2" Residue "Q ARG 139": "NH1" <-> "NH2" Residue "Q ARG 220": "NH1" <-> "NH2" Residue "Q ARG 320": "NH1" <-> "NH2" Residue "Q TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 324": "NH1" <-> "NH2" Residue "Q ARG 333": "NH1" <-> "NH2" Residue "Q ARG 372": "NH1" <-> "NH2" Residue "Q PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 24": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 113": "NH1" <-> "NH2" Residue "R ARG 115": "NH1" <-> "NH2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R ARG 186": "NH1" <-> "NH2" Residue "R ARG 188": "NH1" <-> "NH2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 101": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T ARG 47": "NH1" <-> "NH2" Residue "T ARG 72": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T ARG 75": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "T ARG 97": "NH1" <-> "NH2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 31": "NH1" <-> "NH2" Residue "U ARG 51": "NH1" <-> "NH2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V ARG 64": "NH1" <-> "NH2" Residue "V ARG 71": "NH1" <-> "NH2" Residue "V ARG 113": "NH1" <-> "NH2" Residue "V ARG 115": "NH1" <-> "NH2" Residue "V ARG 186": "NH1" <-> "NH2" Residue "V ARG 188": "NH1" <-> "NH2" Residue "W ARG 38": "NH1" <-> "NH2" Residue "W ARG 51": "NH1" <-> "NH2" Residue "W ARG 95": "NH1" <-> "NH2" Residue "W ARG 103": "NH1" <-> "NH2" Residue "W ARG 139": "NH1" <-> "NH2" Residue "W ARG 220": "NH1" <-> "NH2" Residue "W ARG 320": "NH1" <-> "NH2" Residue "W ARG 324": "NH1" <-> "NH2" Residue "W ARG 333": "NH1" <-> "NH2" Residue "W ARG 372": "NH1" <-> "NH2" Residue "W PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 38": "NH1" <-> "NH2" Residue "X ARG 44": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ASP 80": "OD1" <-> "OD2" Residue "X ARG 95": "NH1" <-> "NH2" Residue "X ARG 103": "NH1" <-> "NH2" Residue "X ARG 139": "NH1" <-> "NH2" Residue "X ARG 220": "NH1" <-> "NH2" Residue "X ARG 320": "NH1" <-> "NH2" Residue "X TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 324": "NH1" <-> "NH2" Residue "X ARG 333": "NH1" <-> "NH2" Residue "X ARG 372": "NH1" <-> "NH2" Residue "X PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 24": "NH1" <-> "NH2" Residue "Y ARG 61": "NH1" <-> "NH2" Residue "Y ARG 64": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 131": "NH1" <-> "NH2" Residue "Y ARG 186": "NH1" <-> "NH2" Residue "Y ARG 188": "NH1" <-> "NH2" Residue "Z ARG 18": "NH1" <-> "NH2" Residue "Z TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 101": "NH1" <-> "NH2" Residue "0 ARG 5": "NH1" <-> "NH2" Residue "0 ARG 47": "NH1" <-> "NH2" Residue "0 ARG 72": "NH1" <-> "NH2" Residue "0 ARG 73": "NH1" <-> "NH2" Residue "0 ARG 75": "NH1" <-> "NH2" Residue "0 ARG 81": "NH1" <-> "NH2" Residue "0 ARG 97": "NH1" <-> "NH2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 ARG 31": "NH1" <-> "NH2" Residue "1 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 60": "NH1" <-> "NH2" Residue "1 ARG 80": "NH1" <-> "NH2" Residue "2 ARG 61": "NH1" <-> "NH2" Residue "2 ARG 64": "NH1" <-> "NH2" Residue "2 ARG 71": "NH1" <-> "NH2" Residue "2 ARG 113": "NH1" <-> "NH2" Residue "2 ARG 115": "NH1" <-> "NH2" Residue "2 ARG 186": "NH1" <-> "NH2" Residue "2 ARG 188": "NH1" <-> "NH2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 ARG 51": "NH1" <-> "NH2" Residue "3 ARG 95": "NH1" <-> "NH2" Residue "3 ARG 103": "NH1" <-> "NH2" Residue "3 ARG 139": "NH1" <-> "NH2" Residue "3 ARG 220": "NH1" <-> "NH2" Residue "3 ARG 320": "NH1" <-> "NH2" Residue "3 ARG 324": "NH1" <-> "NH2" Residue "3 ARG 333": "NH1" <-> "NH2" Residue "3 ARG 372": "NH1" <-> "NH2" Residue "3 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "4 ARG 51": "NH1" <-> "NH2" Residue "4 ASP 80": "OD1" <-> "OD2" Residue "4 ARG 95": "NH1" <-> "NH2" Residue "4 ARG 103": "NH1" <-> "NH2" Residue "4 ARG 139": "NH1" <-> "NH2" Residue "4 ARG 220": "NH1" <-> "NH2" Residue "4 ARG 320": "NH1" <-> "NH2" Residue "4 TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 324": "NH1" <-> "NH2" Residue "4 ARG 333": "NH1" <-> "NH2" Residue "4 ARG 372": "NH1" <-> "NH2" Residue "4 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "5 ARG 61": "NH1" <-> "NH2" Residue "5 ARG 64": "NH1" <-> "NH2" Residue "5 ARG 113": "NH1" <-> "NH2" Residue "5 ARG 115": "NH1" <-> "NH2" Residue "5 ARG 131": "NH1" <-> "NH2" Residue "5 ARG 186": "NH1" <-> "NH2" Residue "5 ARG 188": "NH1" <-> "NH2" Residue "6 ARG 18": "NH1" <-> "NH2" Residue "6 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 101": "NH1" <-> "NH2" Residue "7 ARG 5": "NH1" <-> "NH2" Residue "7 ARG 47": "NH1" <-> "NH2" Residue "7 ARG 72": "NH1" <-> "NH2" Residue "7 ARG 73": "NH1" <-> "NH2" Residue "7 ARG 75": "NH1" <-> "NH2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 ARG 97": "NH1" <-> "NH2" Residue "8 ARG 28": "NH1" <-> "NH2" Residue "8 ARG 31": "NH1" <-> "NH2" Residue "8 ARG 51": "NH1" <-> "NH2" Residue "8 ARG 60": "NH1" <-> "NH2" Residue "8 ARG 80": "NH1" <-> "NH2" Residue "9 ARG 61": "NH1" <-> "NH2" Residue "9 ARG 64": "NH1" <-> "NH2" Residue "9 ARG 71": "NH1" <-> "NH2" Residue "9 ARG 113": "NH1" <-> "NH2" Residue "9 ARG 115": "NH1" <-> "NH2" Residue "9 ARG 186": "NH1" <-> "NH2" Residue "9 ARG 188": "NH1" <-> "NH2" Residue "a ARG 38": "NH1" <-> "NH2" Residue "a ARG 51": "NH1" <-> "NH2" Residue "a ARG 95": "NH1" <-> "NH2" Residue "a ARG 103": "NH1" <-> "NH2" Residue "a ARG 139": "NH1" <-> "NH2" Residue "a ARG 220": "NH1" <-> "NH2" Residue "a ARG 320": "NH1" <-> "NH2" Residue "a ARG 324": "NH1" <-> "NH2" Residue "a ARG 333": "NH1" <-> "NH2" Residue "a ARG 372": "NH1" <-> "NH2" Residue "a PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 38": "NH1" <-> "NH2" Residue "b ARG 44": "NH1" <-> "NH2" Residue "b ARG 51": "NH1" <-> "NH2" Residue "b ASP 80": "OD1" <-> "OD2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "b ARG 103": "NH1" <-> "NH2" Residue "b ARG 139": "NH1" <-> "NH2" Residue "b ARG 220": "NH1" <-> "NH2" Residue "b ARG 320": "NH1" <-> "NH2" Residue "b TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 324": "NH1" <-> "NH2" Residue "b ARG 333": "NH1" <-> "NH2" Residue "b ARG 372": "NH1" <-> "NH2" Residue "b PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 24": "NH1" <-> "NH2" Residue "c ARG 61": "NH1" <-> "NH2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c ARG 115": "NH1" <-> "NH2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 186": "NH1" <-> "NH2" Residue "c ARG 188": "NH1" <-> "NH2" Residue "d ARG 18": "NH1" <-> "NH2" Residue "d TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 101": "NH1" <-> "NH2" Residue "e ARG 5": "NH1" <-> "NH2" Residue "e ARG 47": "NH1" <-> "NH2" Residue "e ARG 72": "NH1" <-> "NH2" Residue "e ARG 73": "NH1" <-> "NH2" Residue "e ARG 75": "NH1" <-> "NH2" Residue "e ARG 81": "NH1" <-> "NH2" Residue "e ARG 97": "NH1" <-> "NH2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 31": "NH1" <-> "NH2" Residue "f ARG 51": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67896 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "A" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "D" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "E" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "H" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "I" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "J" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "K" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "L" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "M" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "N" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "O" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "P" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "Q" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "R" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "S" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "T" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "U" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "V" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "W" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "X" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "Y" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "Z" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "0" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "1" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "2" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "3" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "4" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "5" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "6" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "7" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "8" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "9" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "a" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "b" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "c" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "d" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "e" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "f" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Time building chain proxies: 25.91, per 1000 atoms: 0.38 Number of scatterers: 67896 At special positions: 0 Unit cell: (158.387, 158.387, 248.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 276 16.00 O 12270 8.00 N 12198 7.00 C 43152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.38 Conformation dependent library (CDL) restraints added in 9.1 seconds 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16212 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 102 sheets defined 33.8% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.96 Creating SS restraints... Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP C 21 " --> pdb=" O ALA C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.623A pdb=" N SER C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 165 removed outlier: 3.658A pdb=" N GLN C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL A 30 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.618A pdb=" N MET A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 54 " --> pdb=" O MET A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.953A pdb=" N ARG A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.713A pdb=" N ASN A 257 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 258' Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 344 removed outlier: 4.075A pdb=" N ARG A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 removed outlier: 4.317A pdb=" N VAL A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.748A pdb=" N ASN B 257 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 258' Processing helix chain 'B' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 326 removed outlier: 3.517A pdb=" N ARG B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG B 333 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 361 No H-bonds generated for 'chain 'B' and resid 359 through 361' Processing helix chain 'B' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 389 removed outlier: 4.036A pdb=" N VAL B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 147 removed outlier: 3.788A pdb=" N ALA D 146 " --> pdb=" O SER D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 165 removed outlier: 3.536A pdb=" N PHE D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'F' and resid 5 through 17 removed outlier: 3.532A pdb=" N GLN F 10 " --> pdb=" O ALA F 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU F 17 " --> pdb=" O VAL F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 90 removed outlier: 3.555A pdb=" N LYS F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA G 79 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG H 20 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 54 removed outlier: 3.624A pdb=" N SER H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 165 removed outlier: 3.657A pdb=" N GLN H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'I' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL I 30 " --> pdb=" O THR I 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY I 35 " --> pdb=" O ALA I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 54 removed outlier: 3.617A pdb=" N MET I 50 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG I 51 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE I 54 " --> pdb=" O MET I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA I 72 " --> pdb=" O ALA I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 96 removed outlier: 3.952A pdb=" N ARG I 96 " --> pdb=" O ASP I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU I 116 " --> pdb=" O GLY I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA I 196 " --> pdb=" O SER I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER I 211 " --> pdb=" O ALA I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 250 Processing helix chain 'I' and resid 254 through 258 removed outlier: 3.713A pdb=" N ASN I 257 " --> pdb=" O GLY I 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA I 258 " --> pdb=" O ALA I 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 254 through 258' Processing helix chain 'I' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE I 293 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE I 297 " --> pdb=" O ILE I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE I 304 " --> pdb=" O PRO I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG I 324 " --> pdb=" O ARG I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 344 removed outlier: 4.074A pdb=" N ARG I 333 " --> pdb=" O PRO I 329 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER I 343 " --> pdb=" O ALA I 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY I 344 " --> pdb=" O TRP I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN I 368 " --> pdb=" O VAL I 364 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 369 " --> pdb=" O GLU I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 389 removed outlier: 4.316A pdb=" N VAL I 386 " --> pdb=" O SER I 382 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU I 387 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL J 30 " --> pdb=" O THR J 26 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU J 116 " --> pdb=" O GLY J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP J 202 " --> pdb=" O ALA J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG J 243 " --> pdb=" O GLU J 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS J 251 " --> pdb=" O GLU J 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 258 removed outlier: 3.748A pdb=" N ASN J 257 " --> pdb=" O GLY J 254 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA J 258 " --> pdb=" O ALA J 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 254 through 258' Processing helix chain 'J' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA J 294 " --> pdb=" O ALA J 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE J 304 " --> pdb=" O PRO J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 326 removed outlier: 3.516A pdb=" N ARG J 320 " --> pdb=" O ALA J 316 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG J 324 " --> pdb=" O ARG J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG J 333 " --> pdb=" O PRO J 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER J 343 " --> pdb=" O ALA J 339 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN J 368 " --> pdb=" O VAL J 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU J 369 " --> pdb=" O GLU J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 389 removed outlier: 4.035A pdb=" N VAL J 386 " --> pdb=" O SER J 382 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU J 388 " --> pdb=" O LYS J 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU K 40 " --> pdb=" O ASP K 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER K 41 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA K 45 " --> pdb=" O SER K 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 147 removed outlier: 3.789A pdb=" N ALA K 146 " --> pdb=" O SER K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 165 removed outlier: 3.535A pdb=" N PHE K 156 " --> pdb=" O ALA K 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU K 165 " --> pdb=" O GLN K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'L' and resid 5 through 17 removed outlier: 3.531A pdb=" N GLN L 10 " --> pdb=" O ALA L 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA L 11 " --> pdb=" O GLY L 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU L 17 " --> pdb=" O VAL L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 90 removed outlier: 3.556A pdb=" N LYS L 82 " --> pdb=" O PHE L 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP L 90 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA N 79 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 54 removed outlier: 3.624A pdb=" N SER O 41 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG O 44 " --> pdb=" O LEU O 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA O 45 " --> pdb=" O SER O 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY O 52 " --> pdb=" O ALA O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 165 removed outlier: 3.658A pdb=" N GLN O 161 " --> pdb=" O LEU O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 185 Processing helix chain 'P' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL P 30 " --> pdb=" O THR P 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA P 33 " --> pdb=" O ILE P 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY P 35 " --> pdb=" O ALA P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 54 removed outlier: 3.618A pdb=" N MET P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG P 51 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE P 54 " --> pdb=" O MET P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL P 64 " --> pdb=" O GLY P 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA P 72 " --> pdb=" O ALA P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 96 removed outlier: 3.952A pdb=" N ARG P 96 " --> pdb=" O ASP P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA P 109 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN P 113 " --> pdb=" O ALA P 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU P 116 " --> pdb=" O GLY P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA P 196 " --> pdb=" O SER P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER P 211 " --> pdb=" O ALA P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 250 Processing helix chain 'P' and resid 254 through 258 removed outlier: 3.714A pdb=" N ASN P 257 " --> pdb=" O GLY P 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA P 258 " --> pdb=" O ALA P 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 254 through 258' Processing helix chain 'P' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE P 293 " --> pdb=" O ALA P 289 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE P 297 " --> pdb=" O ILE P 293 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE P 304 " --> pdb=" O PRO P 300 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG P 324 " --> pdb=" O ARG P 320 " (cutoff:3.500A) Processing helix chain 'P' and resid 327 through 344 removed outlier: 4.074A pdb=" N ARG P 333 " --> pdb=" O PRO P 329 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER P 343 " --> pdb=" O ALA P 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY P 344 " --> pdb=" O TRP P 340 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN P 368 " --> pdb=" O VAL P 364 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU P 369 " --> pdb=" O GLU P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 389 removed outlier: 4.316A pdb=" N VAL P 386 " --> pdb=" O SER P 382 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU P 387 " --> pdb=" O GLU P 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL Q 30 " --> pdb=" O THR Q 26 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET Q 32 " --> pdb=" O ARG Q 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA Q 33 " --> pdb=" O ILE Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 54 Processing helix chain 'Q' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL Q 64 " --> pdb=" O GLY Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 96 Processing helix chain 'Q' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU Q 116 " --> pdb=" O GLY Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP Q 202 " --> pdb=" O ALA Q 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG Q 243 " --> pdb=" O GLU Q 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS Q 251 " --> pdb=" O GLU Q 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN Q 253 " --> pdb=" O GLU Q 249 " (cutoff:3.500A) Processing helix chain 'Q' and resid 254 through 258 removed outlier: 3.747A pdb=" N ASN Q 257 " --> pdb=" O GLY Q 254 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA Q 258 " --> pdb=" O ALA Q 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 254 through 258' Processing helix chain 'Q' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA Q 294 " --> pdb=" O ALA Q 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA Q 296 " --> pdb=" O GLU Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE Q 304 " --> pdb=" O PRO Q 300 " (cutoff:3.500A) Processing helix chain 'Q' and resid 315 through 326 removed outlier: 3.516A pdb=" N ARG Q 320 " --> pdb=" O ALA Q 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Q 324 " --> pdb=" O ARG Q 320 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG Q 333 " --> pdb=" O PRO Q 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER Q 343 " --> pdb=" O ALA Q 339 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 361 No H-bonds generated for 'chain 'Q' and resid 359 through 361' Processing helix chain 'Q' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN Q 368 " --> pdb=" O VAL Q 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU Q 369 " --> pdb=" O GLU Q 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 380 through 389 removed outlier: 4.036A pdb=" N VAL Q 386 " --> pdb=" O SER Q 382 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU Q 387 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU Q 388 " --> pdb=" O LYS Q 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU R 40 " --> pdb=" O ASP R 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY R 52 " --> pdb=" O ALA R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 147 removed outlier: 3.788A pdb=" N ALA R 146 " --> pdb=" O SER R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 165 removed outlier: 3.536A pdb=" N PHE R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN R 161 " --> pdb=" O LEU R 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 165 " --> pdb=" O GLN R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'S' and resid 5 through 17 removed outlier: 3.531A pdb=" N GLN S 10 " --> pdb=" O ALA S 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA S 11 " --> pdb=" O GLY S 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU S 17 " --> pdb=" O VAL S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 90 removed outlier: 3.555A pdb=" N LYS S 82 " --> pdb=" O PHE S 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP S 90 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA U 79 " --> pdb=" O THR U 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG U 80 " --> pdb=" O ASP U 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE U 83 " --> pdb=" O ALA U 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG V 20 " --> pdb=" O VAL V 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP V 21 " --> pdb=" O ALA V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 54 removed outlier: 3.623A pdb=" N SER V 41 " --> pdb=" O ALA V 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR V 42 " --> pdb=" O ALA V 38 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG V 44 " --> pdb=" O LEU V 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA V 45 " --> pdb=" O SER V 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA V 49 " --> pdb=" O ALA V 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY V 52 " --> pdb=" O ALA V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 165 removed outlier: 3.658A pdb=" N GLN V 161 " --> pdb=" O LEU V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 185 Processing helix chain 'W' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL W 30 " --> pdb=" O THR W 26 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA W 33 " --> pdb=" O ILE W 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER W 34 " --> pdb=" O VAL W 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY W 35 " --> pdb=" O ALA W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 54 removed outlier: 3.618A pdb=" N MET W 50 " --> pdb=" O THR W 46 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG W 51 " --> pdb=" O VAL W 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE W 54 " --> pdb=" O MET W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL W 64 " --> pdb=" O GLY W 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA W 72 " --> pdb=" O ALA W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 88 through 96 removed outlier: 3.953A pdb=" N ARG W 96 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA W 109 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN W 113 " --> pdb=" O ALA W 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU W 116 " --> pdb=" O GLY W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA W 196 " --> pdb=" O SER W 192 " (cutoff:3.500A) Processing helix chain 'W' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER W 211 " --> pdb=" O ALA W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 250 Processing helix chain 'W' and resid 254 through 258 removed outlier: 3.713A pdb=" N ASN W 257 " --> pdb=" O GLY W 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA W 258 " --> pdb=" O ALA W 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 254 through 258' Processing helix chain 'W' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE W 293 " --> pdb=" O ALA W 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE W 297 " --> pdb=" O ILE W 293 " (cutoff:3.500A) Processing helix chain 'W' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE W 304 " --> pdb=" O PRO W 300 " (cutoff:3.500A) Processing helix chain 'W' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG W 324 " --> pdb=" O ARG W 320 " (cutoff:3.500A) Processing helix chain 'W' and resid 327 through 344 removed outlier: 4.075A pdb=" N ARG W 333 " --> pdb=" O PRO W 329 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER W 343 " --> pdb=" O ALA W 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY W 344 " --> pdb=" O TRP W 340 " (cutoff:3.500A) Processing helix chain 'W' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN W 368 " --> pdb=" O VAL W 364 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU W 369 " --> pdb=" O GLU W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 389 removed outlier: 4.317A pdb=" N VAL W 386 " --> pdb=" O SER W 382 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU W 387 " --> pdb=" O GLU W 383 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL X 30 " --> pdb=" O THR X 26 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET X 32 " --> pdb=" O ARG X 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA X 33 " --> pdb=" O ILE X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 54 Processing helix chain 'X' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL X 64 " --> pdb=" O GLY X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 96 Processing helix chain 'X' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU X 116 " --> pdb=" O GLY X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP X 202 " --> pdb=" O ALA X 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG X 243 " --> pdb=" O GLU X 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS X 251 " --> pdb=" O GLU X 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN X 253 " --> pdb=" O GLU X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 258 removed outlier: 3.748A pdb=" N ASN X 257 " --> pdb=" O GLY X 254 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA X 258 " --> pdb=" O ALA X 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 254 through 258' Processing helix chain 'X' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA X 294 " --> pdb=" O ALA X 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA X 296 " --> pdb=" O GLU X 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE X 304 " --> pdb=" O PRO X 300 " (cutoff:3.500A) Processing helix chain 'X' and resid 315 through 326 removed outlier: 3.517A pdb=" N ARG X 320 " --> pdb=" O ALA X 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG X 324 " --> pdb=" O ARG X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG X 333 " --> pdb=" O PRO X 329 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER X 343 " --> pdb=" O ALA X 339 " (cutoff:3.500A) Processing helix chain 'X' and resid 359 through 361 No H-bonds generated for 'chain 'X' and resid 359 through 361' Processing helix chain 'X' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN X 368 " --> pdb=" O VAL X 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU X 369 " --> pdb=" O GLU X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 380 through 389 removed outlier: 4.036A pdb=" N VAL X 386 " --> pdb=" O SER X 382 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU X 387 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU X 388 " --> pdb=" O LYS X 384 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP Y 21 " --> pdb=" O ALA Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU Y 40 " --> pdb=" O ASP Y 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER Y 41 " --> pdb=" O ALA Y 37 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA Y 45 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA Y 49 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY Y 52 " --> pdb=" O ALA Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 147 removed outlier: 3.788A pdb=" N ALA Y 146 " --> pdb=" O SER Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 165 removed outlier: 3.536A pdb=" N PHE Y 156 " --> pdb=" O ALA Y 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN Y 161 " --> pdb=" O LEU Y 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU Y 165 " --> pdb=" O GLN Y 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 180 through 185 Processing helix chain 'Z' and resid 5 through 17 removed outlier: 3.532A pdb=" N GLN Z 10 " --> pdb=" O ALA Z 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA Z 11 " --> pdb=" O GLY Z 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU Z 17 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 90 removed outlier: 3.555A pdb=" N LYS Z 82 " --> pdb=" O PHE Z 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP Z 90 " --> pdb=" O ALA Z 86 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA 1 79 " --> pdb=" O THR 1 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG 1 80 " --> pdb=" O ASP 1 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE 1 83 " --> pdb=" O ALA 1 79 " (cutoff:3.500A) Processing helix chain '2' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG 2 20 " --> pdb=" O VAL 2 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP 2 21 " --> pdb=" O ALA 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 35 through 54 removed outlier: 3.624A pdb=" N SER 2 41 " --> pdb=" O ALA 2 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR 2 42 " --> pdb=" O ALA 2 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG 2 44 " --> pdb=" O LEU 2 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA 2 45 " --> pdb=" O SER 2 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA 2 49 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY 2 52 " --> pdb=" O ALA 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 148 through 165 removed outlier: 3.657A pdb=" N GLN 2 161 " --> pdb=" O LEU 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 180 through 185 Processing helix chain '3' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL 3 30 " --> pdb=" O THR 3 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA 3 33 " --> pdb=" O ILE 3 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY 3 35 " --> pdb=" O ALA 3 31 " (cutoff:3.500A) Processing helix chain '3' and resid 45 through 54 removed outlier: 3.617A pdb=" N MET 3 50 " --> pdb=" O THR 3 46 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG 3 51 " --> pdb=" O VAL 3 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE 3 54 " --> pdb=" O MET 3 50 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL 3 64 " --> pdb=" O GLY 3 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA 3 72 " --> pdb=" O ALA 3 68 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 96 removed outlier: 3.952A pdb=" N ARG 3 96 " --> pdb=" O ASP 3 92 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA 3 109 " --> pdb=" O GLU 3 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU 3 116 " --> pdb=" O GLY 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA 3 196 " --> pdb=" O SER 3 192 " (cutoff:3.500A) Processing helix chain '3' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER 3 211 " --> pdb=" O ALA 3 207 " (cutoff:3.500A) Processing helix chain '3' and resid 237 through 250 Processing helix chain '3' and resid 254 through 258 removed outlier: 3.713A pdb=" N ASN 3 257 " --> pdb=" O GLY 3 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA 3 258 " --> pdb=" O ALA 3 255 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 254 through 258' Processing helix chain '3' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE 3 293 " --> pdb=" O ALA 3 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE 3 297 " --> pdb=" O ILE 3 293 " (cutoff:3.500A) Processing helix chain '3' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE 3 304 " --> pdb=" O PRO 3 300 " (cutoff:3.500A) Processing helix chain '3' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG 3 324 " --> pdb=" O ARG 3 320 " (cutoff:3.500A) Processing helix chain '3' and resid 327 through 344 removed outlier: 4.074A pdb=" N ARG 3 333 " --> pdb=" O PRO 3 329 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER 3 343 " --> pdb=" O ALA 3 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY 3 344 " --> pdb=" O TRP 3 340 " (cutoff:3.500A) Processing helix chain '3' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN 3 368 " --> pdb=" O VAL 3 364 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 3 369 " --> pdb=" O GLU 3 365 " (cutoff:3.500A) Processing helix chain '3' and resid 380 through 389 removed outlier: 4.316A pdb=" N VAL 3 386 " --> pdb=" O SER 3 382 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU 3 387 " --> pdb=" O GLU 3 383 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL 4 30 " --> pdb=" O THR 4 26 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET 4 32 " --> pdb=" O ARG 4 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA 4 33 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 54 Processing helix chain '4' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL 4 64 " --> pdb=" O GLY 4 60 " (cutoff:3.500A) Processing helix chain '4' and resid 91 through 96 Processing helix chain '4' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU 4 116 " --> pdb=" O GLY 4 112 " (cutoff:3.500A) Processing helix chain '4' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP 4 202 " --> pdb=" O ALA 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG 4 243 " --> pdb=" O GLU 4 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS 4 251 " --> pdb=" O GLU 4 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN 4 253 " --> pdb=" O GLU 4 249 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 258 removed outlier: 3.748A pdb=" N ASN 4 257 " --> pdb=" O GLY 4 254 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA 4 258 " --> pdb=" O ALA 4 255 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 254 through 258' Processing helix chain '4' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA 4 294 " --> pdb=" O ALA 4 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA 4 296 " --> pdb=" O GLU 4 292 " (cutoff:3.500A) Processing helix chain '4' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE 4 304 " --> pdb=" O PRO 4 300 " (cutoff:3.500A) Processing helix chain '4' and resid 315 through 326 removed outlier: 3.516A pdb=" N ARG 4 320 " --> pdb=" O ALA 4 316 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG 4 324 " --> pdb=" O ARG 4 320 " (cutoff:3.500A) Processing helix chain '4' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG 4 333 " --> pdb=" O PRO 4 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER 4 343 " --> pdb=" O ALA 4 339 " (cutoff:3.500A) Processing helix chain '4' and resid 359 through 361 No H-bonds generated for 'chain '4' and resid 359 through 361' Processing helix chain '4' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN 4 368 " --> pdb=" O VAL 4 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU 4 369 " --> pdb=" O GLU 4 365 " (cutoff:3.500A) Processing helix chain '4' and resid 380 through 389 removed outlier: 4.035A pdb=" N VAL 4 386 " --> pdb=" O SER 4 382 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU 4 387 " --> pdb=" O GLU 4 383 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU 4 388 " --> pdb=" O LYS 4 384 " (cutoff:3.500A) Processing helix chain '5' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP 5 21 " --> pdb=" O ALA 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER 5 41 " --> pdb=" O ALA 5 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA 5 45 " --> pdb=" O SER 5 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY 5 52 " --> pdb=" O ALA 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 143 through 147 removed outlier: 3.789A pdb=" N ALA 5 146 " --> pdb=" O SER 5 143 " (cutoff:3.500A) Processing helix chain '5' and resid 148 through 165 removed outlier: 3.535A pdb=" N PHE 5 156 " --> pdb=" O ALA 5 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN 5 161 " --> pdb=" O LEU 5 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU 5 165 " --> pdb=" O GLN 5 161 " (cutoff:3.500A) Processing helix chain '5' and resid 180 through 185 Processing helix chain '6' and resid 5 through 17 removed outlier: 3.531A pdb=" N GLN 6 10 " --> pdb=" O ALA 6 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA 6 11 " --> pdb=" O GLY 6 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU 6 17 " --> pdb=" O VAL 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 78 through 90 removed outlier: 3.556A pdb=" N LYS 6 82 " --> pdb=" O PHE 6 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP 6 90 " --> pdb=" O ALA 6 86 " (cutoff:3.500A) Processing helix chain '8' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA 8 79 " --> pdb=" O THR 8 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG 8 80 " --> pdb=" O ASP 8 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE 8 83 " --> pdb=" O ALA 8 79 " (cutoff:3.500A) Processing helix chain '9' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG 9 20 " --> pdb=" O VAL 9 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP 9 21 " --> pdb=" O ALA 9 17 " (cutoff:3.500A) Processing helix chain '9' and resid 35 through 54 removed outlier: 3.624A pdb=" N SER 9 41 " --> pdb=" O ALA 9 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG 9 44 " --> pdb=" O LEU 9 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA 9 45 " --> pdb=" O SER 9 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA 9 49 " --> pdb=" O ALA 9 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY 9 52 " --> pdb=" O ALA 9 48 " (cutoff:3.500A) Processing helix chain '9' and resid 148 through 165 removed outlier: 3.658A pdb=" N GLN 9 161 " --> pdb=" O LEU 9 157 " (cutoff:3.500A) Processing helix chain '9' and resid 180 through 185 Processing helix chain 'a' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL a 30 " --> pdb=" O THR a 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA a 33 " --> pdb=" O ILE a 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER a 34 " --> pdb=" O VAL a 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY a 35 " --> pdb=" O ALA a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 54 removed outlier: 3.618A pdb=" N MET a 50 " --> pdb=" O THR a 46 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG a 51 " --> pdb=" O VAL a 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE a 54 " --> pdb=" O MET a 50 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL a 64 " --> pdb=" O GLY a 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA a 72 " --> pdb=" O ALA a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 96 removed outlier: 3.952A pdb=" N ARG a 96 " --> pdb=" O ASP a 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA a 109 " --> pdb=" O GLU a 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN a 113 " --> pdb=" O ALA a 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU a 116 " --> pdb=" O GLY a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA a 196 " --> pdb=" O SER a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 250 Processing helix chain 'a' and resid 254 through 258 removed outlier: 3.714A pdb=" N ASN a 257 " --> pdb=" O GLY a 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA a 258 " --> pdb=" O ALA a 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 254 through 258' Processing helix chain 'a' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE a 293 " --> pdb=" O ALA a 289 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE a 297 " --> pdb=" O ILE a 293 " (cutoff:3.500A) Processing helix chain 'a' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE a 304 " --> pdb=" O PRO a 300 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG a 324 " --> pdb=" O ARG a 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 327 through 344 removed outlier: 4.074A pdb=" N ARG a 333 " --> pdb=" O PRO a 329 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER a 343 " --> pdb=" O ALA a 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY a 344 " --> pdb=" O TRP a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN a 368 " --> pdb=" O VAL a 364 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU a 369 " --> pdb=" O GLU a 365 " (cutoff:3.500A) Processing helix chain 'a' and resid 380 through 389 removed outlier: 4.316A pdb=" N VAL a 386 " --> pdb=" O SER a 382 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU a 387 " --> pdb=" O GLU a 383 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL b 30 " --> pdb=" O THR b 26 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET b 32 " --> pdb=" O ARG b 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA b 33 " --> pdb=" O ILE b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 54 Processing helix chain 'b' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL b 64 " --> pdb=" O GLY b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 96 Processing helix chain 'b' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU b 116 " --> pdb=" O GLY b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP b 202 " --> pdb=" O ALA b 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG b 243 " --> pdb=" O GLU b 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS b 251 " --> pdb=" O GLU b 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN b 253 " --> pdb=" O GLU b 249 " (cutoff:3.500A) Processing helix chain 'b' and resid 254 through 258 removed outlier: 3.747A pdb=" N ASN b 257 " --> pdb=" O GLY b 254 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA b 258 " --> pdb=" O ALA b 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 254 through 258' Processing helix chain 'b' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA b 294 " --> pdb=" O ALA b 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA b 296 " --> pdb=" O GLU b 292 " (cutoff:3.500A) Processing helix chain 'b' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE b 304 " --> pdb=" O PRO b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 315 through 326 removed outlier: 3.516A pdb=" N ARG b 320 " --> pdb=" O ALA b 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG b 324 " --> pdb=" O ARG b 320 " (cutoff:3.500A) Processing helix chain 'b' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG b 333 " --> pdb=" O PRO b 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER b 343 " --> pdb=" O ALA b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 359 through 361 No H-bonds generated for 'chain 'b' and resid 359 through 361' Processing helix chain 'b' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN b 368 " --> pdb=" O VAL b 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU b 369 " --> pdb=" O GLU b 365 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 389 removed outlier: 4.036A pdb=" N VAL b 386 " --> pdb=" O SER b 382 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU b 387 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU b 388 " --> pdb=" O LYS b 384 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP c 21 " --> pdb=" O ALA c 17 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU c 40 " --> pdb=" O ASP c 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER c 41 " --> pdb=" O ALA c 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA c 45 " --> pdb=" O SER c 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY c 52 " --> pdb=" O ALA c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 147 removed outlier: 3.788A pdb=" N ALA c 146 " --> pdb=" O SER c 143 " (cutoff:3.500A) Processing helix chain 'c' and resid 148 through 165 removed outlier: 3.536A pdb=" N PHE c 156 " --> pdb=" O ALA c 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN c 161 " --> pdb=" O LEU c 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU c 165 " --> pdb=" O GLN c 161 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 185 Processing helix chain 'd' and resid 5 through 17 removed outlier: 3.531A pdb=" N GLN d 10 " --> pdb=" O ALA d 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA d 11 " --> pdb=" O GLY d 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU d 17 " --> pdb=" O VAL d 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 78 through 90 removed outlier: 3.555A pdb=" N LYS d 82 " --> pdb=" O PHE d 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP d 90 " --> pdb=" O ALA d 86 " (cutoff:3.500A) Processing helix chain 'f' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA f 79 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG f 80 " --> pdb=" O ASP f 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE f 83 " --> pdb=" O ALA f 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG C 61 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 138 " --> pdb=" O ARG C 61 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU C 133 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU C 89 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP C 135 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C 137 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR C 85 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU C 89 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR C 99 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= 3, first strand: chain 'A' and resid 134 through 136 removed outlier: 3.762A pdb=" N GLU A 134 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 122 " --> pdb=" O CYS A 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS A 177 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.797A pdb=" N GLY A 155 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 224 through 227 Processing sheet with id= 6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS B 353 " --> pdb=" O ILE B 77 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 134 through 136 removed outlier: 3.776A pdb=" N GLU B 134 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 177 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY B 155 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 224 through 227 Processing sheet with id= 10, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG D 61 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR D 137 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL D 86 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 91 " --> pdb=" O THR D 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D 99 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 45 through 46 Processing sheet with id= 12, first strand: chain 'F' and resid 62 through 68 removed outlier: 6.297A pdb=" N ARG F 130 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU F 107 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG F 132 " --> pdb=" O VAL F 105 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 85 through 88 removed outlier: 4.274A pdb=" N GLY E 33 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU E 14 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA E 31 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP E 36 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG E 64 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 63 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 17 through 19 Processing sheet with id= 15, first strand: chain 'E' and resid 45 through 48 Processing sheet with id= 16, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.380A pdb=" N ILE G 107 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA G 127 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE G 64 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA G 62 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 10 through 12 Processing sheet with id= 18, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG H 61 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 138 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU H 133 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU H 89 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP H 135 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR H 137 " --> pdb=" O THR H 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR H 85 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU H 89 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR H 99 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 76 through 79 Processing sheet with id= 20, first strand: chain 'I' and resid 134 through 136 removed outlier: 3.762A pdb=" N GLU I 134 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU I 122 " --> pdb=" O CYS I 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS I 177 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 143 through 146 removed outlier: 3.797A pdb=" N GLY I 155 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 224 through 227 Processing sheet with id= 23, first strand: chain 'J' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS J 353 " --> pdb=" O ILE J 77 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 134 through 136 removed outlier: 3.775A pdb=" N GLU J 134 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS J 177 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY J 155 " --> pdb=" O VAL J 146 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 224 through 227 Processing sheet with id= 27, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG K 61 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR K 137 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL K 86 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 91 " --> pdb=" O THR K 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR K 99 " --> pdb=" O LEU K 91 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 45 through 46 Processing sheet with id= 29, first strand: chain 'L' and resid 62 through 68 removed outlier: 6.296A pdb=" N ARG L 130 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU L 107 " --> pdb=" O ARG L 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG L 132 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 85 through 88 removed outlier: 4.275A pdb=" N GLY M 33 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU M 14 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA M 31 " --> pdb=" O GLU M 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP M 36 " --> pdb=" O ARG M 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG M 64 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL M 63 " --> pdb=" O LEU M 102 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 17 through 19 Processing sheet with id= 32, first strand: chain 'M' and resid 45 through 48 Processing sheet with id= 33, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.381A pdb=" N ILE N 107 " --> pdb=" O ALA N 127 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA N 127 " --> pdb=" O ILE N 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE N 64 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA N 62 " --> pdb=" O SER N 128 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'N' and resid 10 through 12 Processing sheet with id= 35, first strand: chain 'O' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG O 61 " --> pdb=" O ALA O 138 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA O 138 " --> pdb=" O ARG O 61 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU O 133 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU O 89 " --> pdb=" O GLU O 133 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP O 135 " --> pdb=" O THR O 87 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR O 137 " --> pdb=" O THR O 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR O 85 " --> pdb=" O THR O 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU O 89 " --> pdb=" O VAL O 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR O 99 " --> pdb=" O LEU O 91 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'P' and resid 76 through 79 Processing sheet with id= 37, first strand: chain 'P' and resid 134 through 136 removed outlier: 3.761A pdb=" N GLU P 134 " --> pdb=" O VAL P 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU P 122 " --> pdb=" O CYS P 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS P 177 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 143 through 146 removed outlier: 3.796A pdb=" N GLY P 155 " --> pdb=" O VAL P 146 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'P' and resid 224 through 227 Processing sheet with id= 40, first strand: chain 'Q' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS Q 353 " --> pdb=" O ILE Q 77 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Q' and resid 134 through 136 removed outlier: 3.776A pdb=" N GLU Q 134 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS Q 177 " --> pdb=" O LEU Q 122 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Q' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY Q 155 " --> pdb=" O VAL Q 146 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Q' and resid 224 through 227 Processing sheet with id= 44, first strand: chain 'R' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG R 61 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR R 137 " --> pdb=" O VAL R 86 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL R 86 " --> pdb=" O THR R 137 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU R 91 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR R 99 " --> pdb=" O LEU R 91 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'S' and resid 45 through 46 Processing sheet with id= 46, first strand: chain 'S' and resid 62 through 68 removed outlier: 6.297A pdb=" N ARG S 130 " --> pdb=" O LEU S 107 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU S 107 " --> pdb=" O ARG S 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG S 132 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'T' and resid 85 through 88 removed outlier: 4.275A pdb=" N GLY T 33 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU T 14 " --> pdb=" O ALA T 31 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA T 31 " --> pdb=" O GLU T 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP T 36 " --> pdb=" O ARG T 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG T 64 " --> pdb=" O TRP T 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL T 63 " --> pdb=" O LEU T 102 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'T' and resid 17 through 19 Processing sheet with id= 49, first strand: chain 'T' and resid 45 through 48 Processing sheet with id= 50, first strand: chain 'U' and resid 10 through 12 removed outlier: 5.381A pdb=" N ILE U 107 " --> pdb=" O ALA U 127 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA U 127 " --> pdb=" O ILE U 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE U 64 " --> pdb=" O MET U 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA U 62 " --> pdb=" O SER U 128 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'U' and resid 10 through 12 Processing sheet with id= 52, first strand: chain 'V' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG V 61 " --> pdb=" O ALA V 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA V 138 " --> pdb=" O ARG V 61 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU V 133 " --> pdb=" O LEU V 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU V 89 " --> pdb=" O GLU V 133 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP V 135 " --> pdb=" O THR V 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR V 137 " --> pdb=" O THR V 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR V 85 " --> pdb=" O THR V 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU V 89 " --> pdb=" O VAL V 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR V 99 " --> pdb=" O LEU V 91 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'W' and resid 76 through 79 Processing sheet with id= 54, first strand: chain 'W' and resid 134 through 136 removed outlier: 3.762A pdb=" N GLU W 134 " --> pdb=" O VAL W 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU W 122 " --> pdb=" O CYS W 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS W 177 " --> pdb=" O LEU W 122 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'W' and resid 143 through 146 removed outlier: 3.797A pdb=" N GLY W 155 " --> pdb=" O VAL W 146 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 224 through 227 Processing sheet with id= 57, first strand: chain 'X' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS X 353 " --> pdb=" O ILE X 77 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'X' and resid 134 through 136 removed outlier: 3.776A pdb=" N GLU X 134 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS X 177 " --> pdb=" O LEU X 122 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'X' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY X 155 " --> pdb=" O VAL X 146 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'X' and resid 224 through 227 Processing sheet with id= 61, first strand: chain 'Y' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG Y 61 " --> pdb=" O ALA Y 138 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR Y 137 " --> pdb=" O VAL Y 86 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL Y 86 " --> pdb=" O THR Y 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU Y 91 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR Y 99 " --> pdb=" O LEU Y 91 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Z' and resid 45 through 46 Processing sheet with id= 63, first strand: chain 'Z' and resid 62 through 68 removed outlier: 6.297A pdb=" N ARG Z 130 " --> pdb=" O LEU Z 107 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU Z 107 " --> pdb=" O ARG Z 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG Z 132 " --> pdb=" O VAL Z 105 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '0' and resid 85 through 88 removed outlier: 4.274A pdb=" N GLY 0 33 " --> pdb=" O LEU 0 12 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU 0 14 " --> pdb=" O ALA 0 31 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA 0 31 " --> pdb=" O GLU 0 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP 0 36 " --> pdb=" O ARG 0 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG 0 64 " --> pdb=" O TRP 0 36 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL 0 63 " --> pdb=" O LEU 0 102 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '0' and resid 17 through 19 Processing sheet with id= 66, first strand: chain '0' and resid 45 through 48 Processing sheet with id= 67, first strand: chain '1' and resid 10 through 12 removed outlier: 5.380A pdb=" N ILE 1 107 " --> pdb=" O ALA 1 127 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA 1 127 " --> pdb=" O ILE 1 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE 1 64 " --> pdb=" O MET 1 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA 1 62 " --> pdb=" O SER 1 128 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '1' and resid 10 through 12 Processing sheet with id= 69, first strand: chain '2' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG 2 61 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA 2 138 " --> pdb=" O ARG 2 61 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU 2 133 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU 2 89 " --> pdb=" O GLU 2 133 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP 2 135 " --> pdb=" O THR 2 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR 2 137 " --> pdb=" O THR 2 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR 2 85 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU 2 89 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR 2 99 " --> pdb=" O LEU 2 91 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '3' and resid 76 through 79 Processing sheet with id= 71, first strand: chain '3' and resid 134 through 136 removed outlier: 3.762A pdb=" N GLU 3 134 " --> pdb=" O VAL 3 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 3 122 " --> pdb=" O CYS 3 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS 3 177 " --> pdb=" O LEU 3 122 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '3' and resid 143 through 146 removed outlier: 3.797A pdb=" N GLY 3 155 " --> pdb=" O VAL 3 146 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '3' and resid 224 through 227 Processing sheet with id= 74, first strand: chain '4' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS 4 353 " --> pdb=" O ILE 4 77 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '4' and resid 134 through 136 removed outlier: 3.775A pdb=" N GLU 4 134 " --> pdb=" O VAL 4 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS 4 177 " --> pdb=" O LEU 4 122 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '4' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY 4 155 " --> pdb=" O VAL 4 146 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '4' and resid 224 through 227 Processing sheet with id= 78, first strand: chain '5' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG 5 61 " --> pdb=" O ALA 5 138 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR 5 137 " --> pdb=" O VAL 5 86 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL 5 86 " --> pdb=" O THR 5 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU 5 91 " --> pdb=" O THR 5 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR 5 99 " --> pdb=" O LEU 5 91 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '6' and resid 45 through 46 Processing sheet with id= 80, first strand: chain '6' and resid 62 through 68 removed outlier: 6.296A pdb=" N ARG 6 130 " --> pdb=" O LEU 6 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU 6 107 " --> pdb=" O ARG 6 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG 6 132 " --> pdb=" O VAL 6 105 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '7' and resid 85 through 88 removed outlier: 4.275A pdb=" N GLY 7 33 " --> pdb=" O LEU 7 12 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU 7 14 " --> pdb=" O ALA 7 31 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA 7 31 " --> pdb=" O GLU 7 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP 7 36 " --> pdb=" O ARG 7 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG 7 64 " --> pdb=" O TRP 7 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL 7 63 " --> pdb=" O LEU 7 102 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '7' and resid 17 through 19 Processing sheet with id= 83, first strand: chain '7' and resid 45 through 48 Processing sheet with id= 84, first strand: chain '8' and resid 10 through 12 removed outlier: 5.381A pdb=" N ILE 8 107 " --> pdb=" O ALA 8 127 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA 8 127 " --> pdb=" O ILE 8 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE 8 64 " --> pdb=" O MET 8 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA 8 62 " --> pdb=" O SER 8 128 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain '8' and resid 10 through 12 Processing sheet with id= 86, first strand: chain '9' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG 9 61 " --> pdb=" O ALA 9 138 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA 9 138 " --> pdb=" O ARG 9 61 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU 9 133 " --> pdb=" O LEU 9 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU 9 89 " --> pdb=" O GLU 9 133 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP 9 135 " --> pdb=" O THR 9 87 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR 9 137 " --> pdb=" O THR 9 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR 9 85 " --> pdb=" O THR 9 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU 9 89 " --> pdb=" O VAL 9 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR 9 99 " --> pdb=" O LEU 9 91 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'a' and resid 76 through 79 Processing sheet with id= 88, first strand: chain 'a' and resid 134 through 136 removed outlier: 3.761A pdb=" N GLU a 134 " --> pdb=" O VAL a 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU a 122 " --> pdb=" O CYS a 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS a 177 " --> pdb=" O LEU a 122 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'a' and resid 143 through 146 removed outlier: 3.796A pdb=" N GLY a 155 " --> pdb=" O VAL a 146 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'a' and resid 224 through 227 Processing sheet with id= 91, first strand: chain 'b' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS b 353 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'b' and resid 134 through 136 removed outlier: 3.776A pdb=" N GLU b 134 " --> pdb=" O VAL b 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS b 177 " --> pdb=" O LEU b 122 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'b' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY b 155 " --> pdb=" O VAL b 146 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'b' and resid 224 through 227 Processing sheet with id= 95, first strand: chain 'c' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG c 61 " --> pdb=" O ALA c 138 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR c 137 " --> pdb=" O VAL c 86 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL c 86 " --> pdb=" O THR c 137 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU c 91 " --> pdb=" O THR c 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR c 99 " --> pdb=" O LEU c 91 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'd' and resid 45 through 46 Processing sheet with id= 97, first strand: chain 'd' and resid 62 through 68 removed outlier: 6.297A pdb=" N ARG d 130 " --> pdb=" O LEU d 107 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU d 107 " --> pdb=" O ARG d 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG d 132 " --> pdb=" O VAL d 105 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'e' and resid 85 through 88 removed outlier: 4.275A pdb=" N GLY e 33 " --> pdb=" O LEU e 12 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU e 14 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA e 31 " --> pdb=" O GLU e 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP e 36 " --> pdb=" O ARG e 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG e 64 " --> pdb=" O TRP e 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL e 63 " --> pdb=" O LEU e 102 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'e' and resid 17 through 19 Processing sheet with id=100, first strand: chain 'e' and resid 45 through 48 Processing sheet with id=101, first strand: chain 'f' and resid 10 through 12 removed outlier: 5.381A pdb=" N ILE f 107 " --> pdb=" O ALA f 127 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA f 127 " --> pdb=" O ILE f 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE f 64 " --> pdb=" O MET f 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA f 62 " --> pdb=" O SER f 128 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'f' and resid 10 through 12 2370 hydrogen bonds defined for protein. 6714 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: 28.61 Time building geometry restraints manager: 22.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 22130 1.34 - 1.46: 12284 1.46 - 1.58: 34490 1.58 - 1.70: 6 1.70 - 1.82: 510 Bond restraints: 69420 Sorted by residual: bond pdb=" N PRO Y 109 " pdb=" CD PRO Y 109 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.90e+01 bond pdb=" N PRO D 109 " pdb=" CD PRO D 109 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.90e+01 bond pdb=" N PRO R 109 " pdb=" CD PRO R 109 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.85e+01 bond pdb=" N PRO c 109 " pdb=" CD PRO c 109 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.85e+01 bond pdb=" N PRO K 109 " pdb=" CD PRO K 109 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.85e+01 ... (remaining 69415 not shown) Histogram of bond angle deviations from ideal: 96.52 - 105.08: 1906 105.08 - 113.64: 38050 113.64 - 122.21: 41544 122.21 - 130.77: 12496 130.77 - 139.33: 402 Bond angle restraints: 94398 Sorted by residual: angle pdb=" N ASP X 150 " pdb=" CA ASP X 150 " pdb=" C ASP X 150 " ideal model delta sigma weight residual 109.50 125.38 -15.88 1.58e+00 4.01e-01 1.01e+02 angle pdb=" N ASP B 150 " pdb=" CA ASP B 150 " pdb=" C ASP B 150 " ideal model delta sigma weight residual 109.50 125.38 -15.88 1.58e+00 4.01e-01 1.01e+02 angle pdb=" N ASP b 150 " pdb=" CA ASP b 150 " pdb=" C ASP b 150 " ideal model delta sigma weight residual 109.50 125.36 -15.86 1.58e+00 4.01e-01 1.01e+02 angle pdb=" N ASP Q 150 " pdb=" CA ASP Q 150 " pdb=" C ASP Q 150 " ideal model delta sigma weight residual 109.50 125.36 -15.86 1.58e+00 4.01e-01 1.01e+02 angle pdb=" N ASP 4 150 " pdb=" CA ASP 4 150 " pdb=" C ASP 4 150 " ideal model delta sigma weight residual 109.50 125.34 -15.84 1.58e+00 4.01e-01 1.01e+02 ... (remaining 94393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.75: 38208 14.75 - 29.51: 2336 29.51 - 44.26: 538 44.26 - 59.02: 48 59.02 - 73.77: 60 Dihedral angle restraints: 41190 sinusoidal: 15828 harmonic: 25362 Sorted by residual: dihedral pdb=" CA ALA D 102 " pdb=" C ALA D 102 " pdb=" N ALA D 103 " pdb=" CA ALA D 103 " ideal model delta harmonic sigma weight residual 180.00 150.61 29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA Y 102 " pdb=" C ALA Y 102 " pdb=" N ALA Y 103 " pdb=" CA ALA Y 103 " ideal model delta harmonic sigma weight residual 180.00 150.61 29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA c 102 " pdb=" C ALA c 102 " pdb=" N ALA c 103 " pdb=" CA ALA c 103 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 41187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 8840 0.087 - 0.174: 1442 0.174 - 0.260: 200 0.260 - 0.347: 6 0.347 - 0.434: 24 Chirality restraints: 10512 Sorted by residual: chirality pdb=" CB ILE W 225 " pdb=" CA ILE W 225 " pdb=" CG1 ILE W 225 " pdb=" CG2 ILE W 225 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CB ILE A 225 " pdb=" CA ILE A 225 " pdb=" CG1 ILE A 225 " pdb=" CG2 ILE A 225 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CB ILE 3 225 " pdb=" CA ILE 3 225 " pdb=" CG1 ILE 3 225 " pdb=" CG2 ILE 3 225 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 10509 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY d 48 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO d 49 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO d 49 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO d 49 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY S 48 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO S 49 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO S 49 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO S 49 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Z 48 " -0.049 5.00e-02 4.00e+02 7.37e-02 8.69e+00 pdb=" N PRO Z 49 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO Z 49 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Z 49 " -0.042 5.00e-02 4.00e+02 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1510 2.67 - 3.23: 60710 3.23 - 3.78: 106932 3.78 - 4.34: 143156 4.34 - 4.90: 239630 Nonbonded interactions: 551938 Sorted by model distance: nonbonded pdb=" OD1 ASP b 150 " pdb=" N GLY b 151 " model vdw 2.110 2.520 nonbonded pdb=" OD1 ASP Q 150 " pdb=" N GLY Q 151 " model vdw 2.110 2.520 nonbonded pdb=" OD1 ASP J 150 " pdb=" N GLY J 151 " model vdw 2.110 2.520 nonbonded pdb=" OD1 ASP 4 150 " pdb=" N GLY 4 151 " model vdw 2.110 2.520 nonbonded pdb=" OD1 ASP X 150 " pdb=" N GLY X 151 " model vdw 2.111 2.520 ... (remaining 551933 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 '0' selection = chain '7' selection = chain 'E' selection = chain 'M' selection = chain 'T' selection = chain 'e' } ncs_group { reference = chain '1' selection = chain '8' selection = chain 'G' selection = chain 'N' selection = chain 'U' selection = chain 'f' } ncs_group { reference = chain '2' selection = (chain '5' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) selection = chain '9' selection = chain 'C' selection = (chain 'D' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) selection = chain 'H' selection = (chain 'K' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) selection = chain 'O' selection = (chain 'R' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) selection = chain 'V' selection = (chain 'Y' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) selection = (chain 'c' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) } ncs_group { reference = (chain '3' and (resid 24 through 85 or resid 90 through 393)) selection = chain '4' selection = (chain 'A' and (resid 24 through 85 or resid 90 through 393)) selection = chain 'B' selection = (chain 'I' and (resid 24 through 85 or resid 90 through 393)) selection = chain 'J' selection = (chain 'P' and (resid 24 through 85 or resid 90 through 393)) selection = chain 'Q' selection = (chain 'W' and (resid 24 through 85 or resid 90 through 393)) selection = chain 'X' selection = (chain 'a' and (resid 24 through 85 or resid 90 through 393)) selection = chain 'b' } ncs_group { reference = chain '6' selection = chain 'F' selection = chain 'L' selection = chain 'S' selection = chain 'Z' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 8.030 Check model and map are aligned: 0.730 Set scattering table: 0.490 Process input model: 140.780 Find NCS groups from input model: 3.880 Set up NCS constraints: 0.540 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.009 0.075 69420 Z= 0.583 Angle : 1.238 15.877 94398 Z= 0.678 Chirality : 0.068 0.434 10512 Planarity : 0.009 0.074 12396 Dihedral : 10.848 73.774 24978 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.83 % Favored : 88.03 % Rotamer: Outliers : 0.54 % Allowed : 6.31 % Favored : 93.15 % 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: -5.85 (0.06), residues: 8874 helix: -4.84 (0.03), residues: 2766 sheet: -2.76 (0.11), residues: 1638 loop : -3.69 (0.07), residues: 4470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP W 370 HIS 0.014 0.003 HIS M 100 PHE 0.049 0.004 PHE S 78 TYR 0.031 0.004 TYR R 162 ARG 0.020 0.002 ARG K 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1969 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1933 time to evaluate : 5.397 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: C 40 LEU cc_start: 0.9229 (tt) cc_final: 0.8987 (tp) REVERT: C 180 VAL cc_start: 0.9266 (t) cc_final: 0.8910 (t) REVERT: A 141 ASP cc_start: 0.7823 (m-30) cc_final: 0.7545 (m-30) REVERT: B 242 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7731 (tm-30) REVERT: B 271 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8346 (ttpp) REVERT: D 32 LEU cc_start: 0.8226 (tp) cc_final: 0.8003 (tp) REVERT: D 90 ARG cc_start: 0.8225 (ptp-110) cc_final: 0.7999 (ptp-170) REVERT: E 108 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7927 (tp30) REVERT: G 35 ASN cc_start: 0.8302 (m-40) cc_final: 0.7982 (m110) REVERT: G 109 SER cc_start: 0.8192 (m) cc_final: 0.7887 (t) REVERT: I 88 HIS cc_start: 0.7017 (t-90) cc_final: 0.6678 (t-90) REVERT: I 119 ASN cc_start: 0.9331 (m-40) cc_final: 0.9118 (m110) REVERT: I 189 TYR cc_start: 0.9266 (m-80) cc_final: 0.8993 (m-80) REVERT: I 202 ASP cc_start: 0.7432 (m-30) cc_final: 0.7191 (m-30) REVERT: I 216 ASP cc_start: 0.7987 (t70) cc_final: 0.7544 (t0) REVERT: I 353 LYS cc_start: 0.8998 (pttm) cc_final: 0.8735 (pttp) REVERT: J 84 ARG cc_start: 0.7548 (mpp80) cc_final: 0.7289 (mtt-85) REVERT: J 242 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7764 (tm-30) REVERT: J 314 ASN cc_start: 0.7688 (p0) cc_final: 0.7446 (p0) REVERT: J 351 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7582 (mt-10) REVERT: L 16 GLN cc_start: 0.9204 (tp40) cc_final: 0.8985 (tp-100) REVERT: L 51 ASP cc_start: 0.7930 (p0) cc_final: 0.7562 (p0) REVERT: M 108 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7817 (tp30) REVERT: N 44 LEU cc_start: 0.8847 (tp) cc_final: 0.8088 (mp) REVERT: N 47 GLN cc_start: 0.6628 (mm110) cc_final: 0.6021 (mm110) REVERT: N 109 SER cc_start: 0.8223 (m) cc_final: 0.7954 (t) REVERT: N 115 SER cc_start: 0.9059 (p) cc_final: 0.8829 (t) REVERT: O 135 ASP cc_start: 0.8140 (p0) cc_final: 0.7497 (p0) REVERT: Q 84 ARG cc_start: 0.7592 (mpp80) cc_final: 0.7367 (mtt-85) REVERT: Q 242 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7665 (tm-30) REVERT: Q 314 ASN cc_start: 0.7824 (p0) cc_final: 0.7571 (p0) REVERT: Q 351 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7594 (mt-10) REVERT: R 2 MET cc_start: 0.7648 (tpp) cc_final: 0.7402 (tpp) REVERT: S 40 LEU cc_start: 0.8359 (tp) cc_final: 0.8130 (tp) REVERT: S 59 THR cc_start: 0.9038 (p) cc_final: 0.8789 (p) REVERT: T 59 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8380 (m-10) REVERT: T 108 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7508 (tm-30) REVERT: U 44 LEU cc_start: 0.8878 (tp) cc_final: 0.8178 (mp) REVERT: U 47 GLN cc_start: 0.6641 (mm110) cc_final: 0.6272 (mm110) REVERT: V 40 LEU cc_start: 0.9220 (tt) cc_final: 0.8991 (tp) REVERT: V 180 VAL cc_start: 0.9265 (t) cc_final: 0.8913 (t) REVERT: W 141 ASP cc_start: 0.7830 (m-30) cc_final: 0.7549 (m-30) REVERT: X 242 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7735 (tm-30) REVERT: X 271 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8338 (ttpp) REVERT: Y 90 ARG cc_start: 0.8229 (ptp-110) cc_final: 0.8001 (ptp-170) REVERT: 0 47 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7734 (ptt180) REVERT: 0 108 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7911 (tp30) REVERT: 1 35 ASN cc_start: 0.8298 (m-40) cc_final: 0.8001 (m110) REVERT: 1 109 SER cc_start: 0.8193 (m) cc_final: 0.7885 (t) REVERT: 3 83 ARG cc_start: 0.6810 (tmt-80) cc_final: 0.6545 (tmt170) REVERT: 3 88 HIS cc_start: 0.7032 (t-90) cc_final: 0.6691 (t-90) REVERT: 3 119 ASN cc_start: 0.9339 (m-40) cc_final: 0.9128 (m110) REVERT: 3 189 TYR cc_start: 0.9261 (m-80) cc_final: 0.8982 (m-80) REVERT: 3 202 ASP cc_start: 0.7425 (m-30) cc_final: 0.7183 (m-30) REVERT: 3 216 ASP cc_start: 0.7993 (t70) cc_final: 0.7554 (t0) REVERT: 3 353 LYS cc_start: 0.9004 (pttm) cc_final: 0.8740 (pttp) REVERT: 4 84 ARG cc_start: 0.7531 (mpp80) cc_final: 0.7166 (mtt-85) REVERT: 4 242 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7747 (tm-30) REVERT: 4 314 ASN cc_start: 0.7692 (p0) cc_final: 0.7468 (p0) REVERT: 4 351 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7562 (mt-10) REVERT: 6 16 GLN cc_start: 0.9198 (tp40) cc_final: 0.8988 (tp-100) REVERT: 6 51 ASP cc_start: 0.7920 (p0) cc_final: 0.7571 (p0) REVERT: 7 108 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7804 (tp30) REVERT: 8 12 LYS cc_start: 0.8451 (ptpp) cc_final: 0.8230 (ptmt) REVERT: 8 47 GLN cc_start: 0.6696 (mm110) cc_final: 0.6117 (mm110) REVERT: 8 109 SER cc_start: 0.8233 (m) cc_final: 0.7949 (t) REVERT: 9 135 ASP cc_start: 0.8137 (p0) cc_final: 0.7507 (p0) REVERT: 9 180 VAL cc_start: 0.9299 (t) cc_final: 0.8985 (t) REVERT: a 141 ASP cc_start: 0.7912 (m-30) cc_final: 0.7710 (m-30) REVERT: b 82 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.4645 (mp0) REVERT: b 84 ARG cc_start: 0.7580 (mpp80) cc_final: 0.7304 (mtt-85) REVERT: b 242 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7659 (tm-30) REVERT: b 314 ASN cc_start: 0.7824 (p0) cc_final: 0.7560 (p0) REVERT: b 351 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7588 (mt-10) REVERT: c 2 MET cc_start: 0.7653 (tpp) cc_final: 0.7413 (tpp) REVERT: d 40 LEU cc_start: 0.8361 (tp) cc_final: 0.8139 (tp) REVERT: d 59 THR cc_start: 0.9012 (p) cc_final: 0.8765 (p) REVERT: e 59 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8374 (m-10) REVERT: e 108 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7523 (tm-30) REVERT: f 44 LEU cc_start: 0.8876 (tp) cc_final: 0.8177 (mp) REVERT: f 47 GLN cc_start: 0.6682 (mm110) cc_final: 0.6310 (mm110) outliers start: 36 outliers final: 18 residues processed: 1957 average time/residue: 0.7226 time to fit residues: 2303.9219 Evaluate side-chains 1400 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1379 time to evaluate : 5.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain F residue 123 ARG Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain L residue 123 ARG Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain P residue 346 LEU Chi-restraints excluded: chain S residue 123 ARG Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain W residue 346 LEU Chi-restraints excluded: chain Z residue 123 ARG Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain 3 residue 346 LEU Chi-restraints excluded: chain 6 residue 123 ARG Chi-restraints excluded: chain 6 residue 125 ILE Chi-restraints excluded: chain a residue 346 LEU Chi-restraints excluded: chain b residue 82 GLU Chi-restraints excluded: chain d residue 123 ARG Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain e residue 59 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 9.9990 chunk 673 optimal weight: 0.9990 chunk 373 optimal weight: 0.6980 chunk 229 optimal weight: 0.6980 chunk 454 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 696 optimal weight: 9.9990 chunk 269 optimal weight: 0.9990 chunk 423 optimal weight: 1.9990 chunk 518 optimal weight: 0.9990 chunk 806 optimal weight: 8.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 204 HIS ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN A 381 ASN B 119 ASN B 204 HIS ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS I 204 HIS ** I 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 358 GLN J 204 HIS J 217 ASN ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS L 15 GLN P 119 ASN P 204 HIS P 233 GLN ** P 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 358 GLN Q 204 HIS Q 217 ASN ** Q 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 283 HIS R 22 HIS S 15 GLN W 79 GLN ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 358 GLN W 381 ASN X 119 ASN X 204 HIS ** X 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 22 HIS 3 204 HIS ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 358 GLN 4 119 ASN 4 204 HIS 4 217 ASN ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 22 HIS 6 15 GLN a 119 ASN a 204 HIS a 233 GLN ** a 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 358 GLN b 204 HIS b 217 ASN ** b 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 22 HIS d 15 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 69420 Z= 0.212 Angle : 0.740 14.876 94398 Z= 0.368 Chirality : 0.047 0.313 10512 Planarity : 0.006 0.065 12396 Dihedral : 6.397 80.209 9919 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.54 % Favored : 91.42 % Rotamer: Outliers : 3.15 % Allowed : 12.68 % Favored : 84.17 % 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: -4.58 (0.07), residues: 8874 helix: -3.00 (0.07), residues: 2856 sheet: -2.57 (0.12), residues: 1674 loop : -3.26 (0.08), residues: 4344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 105 HIS 0.005 0.001 HIS W 88 PHE 0.017 0.002 PHE N 84 TYR 0.024 0.001 TYR P 156 ARG 0.008 0.001 ARG 9 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1758 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1547 time to evaluate : 5.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7619 (mpt-90) cc_final: 0.7393 (mtt180) REVERT: A 164 LYS cc_start: 0.8436 (mmtm) cc_final: 0.8224 (mmtm) REVERT: A 353 LYS cc_start: 0.9204 (pttt) cc_final: 0.8965 (pttp) REVERT: B 242 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B 244 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9007 (tp) REVERT: B 306 ILE cc_start: 0.9005 (mm) cc_final: 0.8800 (mm) REVERT: B 349 GLN cc_start: 0.8161 (tt0) cc_final: 0.7643 (tt0) REVERT: D 90 ARG cc_start: 0.8077 (ptp-110) cc_final: 0.7795 (ptp-170) REVERT: D 113 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7972 (ptm-80) REVERT: F 32 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8052 (p90) REVERT: F 46 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8452 (m) REVERT: F 118 GLU cc_start: 0.7178 (pt0) cc_final: 0.6920 (pt0) REVERT: E 14 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: E 108 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7710 (tm-30) REVERT: E 109 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8052 (mt-10) REVERT: G 7 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8779 (ttpp) REVERT: G 77 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8412 (tm-30) REVERT: H 106 ARG cc_start: 0.8104 (ttp-110) cc_final: 0.7675 (ptt90) REVERT: I 119 ASN cc_start: 0.9227 (m-40) cc_final: 0.8995 (m110) REVERT: I 202 ASP cc_start: 0.7468 (m-30) cc_final: 0.7261 (m-30) REVERT: I 216 ASP cc_start: 0.7824 (t70) cc_final: 0.7388 (t0) REVERT: I 244 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8768 (tt) REVERT: J 79 GLN cc_start: 0.7275 (mt0) cc_final: 0.7022 (mt0) REVERT: J 116 LEU cc_start: 0.9312 (mm) cc_final: 0.9106 (mt) REVERT: J 163 ARG cc_start: 0.7375 (mtt180) cc_final: 0.7139 (mtt180) REVERT: J 216 ASP cc_start: 0.7144 (m-30) cc_final: 0.6832 (m-30) REVERT: J 248 MET cc_start: 0.8693 (tpt) cc_final: 0.8453 (tpt) REVERT: N 44 LEU cc_start: 0.8726 (tp) cc_final: 0.8005 (mp) REVERT: N 47 GLN cc_start: 0.6732 (mm110) cc_final: 0.5853 (mm110) REVERT: N 77 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8309 (tm-30) REVERT: P 88 HIS cc_start: 0.6661 (t-90) cc_final: 0.6419 (t-90) REVERT: P 156 TYR cc_start: 0.9223 (m-80) cc_final: 0.9006 (m-80) REVERT: Q 77 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8636 (pp) REVERT: Q 168 ASP cc_start: 0.7828 (p0) cc_final: 0.7507 (p0) REVERT: Q 242 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7494 (tm-30) REVERT: Q 323 TYR cc_start: 0.8572 (m-80) cc_final: 0.7626 (m-80) REVERT: Q 351 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7561 (mt-10) REVERT: R 2 MET cc_start: 0.7961 (tpp) cc_final: 0.7752 (tpp) REVERT: R 64 ARG cc_start: 0.8256 (ttm110) cc_final: 0.8041 (ttp80) REVERT: S 51 ASP cc_start: 0.7599 (p0) cc_final: 0.7216 (p0) REVERT: T 45 SER cc_start: 0.9062 (p) cc_final: 0.8838 (p) REVERT: T 59 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8351 (m-10) REVERT: U 7 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8711 (ttmt) REVERT: U 44 LEU cc_start: 0.8873 (tp) cc_final: 0.8074 (mp) REVERT: U 77 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8339 (tm-30) REVERT: U 102 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8080 (tm-30) REVERT: W 163 ARG cc_start: 0.7609 (mpt-90) cc_final: 0.7385 (mtt180) REVERT: W 164 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8217 (mmtm) REVERT: W 169 MET cc_start: 0.7884 (mtm) cc_final: 0.7126 (mtm) REVERT: W 353 LYS cc_start: 0.9161 (pttt) cc_final: 0.8930 (pttp) REVERT: X 242 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7576 (tm-30) REVERT: X 244 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9031 (tp) REVERT: X 248 MET cc_start: 0.8735 (tpt) cc_final: 0.8421 (tpt) REVERT: X 306 ILE cc_start: 0.9003 (mm) cc_final: 0.8795 (mm) REVERT: X 349 GLN cc_start: 0.8181 (tt0) cc_final: 0.7676 (tt0) REVERT: Y 90 ARG cc_start: 0.8089 (ptp-110) cc_final: 0.7803 (ptp-170) REVERT: Y 113 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7971 (ptm-80) REVERT: Z 32 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8066 (p90) REVERT: Z 46 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8438 (m) REVERT: Z 118 GLU cc_start: 0.7170 (pt0) cc_final: 0.6908 (pt0) REVERT: 0 47 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7856 (ttp-170) REVERT: 0 108 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7726 (tm-30) REVERT: 1 7 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8780 (ttpp) REVERT: 1 77 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8392 (tm-30) REVERT: 3 119 ASN cc_start: 0.9233 (m-40) cc_final: 0.8940 (m110) REVERT: 3 202 ASP cc_start: 0.7464 (m-30) cc_final: 0.7256 (m-30) REVERT: 3 216 ASP cc_start: 0.7819 (t70) cc_final: 0.7402 (t0) REVERT: 3 244 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8780 (tt) REVERT: 4 116 LEU cc_start: 0.9315 (mm) cc_final: 0.9093 (mt) REVERT: 4 163 ARG cc_start: 0.7423 (mtt180) cc_final: 0.7166 (mtt180) REVERT: 4 215 LEU cc_start: 0.9172 (mt) cc_final: 0.8969 (mt) REVERT: 4 216 ASP cc_start: 0.7161 (m-30) cc_final: 0.6854 (m-30) REVERT: 4 242 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7635 (tm-30) REVERT: 4 248 MET cc_start: 0.8713 (tpt) cc_final: 0.8474 (tpt) REVERT: 4 351 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7652 (mt-10) REVERT: 6 51 ASP cc_start: 0.7556 (p0) cc_final: 0.7254 (p0) REVERT: 8 47 GLN cc_start: 0.6822 (mm110) cc_final: 0.5955 (mm110) REVERT: 8 77 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8339 (tm-30) REVERT: a 156 TYR cc_start: 0.9222 (m-80) cc_final: 0.9000 (m-80) REVERT: b 168 ASP cc_start: 0.7818 (p0) cc_final: 0.7497 (p0) REVERT: b 242 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7495 (tm-30) REVERT: b 323 TYR cc_start: 0.8571 (m-80) cc_final: 0.7631 (m-80) REVERT: c 2 MET cc_start: 0.7967 (tpp) cc_final: 0.7757 (tpp) REVERT: c 64 ARG cc_start: 0.8247 (ttm110) cc_final: 0.8040 (ttp80) REVERT: d 51 ASP cc_start: 0.7592 (p0) cc_final: 0.7229 (p0) REVERT: e 59 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8350 (m-10) REVERT: e 108 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7889 (tp30) REVERT: f 7 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8713 (ttmt) REVERT: f 44 LEU cc_start: 0.8869 (tp) cc_final: 0.8073 (mp) REVERT: f 77 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8332 (tm-30) REVERT: f 102 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8069 (tm-30) outliers start: 211 outliers final: 86 residues processed: 1691 average time/residue: 0.6639 time to fit residues: 1899.1866 Evaluate side-chains 1471 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1369 time to evaluate : 5.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 245 ILE Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 34 GLU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 45 ASP Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 244 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 102 GLN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain U residue 115 SER Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 159 THR Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 346 LEU Chi-restraints excluded: chain X residue 244 LEU Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 113 ARG Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Z residue 32 TYR Chi-restraints excluded: chain Z residue 46 SER Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain 0 residue 57 VAL Chi-restraints excluded: chain 1 residue 12 LYS Chi-restraints excluded: chain 1 residue 111 ASP Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 3 residue 45 ASP Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 244 LEU Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 245 ILE Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 6 residue 70 SER Chi-restraints excluded: chain 6 residue 125 ILE Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 57 VAL Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 7 residue 110 VAL Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 111 ASP Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 101 VAL Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 303 LEU Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 244 LEU Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 59 PHE Chi-restraints excluded: chain f residue 12 LYS Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 111 ASP Chi-restraints excluded: chain f residue 115 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 448 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 671 optimal weight: 0.0870 chunk 549 optimal weight: 10.0000 chunk 222 optimal weight: 0.7980 chunk 807 optimal weight: 0.9980 chunk 872 optimal weight: 4.9990 chunk 719 optimal weight: 0.9990 chunk 801 optimal weight: 20.0000 chunk 275 optimal weight: 0.9980 chunk 648 optimal weight: 9.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 HIS A 233 GLN A 253 GLN B 195 GLN B 217 ASN B 233 GLN ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS I 233 GLN I 253 GLN J 217 ASN ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 HIS ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 233 GLN P 253 GLN Q 195 GLN Q 217 ASN ** Q 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 HIS W 253 GLN X 217 ASN X 233 GLN ** X 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 283 HIS Z 10 GLN 3 233 GLN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 233 GLN a 253 GLN b 195 GLN b 217 ASN ** b 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 283 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 69420 Z= 0.179 Angle : 0.670 13.769 94398 Z= 0.328 Chirality : 0.045 0.285 10512 Planarity : 0.005 0.072 12396 Dihedral : 5.557 43.530 9884 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 4.20 % Allowed : 13.56 % Favored : 82.24 % 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: -3.72 (0.08), residues: 8874 helix: -1.81 (0.09), residues: 2844 sheet: -2.14 (0.12), residues: 1542 loop : -3.08 (0.08), residues: 4488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 5 105 HIS 0.010 0.001 HIS 3 88 PHE 0.017 0.002 PHE 4 322 TYR 0.015 0.001 TYR W 156 ARG 0.006 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1745 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1464 time to evaluate : 5.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7863 (mtt) cc_final: 0.7409 (mtt) REVERT: A 164 LYS cc_start: 0.8394 (mmtm) cc_final: 0.8149 (mmtm) REVERT: A 353 LYS cc_start: 0.9221 (pttt) cc_final: 0.9006 (pttp) REVERT: A 367 ASP cc_start: 0.7594 (m-30) cc_final: 0.7389 (m-30) REVERT: B 116 LEU cc_start: 0.9164 (mm) cc_final: 0.8908 (mt) REVERT: B 242 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 244 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8932 (tp) REVERT: B 257 ASN cc_start: 0.9038 (m-40) cc_final: 0.8784 (m110) REVERT: B 280 MET cc_start: 0.8152 (mpp) cc_final: 0.7947 (mpp) REVERT: B 349 GLN cc_start: 0.8115 (tt0) cc_final: 0.7663 (tt0) REVERT: D 107 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7537 (tt) REVERT: D 113 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7752 (ptt-90) REVERT: F 32 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.7932 (p90) REVERT: F 46 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8401 (m) REVERT: F 118 GLU cc_start: 0.7268 (pt0) cc_final: 0.7056 (pt0) REVERT: G 7 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8697 (tttt) REVERT: G 77 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8336 (tm-30) REVERT: G 85 ASP cc_start: 0.8340 (m-30) cc_final: 0.7755 (m-30) REVERT: G 106 MET cc_start: 0.7113 (ptm) cc_final: 0.6870 (ptm) REVERT: H 75 MET cc_start: 0.7621 (mmt) cc_final: 0.7352 (mmt) REVERT: H 106 ARG cc_start: 0.8083 (ttp-110) cc_final: 0.7722 (ptt90) REVERT: I 88 HIS cc_start: 0.7096 (t-90) cc_final: 0.6854 (t-90) REVERT: I 108 GLU cc_start: 0.7546 (pt0) cc_final: 0.7124 (tt0) REVERT: I 216 ASP cc_start: 0.7748 (t70) cc_final: 0.7352 (t0) REVERT: I 323 TYR cc_start: 0.8862 (m-80) cc_final: 0.8590 (m-80) REVERT: I 349 GLN cc_start: 0.8570 (tt0) cc_final: 0.8324 (mm-40) REVERT: I 353 LYS cc_start: 0.9127 (pttp) cc_final: 0.8701 (ptpp) REVERT: I 367 ASP cc_start: 0.7576 (m-30) cc_final: 0.7344 (m-30) REVERT: I 381 ASN cc_start: 0.8492 (m-40) cc_final: 0.8134 (m-40) REVERT: J 116 LEU cc_start: 0.9174 (mm) cc_final: 0.8902 (mt) REVERT: J 142 ARG cc_start: 0.8262 (mtm180) cc_final: 0.7910 (mtm180) REVERT: J 143 MET cc_start: 0.8416 (tpp) cc_final: 0.8083 (ttt) REVERT: J 163 ARG cc_start: 0.7433 (mtt180) cc_final: 0.7118 (mtt180) REVERT: J 306 ILE cc_start: 0.9186 (mm) cc_final: 0.8893 (mm) REVERT: M 108 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7811 (tp30) REVERT: N 47 GLN cc_start: 0.6766 (mm110) cc_final: 0.5882 (mm110) REVERT: N 77 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8233 (tm-30) REVERT: N 81 GLN cc_start: 0.8479 (tp40) cc_final: 0.8077 (tp40) REVERT: O 90 ARG cc_start: 0.7406 (mtm110) cc_final: 0.6808 (mtm110) REVERT: P 156 TYR cc_start: 0.9192 (m-80) cc_final: 0.8949 (m-80) REVERT: P 367 ASP cc_start: 0.7540 (m-30) cc_final: 0.7306 (m-30) REVERT: Q 77 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8661 (pp) REVERT: Q 116 LEU cc_start: 0.9191 (mm) cc_final: 0.8884 (mt) REVERT: Q 142 ARG cc_start: 0.8497 (mtm180) cc_final: 0.8055 (mtm180) REVERT: Q 143 MET cc_start: 0.8456 (tpp) cc_final: 0.8126 (ttt) REVERT: Q 168 ASP cc_start: 0.7833 (p0) cc_final: 0.7625 (p0) REVERT: Q 242 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7428 (tm-30) REVERT: Q 323 TYR cc_start: 0.8562 (m-80) cc_final: 0.7652 (m-80) REVERT: R 64 ARG cc_start: 0.8210 (ttm110) cc_final: 0.8000 (ttp80) REVERT: S 51 ASP cc_start: 0.7431 (p0) cc_final: 0.7033 (p0) REVERT: T 45 SER cc_start: 0.9057 (p) cc_final: 0.8480 (t) REVERT: T 59 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8280 (m-10) REVERT: T 108 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7420 (tm-30) REVERT: U 44 LEU cc_start: 0.8838 (tp) cc_final: 0.8087 (mp) REVERT: U 77 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8304 (tm-30) REVERT: U 102 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: W 50 MET cc_start: 0.7866 (mtt) cc_final: 0.7414 (mtt) REVERT: W 353 LYS cc_start: 0.9185 (pttt) cc_final: 0.8969 (pttp) REVERT: W 367 ASP cc_start: 0.7586 (m-30) cc_final: 0.7365 (m-30) REVERT: X 116 LEU cc_start: 0.9165 (mm) cc_final: 0.8910 (mt) REVERT: X 242 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7537 (tm-30) REVERT: X 244 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9047 (tp) REVERT: X 280 MET cc_start: 0.8148 (mpp) cc_final: 0.7928 (mpp) REVERT: X 349 GLN cc_start: 0.8087 (tt0) cc_final: 0.7698 (tt0) REVERT: Y 107 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7560 (tt) REVERT: Y 113 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7757 (ptt-90) REVERT: Z 32 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7952 (p90) REVERT: Z 46 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8380 (m) REVERT: Z 118 GLU cc_start: 0.7279 (pt0) cc_final: 0.6990 (pt0) REVERT: 0 108 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7710 (tm-30) REVERT: 1 7 LYS cc_start: 0.8975 (mtpp) cc_final: 0.8688 (tttt) REVERT: 1 77 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8300 (tm-30) REVERT: 3 108 GLU cc_start: 0.7554 (pt0) cc_final: 0.7153 (tt0) REVERT: 3 216 ASP cc_start: 0.7752 (t70) cc_final: 0.7367 (t0) REVERT: 3 323 TYR cc_start: 0.8870 (m-80) cc_final: 0.8606 (m-80) REVERT: 3 349 GLN cc_start: 0.8597 (tt0) cc_final: 0.8360 (mm-40) REVERT: 3 353 LYS cc_start: 0.9206 (pttt) cc_final: 0.8940 (ptpp) REVERT: 3 367 ASP cc_start: 0.7571 (m-30) cc_final: 0.7343 (m-30) REVERT: 3 381 ASN cc_start: 0.8494 (m-40) cc_final: 0.8149 (m-40) REVERT: 4 116 LEU cc_start: 0.9173 (mm) cc_final: 0.8898 (mt) REVERT: 4 133 ARG cc_start: 0.8188 (mmp80) cc_final: 0.7735 (mmp-170) REVERT: 4 142 ARG cc_start: 0.8269 (mtm180) cc_final: 0.7908 (mtm180) REVERT: 4 143 MET cc_start: 0.8401 (tpp) cc_final: 0.8052 (ttt) REVERT: 4 163 ARG cc_start: 0.7417 (mtt180) cc_final: 0.7071 (mtt180) REVERT: 4 168 ASP cc_start: 0.7900 (p0) cc_final: 0.7692 (p0) REVERT: 4 242 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7603 (tm-30) REVERT: 4 306 ILE cc_start: 0.9177 (mm) cc_final: 0.8882 (mm) REVERT: 5 122 MET cc_start: 0.6640 (mtp) cc_final: 0.6401 (mtt) REVERT: 7 108 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7780 (tp30) REVERT: 8 47 GLN cc_start: 0.6834 (mm110) cc_final: 0.5959 (mm110) REVERT: 8 77 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8267 (tm-30) REVERT: 8 81 GLN cc_start: 0.8488 (tp40) cc_final: 0.8092 (tp40) REVERT: 9 90 ARG cc_start: 0.7414 (mtm110) cc_final: 0.6816 (mtm110) REVERT: a 156 TYR cc_start: 0.9193 (m-80) cc_final: 0.8929 (m-80) REVERT: a 367 ASP cc_start: 0.7537 (m-30) cc_final: 0.7306 (m-30) REVERT: b 116 LEU cc_start: 0.9190 (mm) cc_final: 0.8876 (mt) REVERT: b 142 ARG cc_start: 0.8479 (mtm180) cc_final: 0.8032 (mtm180) REVERT: b 143 MET cc_start: 0.8435 (tpp) cc_final: 0.8112 (ttt) REVERT: b 168 ASP cc_start: 0.7828 (p0) cc_final: 0.7617 (p0) REVERT: b 242 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7446 (tm-30) REVERT: b 323 TYR cc_start: 0.8557 (m-80) cc_final: 0.7654 (m-80) REVERT: d 51 ASP cc_start: 0.7426 (p0) cc_final: 0.7045 (p0) REVERT: e 59 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8263 (m-10) REVERT: e 108 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7803 (tp30) REVERT: f 38 THR cc_start: 0.8909 (t) cc_final: 0.8680 (t) REVERT: f 77 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8313 (tm-30) REVERT: f 102 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: f 106 MET cc_start: 0.7780 (ptm) cc_final: 0.7545 (ptm) outliers start: 281 outliers final: 148 residues processed: 1637 average time/residue: 0.6885 time to fit residues: 1923.3830 Evaluate side-chains 1523 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1360 time to evaluate : 5.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain J residue 381 ASN Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain P residue 233 GLN Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain P residue 326 THR Chi-restraints excluded: chain P residue 346 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain T residue 103 SER Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 102 GLN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain W residue 159 THR Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 346 LEU Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 244 LEU Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 107 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 113 ARG Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Z residue 10 GLN Chi-restraints excluded: chain Z residue 32 TYR Chi-restraints excluded: chain Z residue 46 SER Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain 0 residue 57 VAL Chi-restraints excluded: chain 0 residue 103 SER Chi-restraints excluded: chain 1 residue 12 LYS Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 1 residue 102 GLN Chi-restraints excluded: chain 1 residue 111 ASP Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 117 GLU Chi-restraints excluded: chain 3 residue 45 ASP Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 346 LEU Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 381 ASN Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 189 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 6 residue 70 SER Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 6 residue 125 ILE Chi-restraints excluded: chain 7 residue 57 VAL Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 111 ASP Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 77 THR Chi-restraints excluded: chain 9 residue 123 LEU Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 117 SER Chi-restraints excluded: chain a residue 191 LEU Chi-restraints excluded: chain a residue 233 GLN Chi-restraints excluded: chain a residue 303 LEU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 346 LEU Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 189 THR Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 80 THR Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 59 PHE Chi-restraints excluded: chain e residue 103 SER Chi-restraints excluded: chain f residue 12 LYS Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 111 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 798 optimal weight: 3.9990 chunk 607 optimal weight: 0.8980 chunk 419 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 385 optimal weight: 0.0770 chunk 542 optimal weight: 7.9990 chunk 810 optimal weight: 3.9990 chunk 858 optimal weight: 5.9990 chunk 423 optimal weight: 6.9990 chunk 768 optimal weight: 0.5980 chunk 231 optimal weight: 0.0770 overall best weight: 0.9298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN B 178 HIS B 217 ASN H 22 HIS I 233 GLN J 217 ASN J 233 GLN P 233 GLN Q 217 ASN W 204 HIS X 178 HIS X 217 ASN Z 10 GLN 2 22 HIS 3 233 GLN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN 9 22 HIS a 233 GLN b 217 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 69420 Z= 0.181 Angle : 0.650 13.530 94398 Z= 0.316 Chirality : 0.045 0.292 10512 Planarity : 0.005 0.072 12396 Dihedral : 5.294 44.566 9884 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.23 % Favored : 92.70 % Rotamer: Outliers : 4.33 % Allowed : 14.66 % Favored : 81.00 % 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: -3.22 (0.08), residues: 8874 helix: -1.09 (0.09), residues: 2862 sheet: -2.07 (0.12), residues: 1560 loop : -2.92 (0.08), residues: 4452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 5 105 HIS 0.010 0.001 HIS P 88 PHE 0.022 0.002 PHE U 98 TYR 0.019 0.001 TYR 8 122 ARG 0.006 0.000 ARG a 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1715 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1425 time to evaluate : 5.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7988 (mtt) cc_final: 0.7597 (mtt) REVERT: A 276 SER cc_start: 0.7665 (OUTLIER) cc_final: 0.7409 (t) REVERT: A 353 LYS cc_start: 0.9189 (pttt) cc_final: 0.8936 (pttp) REVERT: A 367 ASP cc_start: 0.7698 (m-30) cc_final: 0.7451 (m-30) REVERT: B 116 LEU cc_start: 0.9181 (mm) cc_final: 0.8903 (mt) REVERT: B 242 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 257 ASN cc_start: 0.9019 (m-40) cc_final: 0.8787 (m110) REVERT: B 271 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8578 (ttpp) REVERT: B 273 MET cc_start: 0.8864 (mpt) cc_final: 0.8601 (mmt) REVERT: B 349 GLN cc_start: 0.8087 (tt0) cc_final: 0.7632 (tt0) REVERT: D 107 LEU cc_start: 0.7974 (tt) cc_final: 0.7385 (tt) REVERT: D 113 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7764 (ptt-90) REVERT: F 32 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7806 (p90) REVERT: F 46 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8368 (m) REVERT: F 118 GLU cc_start: 0.7027 (pt0) cc_final: 0.6779 (pt0) REVERT: E 108 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7649 (tm-30) REVERT: G 7 LYS cc_start: 0.8967 (mtpp) cc_final: 0.8698 (tttt) REVERT: G 77 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8428 (tm-30) REVERT: G 85 ASP cc_start: 0.8316 (m-30) cc_final: 0.7744 (m-30) REVERT: H 75 MET cc_start: 0.7619 (mmt) cc_final: 0.7376 (mmt) REVERT: H 106 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7579 (ptt90) REVERT: I 108 GLU cc_start: 0.7605 (pt0) cc_final: 0.7169 (tt0) REVERT: I 216 ASP cc_start: 0.7680 (t70) cc_final: 0.7335 (t0) REVERT: I 349 GLN cc_start: 0.8537 (tt0) cc_final: 0.8313 (mm-40) REVERT: I 367 ASP cc_start: 0.7552 (m-30) cc_final: 0.7295 (m-30) REVERT: I 381 ASN cc_start: 0.8498 (m-40) cc_final: 0.8070 (m-40) REVERT: J 116 LEU cc_start: 0.9149 (mm) cc_final: 0.8888 (mt) REVERT: J 142 ARG cc_start: 0.8268 (mtm180) cc_final: 0.7940 (mtm180) REVERT: J 143 MET cc_start: 0.8408 (tpp) cc_final: 0.8047 (ttt) REVERT: J 306 ILE cc_start: 0.9167 (mm) cc_final: 0.8885 (mm) REVERT: L 46 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8239 (m) REVERT: M 108 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7851 (tp30) REVERT: N 47 GLN cc_start: 0.6827 (mm110) cc_final: 0.5944 (mm110) REVERT: N 77 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8186 (tm-30) REVERT: N 81 GLN cc_start: 0.8539 (tp40) cc_final: 0.8101 (tp40) REVERT: O 2 MET cc_start: 0.7650 (tpt) cc_final: 0.7404 (tpt) REVERT: O 90 ARG cc_start: 0.7319 (mtm110) cc_final: 0.6734 (mtm110) REVERT: P 156 TYR cc_start: 0.9210 (m-80) cc_final: 0.8938 (m-80) REVERT: P 276 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.7384 (t) REVERT: P 367 ASP cc_start: 0.7576 (m-30) cc_final: 0.7274 (m-30) REVERT: Q 77 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8595 (pp) REVERT: Q 116 LEU cc_start: 0.9167 (mm) cc_final: 0.8907 (mt) REVERT: Q 142 ARG cc_start: 0.8410 (mtm180) cc_final: 0.7989 (mtm180) REVERT: Q 143 MET cc_start: 0.8451 (tpp) cc_final: 0.8109 (ttt) REVERT: Q 168 ASP cc_start: 0.7818 (p0) cc_final: 0.7589 (p0) REVERT: Q 242 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7421 (tm-30) REVERT: R 64 ARG cc_start: 0.8292 (ttm110) cc_final: 0.8077 (ttp80) REVERT: T 45 SER cc_start: 0.9052 (p) cc_final: 0.8827 (p) REVERT: T 59 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: U 77 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8294 (tm-30) REVERT: U 102 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: V 90 ARG cc_start: 0.7184 (mtp85) cc_final: 0.6972 (mtp85) REVERT: W 50 MET cc_start: 0.7938 (mtt) cc_final: 0.7525 (mtt) REVERT: W 276 SER cc_start: 0.7657 (OUTLIER) cc_final: 0.7400 (t) REVERT: W 350 ILE cc_start: 0.8541 (mm) cc_final: 0.8296 (mm) REVERT: W 367 ASP cc_start: 0.7686 (m-30) cc_final: 0.7451 (m-30) REVERT: X 116 LEU cc_start: 0.9194 (mm) cc_final: 0.8917 (mt) REVERT: X 163 ARG cc_start: 0.6349 (mtp85) cc_final: 0.6138 (mtp85) REVERT: X 242 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7526 (tm-30) REVERT: X 271 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8640 (ttpp) REVERT: X 273 MET cc_start: 0.8851 (mpt) cc_final: 0.8612 (mmt) REVERT: X 349 GLN cc_start: 0.8083 (tt0) cc_final: 0.7689 (tt0) REVERT: Y 107 LEU cc_start: 0.7983 (tt) cc_final: 0.7399 (tt) REVERT: Y 113 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7750 (ptt-90) REVERT: Z 32 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.7821 (p90) REVERT: Z 46 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8319 (m) REVERT: Z 118 GLU cc_start: 0.7251 (pt0) cc_final: 0.7048 (pt0) REVERT: 0 108 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7714 (tm-30) REVERT: 1 7 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8697 (tttt) REVERT: 1 77 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8311 (tm-30) REVERT: 3 108 GLU cc_start: 0.7590 (pt0) cc_final: 0.7200 (tt0) REVERT: 3 216 ASP cc_start: 0.7674 (t70) cc_final: 0.7345 (t0) REVERT: 3 349 GLN cc_start: 0.8584 (tt0) cc_final: 0.8349 (mm-40) REVERT: 3 353 LYS cc_start: 0.9152 (pttt) cc_final: 0.8925 (ptpp) REVERT: 3 367 ASP cc_start: 0.7553 (m-30) cc_final: 0.7290 (m-30) REVERT: 3 381 ASN cc_start: 0.8501 (m-40) cc_final: 0.8081 (m-40) REVERT: 4 116 LEU cc_start: 0.9145 (mm) cc_final: 0.8885 (mt) REVERT: 4 133 ARG cc_start: 0.8195 (mmp80) cc_final: 0.7730 (mmp-170) REVERT: 4 143 MET cc_start: 0.8377 (tpp) cc_final: 0.7991 (ttt) REVERT: 4 216 ASP cc_start: 0.7208 (m-30) cc_final: 0.6991 (m-30) REVERT: 4 242 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7601 (tm-30) REVERT: 5 122 MET cc_start: 0.6569 (mtp) cc_final: 0.6355 (mtt) REVERT: 6 46 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8254 (m) REVERT: 7 108 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7808 (tp30) REVERT: 8 47 GLN cc_start: 0.6884 (mm110) cc_final: 0.5994 (mm110) REVERT: 8 81 GLN cc_start: 0.8560 (tp40) cc_final: 0.8112 (tp40) REVERT: 9 90 ARG cc_start: 0.7323 (mtm110) cc_final: 0.6740 (mtm110) REVERT: a 156 TYR cc_start: 0.9213 (m-80) cc_final: 0.8947 (m-80) REVERT: a 169 MET cc_start: 0.7596 (mtm) cc_final: 0.6782 (mtm) REVERT: a 276 SER cc_start: 0.7620 (OUTLIER) cc_final: 0.7408 (t) REVERT: a 353 LYS cc_start: 0.9130 (pttt) cc_final: 0.8903 (pttt) REVERT: a 367 ASP cc_start: 0.7576 (m-30) cc_final: 0.7296 (m-30) REVERT: b 116 LEU cc_start: 0.9161 (mm) cc_final: 0.8890 (mt) REVERT: b 142 ARG cc_start: 0.8399 (mtm180) cc_final: 0.7970 (mtm180) REVERT: b 143 MET cc_start: 0.8437 (tpp) cc_final: 0.8072 (ttt) REVERT: b 168 ASP cc_start: 0.7812 (p0) cc_final: 0.7597 (p0) REVERT: b 242 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7434 (tm-30) REVERT: b 323 TYR cc_start: 0.8619 (m-80) cc_final: 0.7781 (m-80) REVERT: b 349 GLN cc_start: 0.8064 (tp40) cc_final: 0.7715 (tp40) REVERT: c 68 THR cc_start: 0.8864 (p) cc_final: 0.8625 (t) REVERT: e 59 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: e 108 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7897 (tp30) REVERT: f 77 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8330 (tm-30) REVERT: f 102 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: f 106 MET cc_start: 0.7618 (ptm) cc_final: 0.7360 (ptm) outliers start: 290 outliers final: 195 residues processed: 1592 average time/residue: 0.6627 time to fit residues: 1793.5859 Evaluate side-chains 1540 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1328 time to evaluate : 5.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 249 GLU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 45 ASP Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 117 SER Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 191 LEU Chi-restraints excluded: chain P residue 276 SER Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain P residue 326 THR Chi-restraints excluded: chain P residue 346 LEU Chi-restraints excluded: chain P residue 349 GLN Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain R residue 31 ASP Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 102 GLN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 159 THR Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 276 SER Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 346 LEU Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 113 ARG Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 32 TYR Chi-restraints excluded: chain Z residue 46 SER Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 100 SER Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 0 residue 57 VAL Chi-restraints excluded: chain 0 residue 103 SER Chi-restraints excluded: chain 1 residue 12 LYS Chi-restraints excluded: chain 1 residue 93 VAL Chi-restraints excluded: chain 1 residue 102 GLN Chi-restraints excluded: chain 1 residue 111 ASP Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 43 LEU Chi-restraints excluded: chain 2 residue 77 THR Chi-restraints excluded: chain 2 residue 123 LEU Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 3 residue 45 ASP Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 303 LEU Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 346 LEU Chi-restraints excluded: chain 4 residue 32 MET Chi-restraints excluded: chain 4 residue 77 ILE Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 189 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 6 residue 46 SER Chi-restraints excluded: chain 6 residue 70 SER Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 6 residue 117 VAL Chi-restraints excluded: chain 6 residue 125 ILE Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 57 VAL Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 111 ASP Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 101 VAL Chi-restraints excluded: chain 9 residue 123 LEU Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 108 GLU Chi-restraints excluded: chain a residue 117 SER Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 191 LEU Chi-restraints excluded: chain a residue 276 SER Chi-restraints excluded: chain a residue 303 LEU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 346 LEU Chi-restraints excluded: chain a residue 349 GLN Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 189 THR Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 80 THR Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 117 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 59 PHE Chi-restraints excluded: chain f residue 12 LYS Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 111 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 714 optimal weight: 9.9990 chunk 487 optimal weight: 4.9990 chunk 12 optimal weight: 0.0030 chunk 639 optimal weight: 0.9990 chunk 354 optimal weight: 10.0000 chunk 732 optimal weight: 20.0000 chunk 593 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 438 optimal weight: 0.3980 chunk 770 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 overall best weight: 2.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 178 HIS B 195 GLN B 240 GLN D 76 GLN I 233 GLN J 217 ASN J 283 HIS ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 233 GLN Q 57 ASN Q 195 GLN Q 217 ASN W 204 HIS X 119 ASN X 178 HIS X 195 GLN X 217 ASN X 240 GLN 3 119 ASN 3 233 GLN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN 4 283 HIS a 233 GLN b 195 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 69420 Z= 0.273 Angle : 0.679 14.261 94398 Z= 0.330 Chirality : 0.046 0.272 10512 Planarity : 0.005 0.061 12396 Dihedral : 5.270 43.805 9884 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.01 % Favored : 91.92 % Rotamer: Outliers : 5.05 % Allowed : 15.22 % Favored : 79.73 % 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: -2.99 (0.08), residues: 8874 helix: -0.78 (0.10), residues: 2886 sheet: -2.17 (0.12), residues: 1686 loop : -2.79 (0.08), residues: 4302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 72 HIS 0.006 0.001 HIS B 178 PHE 0.021 0.002 PHE 6 78 TYR 0.020 0.001 TYR G 122 ARG 0.008 0.000 ARG Q 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1712 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1374 time to evaluate : 5.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8067 (mtt) cc_final: 0.7696 (mtt) REVERT: A 353 LYS cc_start: 0.9190 (pttt) cc_final: 0.8914 (pttp) REVERT: A 367 ASP cc_start: 0.7769 (m-30) cc_final: 0.7556 (m-30) REVERT: B 116 LEU cc_start: 0.9205 (mm) cc_final: 0.8941 (mt) REVERT: B 215 LEU cc_start: 0.9121 (mt) cc_final: 0.8874 (mt) REVERT: B 242 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 271 LYS cc_start: 0.8943 (ttpp) cc_final: 0.8634 (ttpp) REVERT: B 349 GLN cc_start: 0.8056 (tt0) cc_final: 0.7649 (tt0) REVERT: D 113 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7851 (ptt-90) REVERT: D 165 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8483 (pp) REVERT: F 32 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.7811 (p90) REVERT: F 46 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8405 (m) REVERT: F 118 GLU cc_start: 0.7131 (pt0) cc_final: 0.6887 (pt0) REVERT: E 108 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7639 (tm-30) REVERT: G 77 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8389 (tm-30) REVERT: G 106 MET cc_start: 0.8017 (ptm) cc_final: 0.7321 (ptm) REVERT: G 126 MET cc_start: 0.8099 (mmm) cc_final: 0.6821 (mmm) REVERT: H 106 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7662 (ptt90) REVERT: I 108 GLU cc_start: 0.7599 (pt0) cc_final: 0.7201 (tt0) REVERT: I 164 LYS cc_start: 0.8474 (mmtp) cc_final: 0.8250 (mmtm) REVERT: I 216 ASP cc_start: 0.7742 (t70) cc_final: 0.7383 (t0) REVERT: I 349 GLN cc_start: 0.8568 (tt0) cc_final: 0.8352 (mm-40) REVERT: I 367 ASP cc_start: 0.7618 (m-30) cc_final: 0.7299 (m-30) REVERT: J 116 LEU cc_start: 0.9208 (mm) cc_final: 0.9007 (mt) REVERT: J 142 ARG cc_start: 0.8295 (mtm180) cc_final: 0.7946 (mtm180) REVERT: J 143 MET cc_start: 0.8432 (tpp) cc_final: 0.8044 (ttt) REVERT: L 46 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8374 (m) REVERT: N 47 GLN cc_start: 0.6818 (mm110) cc_final: 0.5893 (mm110) REVERT: N 81 GLN cc_start: 0.8521 (tp40) cc_final: 0.8076 (tp40) REVERT: N 134 PHE cc_start: 0.8256 (t80) cc_final: 0.7760 (t80) REVERT: O 2 MET cc_start: 0.7827 (tpt) cc_final: 0.7594 (tpt) REVERT: O 90 ARG cc_start: 0.7329 (mtm110) cc_final: 0.6667 (mtm110) REVERT: P 156 TYR cc_start: 0.9256 (m-80) cc_final: 0.9039 (m-80) REVERT: P 169 MET cc_start: 0.7580 (mtm) cc_final: 0.6742 (mtm) REVERT: P 226 ILE cc_start: 0.9136 (mm) cc_final: 0.8785 (mm) REVERT: P 276 SER cc_start: 0.7693 (OUTLIER) cc_final: 0.7469 (t) REVERT: P 367 ASP cc_start: 0.7668 (m-30) cc_final: 0.7356 (m-30) REVERT: Q 57 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8412 (p0) REVERT: Q 116 LEU cc_start: 0.9204 (mm) cc_final: 0.8982 (mt) REVERT: Q 142 ARG cc_start: 0.8509 (mtm180) cc_final: 0.8060 (mtm180) REVERT: Q 143 MET cc_start: 0.8541 (tpp) cc_final: 0.8019 (ttt) REVERT: Q 168 ASP cc_start: 0.7807 (p0) cc_final: 0.7601 (p0) REVERT: Q 242 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7461 (tm-30) REVERT: S 32 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.7656 (p90) REVERT: T 45 SER cc_start: 0.9065 (p) cc_final: 0.8850 (p) REVERT: T 59 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8083 (m-10) REVERT: U 77 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8344 (tm-30) REVERT: U 102 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: V 90 ARG cc_start: 0.7245 (mtp85) cc_final: 0.7011 (mtp85) REVERT: W 50 MET cc_start: 0.8061 (mtt) cc_final: 0.7685 (mtt) REVERT: W 350 ILE cc_start: 0.8580 (mm) cc_final: 0.8277 (mm) REVERT: W 353 LYS cc_start: 0.9234 (pttt) cc_final: 0.8871 (ptpp) REVERT: W 367 ASP cc_start: 0.7764 (m-30) cc_final: 0.7532 (m-30) REVERT: X 116 LEU cc_start: 0.9219 (mm) cc_final: 0.8970 (mt) REVERT: X 242 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7578 (tm-30) REVERT: X 271 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8633 (ttpp) REVERT: X 349 GLN cc_start: 0.8066 (tt0) cc_final: 0.7669 (tt0) REVERT: Y 113 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7780 (ptt-90) REVERT: Y 165 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8497 (pp) REVERT: Z 32 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7928 (p90) REVERT: 0 108 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7699 (tm-30) REVERT: 1 126 MET cc_start: 0.8106 (mmm) cc_final: 0.6915 (mmm) REVERT: 2 106 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7673 (ptt90) REVERT: 3 108 GLU cc_start: 0.7612 (pt0) cc_final: 0.7230 (tt0) REVERT: 3 164 LYS cc_start: 0.8453 (mmtp) cc_final: 0.8250 (mmtm) REVERT: 3 216 ASP cc_start: 0.7739 (t70) cc_final: 0.7413 (t0) REVERT: 3 349 GLN cc_start: 0.8591 (tt0) cc_final: 0.8366 (mm-40) REVERT: 3 367 ASP cc_start: 0.7609 (m-30) cc_final: 0.7291 (m-30) REVERT: 4 116 LEU cc_start: 0.9212 (mm) cc_final: 0.9002 (mt) REVERT: 4 133 ARG cc_start: 0.8257 (mmp80) cc_final: 0.7796 (mmp-170) REVERT: 4 143 MET cc_start: 0.8469 (tpp) cc_final: 0.8054 (ttt) REVERT: 4 163 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7028 (mtt-85) REVERT: 4 242 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7623 (tm-30) REVERT: 4 306 ILE cc_start: 0.9197 (mm) cc_final: 0.8904 (mm) REVERT: 5 122 MET cc_start: 0.6517 (mtp) cc_final: 0.6311 (mtt) REVERT: 6 46 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8380 (m) REVERT: 8 47 GLN cc_start: 0.6880 (mm110) cc_final: 0.5999 (mm110) REVERT: 8 81 GLN cc_start: 0.8491 (tp40) cc_final: 0.8052 (tp40) REVERT: 9 2 MET cc_start: 0.7886 (tpt) cc_final: 0.7651 (tpt) REVERT: 9 90 ARG cc_start: 0.7336 (mtm110) cc_final: 0.6684 (mtm110) REVERT: a 156 TYR cc_start: 0.9259 (m-80) cc_final: 0.9043 (m-80) REVERT: a 169 MET cc_start: 0.7561 (mtm) cc_final: 0.6744 (mtm) REVERT: a 226 ILE cc_start: 0.9145 (mm) cc_final: 0.8783 (mm) REVERT: a 276 SER cc_start: 0.7705 (OUTLIER) cc_final: 0.7502 (t) REVERT: a 367 ASP cc_start: 0.7668 (m-30) cc_final: 0.7359 (m-30) REVERT: b 116 LEU cc_start: 0.9203 (mm) cc_final: 0.8980 (mt) REVERT: b 142 ARG cc_start: 0.8502 (mtm180) cc_final: 0.8011 (mtm180) REVERT: b 143 MET cc_start: 0.8520 (tpp) cc_final: 0.8045 (ttt) REVERT: b 168 ASP cc_start: 0.7842 (p0) cc_final: 0.7627 (p0) REVERT: b 242 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7482 (tm-30) REVERT: b 273 MET cc_start: 0.8733 (mpt) cc_final: 0.8533 (mmt) REVERT: d 32 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.7640 (p90) REVERT: e 59 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8208 (m-10) REVERT: e 108 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7617 (tp30) REVERT: f 98 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7905 (t80) REVERT: f 102 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7878 (tm-30) outliers start: 338 outliers final: 253 residues processed: 1573 average time/residue: 0.6595 time to fit residues: 1754.2829 Evaluate side-chains 1599 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1327 time to evaluate : 5.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain F residue 3 TYR Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 233 GLN Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 239 GLU Chi-restraints excluded: chain J residue 249 GLU Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 34 GLU Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 45 ASP Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 276 SER Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain P residue 326 THR Chi-restraints excluded: chain P residue 346 LEU Chi-restraints excluded: chain P residue 349 GLN Chi-restraints excluded: chain Q residue 57 ASN Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain U residue 12 LYS Chi-restraints excluded: chain U residue 47 GLN Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 102 GLN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 85 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain W residue 159 THR Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 177 CYS Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 346 LEU Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 222 SER Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 75 MET Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 113 ARG Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain Y residue 165 LEU Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Z residue 3 TYR Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 32 TYR Chi-restraints excluded: chain Z residue 46 SER Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 0 residue 57 VAL Chi-restraints excluded: chain 1 residue 12 LYS Chi-restraints excluded: chain 1 residue 13 LEU Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 102 GLN Chi-restraints excluded: chain 1 residue 111 ASP Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 43 LEU Chi-restraints excluded: chain 2 residue 77 THR Chi-restraints excluded: chain 2 residue 85 THR Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 123 LEU Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 3 residue 45 ASP Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 154 VAL Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 233 GLN Chi-restraints excluded: chain 3 residue 303 LEU Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 346 LEU Chi-restraints excluded: chain 4 residue 32 MET Chi-restraints excluded: chain 4 residue 77 ILE Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 159 THR Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 5 residue 41 SER Chi-restraints excluded: chain 5 residue 137 THR Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 189 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 6 residue 46 SER Chi-restraints excluded: chain 6 residue 51 ASP Chi-restraints excluded: chain 6 residue 70 SER Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 6 residue 117 VAL Chi-restraints excluded: chain 6 residue 125 ILE Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 45 SER Chi-restraints excluded: chain 7 residue 57 VAL Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 7 residue 103 SER Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 111 ASP Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 43 LEU Chi-restraints excluded: chain 9 residue 85 THR Chi-restraints excluded: chain 9 residue 99 THR Chi-restraints excluded: chain 9 residue 101 VAL Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 123 LEU Chi-restraints excluded: chain 9 residue 135 ASP Chi-restraints excluded: chain 9 residue 137 THR Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 108 GLU Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 276 SER Chi-restraints excluded: chain a residue 303 LEU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 346 LEU Chi-restraints excluded: chain a residue 349 GLN Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 189 THR Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 32 TYR Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 59 THR Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 117 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 59 PHE Chi-restraints excluded: chain f residue 12 LYS Chi-restraints excluded: chain f residue 38 THR Chi-restraints excluded: chain f residue 39 VAL Chi-restraints excluded: chain f residue 47 GLN Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 98 PHE Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 111 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 288 optimal weight: 3.9990 chunk 772 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 503 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 859 optimal weight: 3.9990 chunk 713 optimal weight: 0.0870 chunk 397 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 284 optimal weight: 7.9990 chunk 451 optimal weight: 0.0770 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 119 ASN B 195 GLN B 217 ASN B 253 GLN J 217 ASN P 233 GLN Q 195 GLN Q 217 ASN R 76 GLN ** W 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 119 ASN X 195 GLN ** X 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 253 GLN Y 76 GLN 3 79 GLN 3 119 ASN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN 4 233 GLN ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 233 GLN b 195 GLN b 217 ASN c 76 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 69420 Z= 0.264 Angle : 0.675 14.304 94398 Z= 0.327 Chirality : 0.046 0.307 10512 Planarity : 0.005 0.064 12396 Dihedral : 5.265 44.293 9884 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.83 % Favored : 92.10 % Rotamer: Outliers : 5.55 % Allowed : 15.10 % Favored : 79.36 % 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: -2.74 (0.08), residues: 8874 helix: -0.54 (0.10), residues: 2886 sheet: -1.90 (0.12), residues: 1626 loop : -2.72 (0.09), residues: 4362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 72 HIS 0.004 0.001 HIS I 178 PHE 0.020 0.002 PHE 6 78 TYR 0.021 0.001 TYR N 122 ARG 0.007 0.000 ARG a 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1731 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 371 poor density : 1360 time to evaluate : 5.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7130 (mtm180) REVERT: A 302 MET cc_start: 0.8412 (ptm) cc_final: 0.8162 (ttt) REVERT: A 367 ASP cc_start: 0.7780 (m-30) cc_final: 0.7560 (m-30) REVERT: B 116 LEU cc_start: 0.9218 (mm) cc_final: 0.8968 (mt) REVERT: B 242 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 271 LYS cc_start: 0.8899 (ttpp) cc_final: 0.8621 (ttpp) REVERT: B 349 GLN cc_start: 0.8030 (tt0) cc_final: 0.7620 (tt0) REVERT: D 107 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7547 (tt) REVERT: D 165 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8501 (pp) REVERT: F 32 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7958 (p90) REVERT: F 46 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8370 (m) REVERT: E 108 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7781 (tp30) REVERT: G 102 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: I 108 GLU cc_start: 0.7609 (pt0) cc_final: 0.7211 (tt0) REVERT: I 164 LYS cc_start: 0.8522 (mmtp) cc_final: 0.8203 (mmtm) REVERT: I 216 ASP cc_start: 0.7751 (t70) cc_final: 0.7383 (t0) REVERT: I 349 GLN cc_start: 0.8572 (tt0) cc_final: 0.8358 (mm-40) REVERT: I 367 ASP cc_start: 0.7649 (m-30) cc_final: 0.7292 (m-30) REVERT: J 116 LEU cc_start: 0.9187 (mm) cc_final: 0.8975 (mt) REVERT: J 142 ARG cc_start: 0.8331 (mtm180) cc_final: 0.7999 (mtm180) REVERT: J 143 MET cc_start: 0.8466 (tpp) cc_final: 0.8105 (ttt) REVERT: J 306 ILE cc_start: 0.9203 (mm) cc_final: 0.8899 (mm) REVERT: L 46 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8386 (m) REVERT: N 47 GLN cc_start: 0.6817 (mm110) cc_final: 0.5908 (mm110) REVERT: N 98 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: N 134 PHE cc_start: 0.8281 (t80) cc_final: 0.7734 (t80) REVERT: O 2 MET cc_start: 0.7882 (tpt) cc_final: 0.7678 (tpt) REVERT: O 90 ARG cc_start: 0.7416 (mtm110) cc_final: 0.6823 (mtm110) REVERT: O 125 MET cc_start: 0.7123 (mpp) cc_final: 0.6776 (mpp) REVERT: P 156 TYR cc_start: 0.9269 (m-80) cc_final: 0.9048 (m-80) REVERT: P 169 MET cc_start: 0.7488 (mtm) cc_final: 0.6739 (mtm) REVERT: P 276 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.7526 (t) REVERT: P 302 MET cc_start: 0.8421 (ptm) cc_final: 0.8110 (ttt) REVERT: P 353 LYS cc_start: 0.9180 (pttt) cc_final: 0.8877 (pttt) REVERT: P 367 ASP cc_start: 0.7684 (m-30) cc_final: 0.7355 (m-30) REVERT: Q 57 ASN cc_start: 0.8732 (p0) cc_final: 0.8484 (p0) REVERT: Q 116 LEU cc_start: 0.9210 (mm) cc_final: 0.8986 (mt) REVERT: Q 142 ARG cc_start: 0.8530 (mtm180) cc_final: 0.8063 (mtm180) REVERT: Q 143 MET cc_start: 0.8553 (tpp) cc_final: 0.8049 (ttt) REVERT: Q 163 ARG cc_start: 0.6588 (mtt-85) cc_final: 0.6327 (mtt-85) REVERT: Q 168 ASP cc_start: 0.7849 (p0) cc_final: 0.7642 (p0) REVERT: Q 242 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7465 (tm-30) REVERT: R 68 THR cc_start: 0.8816 (p) cc_final: 0.8557 (t) REVERT: R 75 MET cc_start: 0.5905 (pp-130) cc_final: 0.5451 (pp-130) REVERT: S 32 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7716 (p90) REVERT: T 45 SER cc_start: 0.9091 (p) cc_final: 0.8869 (p) REVERT: T 59 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8102 (m-10) REVERT: U 77 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8345 (tm-30) REVERT: U 98 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7907 (t80) REVERT: U 102 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: V 90 ARG cc_start: 0.7312 (mtp85) cc_final: 0.7098 (mtp85) REVERT: W 302 MET cc_start: 0.8397 (ptm) cc_final: 0.8150 (ttt) REVERT: W 367 ASP cc_start: 0.7773 (m-30) cc_final: 0.7544 (m-30) REVERT: X 116 LEU cc_start: 0.9223 (mm) cc_final: 0.8971 (mt) REVERT: X 242 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7577 (tm-30) REVERT: X 271 LYS cc_start: 0.8905 (ttpp) cc_final: 0.8616 (ttpp) REVERT: X 349 GLN cc_start: 0.8046 (tt0) cc_final: 0.7661 (tt0) REVERT: Y 107 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7568 (tt) REVERT: Y 113 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7920 (ptt-90) REVERT: Y 165 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8511 (pp) REVERT: Z 32 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7982 (p90) REVERT: 0 108 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7688 (tm-30) REVERT: 3 108 GLU cc_start: 0.7615 (pt0) cc_final: 0.7243 (tt0) REVERT: 3 164 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8137 (mmtm) REVERT: 3 216 ASP cc_start: 0.7741 (t70) cc_final: 0.7387 (t0) REVERT: 3 226 ILE cc_start: 0.9129 (mm) cc_final: 0.8925 (mm) REVERT: 3 349 GLN cc_start: 0.8586 (tt0) cc_final: 0.8358 (mm-40) REVERT: 3 367 ASP cc_start: 0.7633 (m-30) cc_final: 0.7300 (m-30) REVERT: 3 381 ASN cc_start: 0.8470 (m-40) cc_final: 0.8093 (m-40) REVERT: 4 116 LEU cc_start: 0.9191 (mm) cc_final: 0.8954 (mt) REVERT: 4 133 ARG cc_start: 0.8264 (mmp80) cc_final: 0.7802 (mmp-170) REVERT: 4 143 MET cc_start: 0.8447 (tpp) cc_final: 0.8016 (ttt) REVERT: 4 163 ARG cc_start: 0.7512 (mpt180) cc_final: 0.7062 (mtt-85) REVERT: 4 242 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7624 (tm-30) REVERT: 4 306 ILE cc_start: 0.9184 (mm) cc_final: 0.8893 (mm) REVERT: 6 46 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8386 (m) REVERT: 8 47 GLN cc_start: 0.6881 (mm110) cc_final: 0.5994 (mm110) REVERT: 8 98 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: 8 126 MET cc_start: 0.8621 (mpp) cc_final: 0.8149 (mpp) REVERT: 9 90 ARG cc_start: 0.7427 (mtm110) cc_final: 0.6841 (mtm110) REVERT: a 156 TYR cc_start: 0.9278 (m-80) cc_final: 0.9055 (m-80) REVERT: a 169 MET cc_start: 0.7768 (mtm) cc_final: 0.6972 (mtm) REVERT: a 302 MET cc_start: 0.8426 (ptm) cc_final: 0.8111 (ttt) REVERT: a 367 ASP cc_start: 0.7684 (m-30) cc_final: 0.7358 (m-30) REVERT: b 116 LEU cc_start: 0.9208 (mm) cc_final: 0.8976 (mt) REVERT: b 143 MET cc_start: 0.8512 (tpp) cc_final: 0.8061 (ttt) REVERT: b 168 ASP cc_start: 0.7803 (p0) cc_final: 0.7602 (p0) REVERT: b 242 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7472 (tm-30) REVERT: c 75 MET cc_start: 0.5967 (pp-130) cc_final: 0.5458 (pp-130) REVERT: d 32 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.7706 (p90) REVERT: e 59 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8152 (m-10) REVERT: e 108 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7617 (tp30) REVERT: f 98 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7898 (t80) REVERT: f 102 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7915 (tm-30) outliers start: 371 outliers final: 273 residues processed: 1590 average time/residue: 0.6970 time to fit residues: 1895.7738 Evaluate side-chains 1618 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1323 time to evaluate : 5.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 239 GLU Chi-restraints excluded: chain J residue 249 GLU Chi-restraints excluded: chain J residue 292 GLU Chi-restraints excluded: chain J residue 356 LEU Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 45 ASP Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 276 SER Chi-restraints excluded: chain P residue 326 THR Chi-restraints excluded: chain P residue 346 LEU Chi-restraints excluded: chain P residue 349 GLN Chi-restraints excluded: chain P residue 386 VAL Chi-restraints excluded: chain Q residue 159 THR Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain R residue 31 ASP Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 47 GLN Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 102 GLN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 85 THR Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 137 THR Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain W residue 159 THR Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 177 CYS Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 346 LEU Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 222 SER Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 75 MET Chi-restraints excluded: chain Y residue 107 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 113 ARG Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain Y residue 165 LEU Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Z residue 3 TYR Chi-restraints excluded: chain Z residue 10 GLN Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 32 TYR Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 46 SER Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 100 SER Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 0 residue 57 VAL Chi-restraints excluded: chain 1 residue 12 LYS Chi-restraints excluded: chain 1 residue 13 LEU Chi-restraints excluded: chain 1 residue 52 GLU Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 102 GLN Chi-restraints excluded: chain 1 residue 111 ASP Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 43 LEU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 111 MET Chi-restraints excluded: chain 2 residue 123 LEU Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 3 residue 45 ASP Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 303 LEU Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 346 LEU Chi-restraints excluded: chain 3 residue 386 VAL Chi-restraints excluded: chain 4 residue 32 MET Chi-restraints excluded: chain 4 residue 77 ILE Chi-restraints excluded: chain 4 residue 145 VAL Chi-restraints excluded: chain 4 residue 159 THR Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 191 LEU Chi-restraints excluded: chain 4 residue 225 ILE Chi-restraints excluded: chain 4 residue 239 GLU Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 4 residue 292 GLU Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 4 residue 373 ILE Chi-restraints excluded: chain 5 residue 111 MET Chi-restraints excluded: chain 5 residue 137 THR Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 189 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 6 residue 32 TYR Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 6 residue 46 SER Chi-restraints excluded: chain 6 residue 51 ASP Chi-restraints excluded: chain 6 residue 70 SER Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 6 residue 117 VAL Chi-restraints excluded: chain 6 residue 125 ILE Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 45 SER Chi-restraints excluded: chain 7 residue 57 VAL Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 7 residue 103 SER Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 98 PHE Chi-restraints excluded: chain 8 residue 111 ASP Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 43 LEU Chi-restraints excluded: chain 9 residue 77 THR Chi-restraints excluded: chain 9 residue 99 THR Chi-restraints excluded: chain 9 residue 101 VAL Chi-restraints excluded: chain 9 residue 123 LEU Chi-restraints excluded: chain 9 residue 135 ASP Chi-restraints excluded: chain 9 residue 137 THR Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 108 GLU Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 346 LEU Chi-restraints excluded: chain a residue 349 GLN Chi-restraints excluded: chain a residue 386 VAL Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 189 THR Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 32 TYR Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 59 THR Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 117 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 59 PHE Chi-restraints excluded: chain f residue 12 LYS Chi-restraints excluded: chain f residue 47 GLN Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 98 PHE Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 111 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 828 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 489 optimal weight: 2.9990 chunk 627 optimal weight: 8.9990 chunk 486 optimal weight: 5.9990 chunk 723 optimal weight: 5.9990 chunk 479 optimal weight: 6.9990 chunk 855 optimal weight: 0.9980 chunk 535 optimal weight: 0.8980 chunk 521 optimal weight: 1.9990 chunk 395 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 195 GLN I 119 ASN I 233 GLN J 217 ASN K 76 GLN P 233 GLN Q 195 GLN Q 217 ASN X 119 ASN X 195 GLN ** 2 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 119 ASN 3 233 GLN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN 5 76 GLN a 233 GLN b 195 GLN b 217 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 69420 Z= 0.241 Angle : 0.667 14.157 94398 Z= 0.322 Chirality : 0.046 0.344 10512 Planarity : 0.005 0.063 12396 Dihedral : 5.179 44.937 9884 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.08 % Rotamer: Outliers : 5.67 % Allowed : 15.75 % Favored : 78.58 % 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: -2.55 (0.09), residues: 8874 helix: -0.32 (0.10), residues: 2886 sheet: -1.80 (0.12), residues: 1488 loop : -2.65 (0.09), residues: 4500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 72 HIS 0.004 0.001 HIS 3 178 PHE 0.020 0.002 PHE F 78 TYR 0.024 0.001 TYR f 122 ARG 0.008 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1748 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 379 poor density : 1369 time to evaluate : 6.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ARG cc_start: 0.7515 (mtp85) cc_final: 0.7109 (mtm180) REVERT: A 110 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9145 (tt) REVERT: B 116 LEU cc_start: 0.9208 (mm) cc_final: 0.8952 (mt) REVERT: B 242 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7589 (tm-30) REVERT: B 271 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8691 (ttpp) REVERT: B 349 GLN cc_start: 0.7989 (tt0) cc_final: 0.7580 (tt0) REVERT: D 107 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7608 (tt) REVERT: D 113 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7905 (ptt-90) REVERT: D 165 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8488 (pp) REVERT: F 32 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7948 (p90) REVERT: F 46 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8364 (m) REVERT: E 108 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7799 (tp30) REVERT: H 106 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7675 (ptt90) REVERT: I 108 GLU cc_start: 0.7697 (pt0) cc_final: 0.7310 (tt0) REVERT: I 143 MET cc_start: 0.8762 (mmt) cc_final: 0.8492 (mmt) REVERT: I 164 LYS cc_start: 0.8540 (mmtp) cc_final: 0.8216 (mmtm) REVERT: I 216 ASP cc_start: 0.7715 (t70) cc_final: 0.7365 (t0) REVERT: I 349 GLN cc_start: 0.8555 (tt0) cc_final: 0.8321 (mm-40) REVERT: I 367 ASP cc_start: 0.7671 (m-30) cc_final: 0.7325 (m-30) REVERT: J 116 LEU cc_start: 0.9243 (mm) cc_final: 0.9039 (mt) REVERT: J 142 ARG cc_start: 0.8334 (mtm180) cc_final: 0.7999 (mtm180) REVERT: J 143 MET cc_start: 0.8380 (tpp) cc_final: 0.8068 (ttt) REVERT: J 271 LYS cc_start: 0.8984 (ttpp) cc_final: 0.8749 (ttpp) REVERT: J 306 ILE cc_start: 0.9188 (mm) cc_final: 0.8878 (mm) REVERT: L 46 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8369 (m) REVERT: N 47 GLN cc_start: 0.6853 (mm110) cc_final: 0.5892 (mm110) REVERT: N 98 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7925 (m-80) REVERT: N 106 MET cc_start: 0.8207 (ptm) cc_final: 0.7986 (ptm) REVERT: O 90 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7051 (mtm-85) REVERT: O 125 MET cc_start: 0.7155 (mpp) cc_final: 0.6787 (mpp) REVERT: P 169 MET cc_start: 0.7688 (mtm) cc_final: 0.6893 (mtm) REVERT: P 302 MET cc_start: 0.8409 (ptm) cc_final: 0.8101 (ttt) REVERT: P 367 ASP cc_start: 0.7700 (m-30) cc_final: 0.7378 (m-30) REVERT: Q 116 LEU cc_start: 0.9204 (mm) cc_final: 0.8966 (mt) REVERT: Q 142 ARG cc_start: 0.8562 (mtm180) cc_final: 0.8082 (mtm180) REVERT: Q 143 MET cc_start: 0.8495 (tpp) cc_final: 0.8146 (ttt) REVERT: Q 168 ASP cc_start: 0.7966 (p0) cc_final: 0.7681 (p0) REVERT: Q 242 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7458 (tm-30) REVERT: Q 271 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8556 (ttpp) REVERT: R 105 TRP cc_start: 0.8060 (p-90) cc_final: 0.7669 (p-90) REVERT: S 32 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.7702 (p90) REVERT: T 45 SER cc_start: 0.9070 (p) cc_final: 0.8847 (p) REVERT: T 59 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: U 98 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7911 (t80) REVERT: U 102 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: V 90 ARG cc_start: 0.7319 (mtp85) cc_final: 0.7103 (mtp85) REVERT: W 110 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9156 (tt) REVERT: W 353 LYS cc_start: 0.9173 (pttt) cc_final: 0.8869 (ptpp) REVERT: W 367 ASP cc_start: 0.7785 (m-30) cc_final: 0.7583 (m-30) REVERT: X 116 LEU cc_start: 0.9210 (mm) cc_final: 0.8948 (mt) REVERT: X 242 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7570 (tm-30) REVERT: X 271 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8673 (ttpp) REVERT: X 349 GLN cc_start: 0.8069 (tt0) cc_final: 0.7658 (tt0) REVERT: Y 107 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7635 (tt) REVERT: Y 165 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8500 (pp) REVERT: Z 32 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7966 (p90) REVERT: Z 46 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8375 (m) REVERT: 0 108 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7677 (tm-30) REVERT: 3 108 GLU cc_start: 0.7715 (pt0) cc_final: 0.7339 (tt0) REVERT: 3 143 MET cc_start: 0.8755 (mmt) cc_final: 0.8489 (mmt) REVERT: 3 164 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8116 (mmtm) REVERT: 3 216 ASP cc_start: 0.7710 (t70) cc_final: 0.7389 (t0) REVERT: 3 349 GLN cc_start: 0.8567 (tt0) cc_final: 0.8320 (mm-40) REVERT: 3 367 ASP cc_start: 0.7674 (m-30) cc_final: 0.7327 (m-30) REVERT: 4 116 LEU cc_start: 0.9186 (mm) cc_final: 0.8977 (mt) REVERT: 4 133 ARG cc_start: 0.8299 (mmp80) cc_final: 0.7835 (mmp-170) REVERT: 4 242 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7622 (tm-30) REVERT: 4 306 ILE cc_start: 0.9168 (mm) cc_final: 0.8861 (mm) REVERT: 6 46 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8388 (m) REVERT: 8 47 GLN cc_start: 0.6905 (mm110) cc_final: 0.5976 (mm110) REVERT: 8 98 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: 8 106 MET cc_start: 0.8201 (ptm) cc_final: 0.7979 (ptm) REVERT: 8 134 PHE cc_start: 0.8287 (t80) cc_final: 0.7693 (t80) REVERT: 9 90 ARG cc_start: 0.7748 (mtm110) cc_final: 0.7079 (mtm-85) REVERT: a 169 MET cc_start: 0.7668 (mtm) cc_final: 0.6884 (mtm) REVERT: a 367 ASP cc_start: 0.7696 (m-30) cc_final: 0.7379 (m-30) REVERT: b 116 LEU cc_start: 0.9199 (mm) cc_final: 0.8981 (mt) REVERT: b 143 MET cc_start: 0.8423 (tpp) cc_final: 0.8136 (ttt) REVERT: b 168 ASP cc_start: 0.7992 (p0) cc_final: 0.7719 (p0) REVERT: b 242 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7475 (tm-30) REVERT: b 273 MET cc_start: 0.8813 (mpt) cc_final: 0.8073 (mpt) REVERT: c 105 TRP cc_start: 0.8024 (p-90) cc_final: 0.7656 (p-90) REVERT: d 32 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.7690 (p90) REVERT: e 59 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8055 (m-10) REVERT: e 108 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7673 (tp30) REVERT: f 98 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7999 (t80) REVERT: f 102 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7895 (tm-30) outliers start: 379 outliers final: 291 residues processed: 1596 average time/residue: 0.6470 time to fit residues: 1750.1050 Evaluate side-chains 1643 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1329 time to evaluate : 5.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 233 GLN Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 239 GLU Chi-restraints excluded: chain J residue 249 GLU Chi-restraints excluded: chain J residue 292 GLU Chi-restraints excluded: chain J residue 359 VAL Chi-restraints excluded: chain K residue 4 ASN Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 115 SER Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 45 ASP Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 177 CYS Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 233 GLN Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain P residue 326 THR Chi-restraints excluded: chain P residue 346 LEU Chi-restraints excluded: chain P residue 349 GLN Chi-restraints excluded: chain P residue 386 VAL Chi-restraints excluded: chain Q residue 159 THR Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 235 VAL Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain Q residue 373 ILE Chi-restraints excluded: chain R residue 31 ASP Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain U residue 47 GLN Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 102 GLN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 85 THR Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 137 THR Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain W residue 159 THR Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 177 CYS Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 346 LEU Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 222 SER Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 75 MET Chi-restraints excluded: chain Y residue 107 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain Y residue 165 LEU Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Z residue 3 TYR Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 32 TYR Chi-restraints excluded: chain Z residue 46 SER Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 100 SER Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain 0 residue 57 VAL Chi-restraints excluded: chain 1 residue 12 LYS Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 102 GLN Chi-restraints excluded: chain 1 residue 111 ASP Chi-restraints excluded: chain 1 residue 115 SER Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 43 LEU Chi-restraints excluded: chain 2 residue 77 THR Chi-restraints excluded: chain 2 residue 85 THR Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 111 MET Chi-restraints excluded: chain 2 residue 123 LEU Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 3 residue 45 ASP Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 154 VAL Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 233 GLN Chi-restraints excluded: chain 3 residue 303 LEU Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 346 LEU Chi-restraints excluded: chain 3 residue 386 VAL Chi-restraints excluded: chain 4 residue 32 MET Chi-restraints excluded: chain 4 residue 77 ILE Chi-restraints excluded: chain 4 residue 159 THR Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 191 LEU Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 239 GLU Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 4 residue 292 GLU Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 4 residue 359 VAL Chi-restraints excluded: chain 5 residue 111 MET Chi-restraints excluded: chain 5 residue 137 THR Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 189 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 6 residue 32 TYR Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 6 residue 46 SER Chi-restraints excluded: chain 6 residue 51 ASP Chi-restraints excluded: chain 6 residue 70 SER Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 6 residue 117 VAL Chi-restraints excluded: chain 6 residue 125 ILE Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 45 SER Chi-restraints excluded: chain 7 residue 57 VAL Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 7 residue 103 SER Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 98 PHE Chi-restraints excluded: chain 8 residue 111 ASP Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 43 LEU Chi-restraints excluded: chain 9 residue 68 THR Chi-restraints excluded: chain 9 residue 77 THR Chi-restraints excluded: chain 9 residue 99 THR Chi-restraints excluded: chain 9 residue 101 VAL Chi-restraints excluded: chain 9 residue 123 LEU Chi-restraints excluded: chain 9 residue 135 ASP Chi-restraints excluded: chain 9 residue 137 THR Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 108 GLU Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 177 CYS Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 191 LEU Chi-restraints excluded: chain a residue 233 GLN Chi-restraints excluded: chain a residue 303 LEU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 346 LEU Chi-restraints excluded: chain a residue 349 GLN Chi-restraints excluded: chain a residue 386 VAL Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain b residue 373 ILE Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 189 THR Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 32 TYR Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 59 THR Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 117 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain e residue 57 VAL Chi-restraints excluded: chain e residue 59 PHE Chi-restraints excluded: chain f residue 47 GLN Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 98 PHE Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 111 ASP Chi-restraints excluded: chain f residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 529 optimal weight: 0.4980 chunk 341 optimal weight: 2.9990 chunk 511 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 165 optimal weight: 0.9980 chunk 544 optimal weight: 6.9990 chunk 583 optimal weight: 0.6980 chunk 423 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 672 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 119 ASN B 195 GLN B 217 ASN I 119 ASN J 217 ASN Q 195 GLN Q 217 ASN X 119 ASN X 195 GLN ** 2 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN a 233 GLN b 195 GLN b 217 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 69420 Z= 0.197 Angle : 0.650 13.657 94398 Z= 0.313 Chirality : 0.045 0.369 10512 Planarity : 0.005 0.064 12396 Dihedral : 5.074 46.407 9884 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 5.14 % Allowed : 16.76 % Favored : 78.10 % 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: -2.36 (0.09), residues: 8874 helix: -0.03 (0.10), residues: 2862 sheet: -1.80 (0.12), residues: 1482 loop : -2.58 (0.09), residues: 4530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 72 HIS 0.004 0.001 HIS A 178 PHE 0.015 0.001 PHE 6 78 TYR 0.024 0.001 TYR U 122 ARG 0.007 0.000 ARG O 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1703 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1359 time to evaluate : 5.479 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: C 90 ARG cc_start: 0.7552 (mtp85) cc_final: 0.7243 (mtm180) REVERT: A 110 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9146 (tt) REVERT: B 96 ARG cc_start: 0.8447 (tpm170) cc_final: 0.8231 (tpm170) REVERT: B 116 LEU cc_start: 0.9177 (mm) cc_final: 0.8929 (mt) REVERT: B 242 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7552 (tm-30) REVERT: B 271 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8631 (ttpp) REVERT: B 349 GLN cc_start: 0.7972 (tt0) cc_final: 0.7585 (tt0) REVERT: D 2 MET cc_start: 0.8044 (tpp) cc_final: 0.7824 (tmm) REVERT: D 107 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7334 (tt) REVERT: D 113 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7882 (ptt-90) REVERT: D 165 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8467 (pp) REVERT: F 32 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7971 (p90) REVERT: F 46 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8391 (m) REVERT: E 108 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7821 (tp30) REVERT: H 75 MET cc_start: 0.8005 (mmt) cc_final: 0.7723 (mmt) REVERT: I 108 GLU cc_start: 0.7663 (pt0) cc_final: 0.7293 (tt0) REVERT: I 164 LYS cc_start: 0.8584 (mmtp) cc_final: 0.8246 (mmtm) REVERT: I 216 ASP cc_start: 0.7690 (t70) cc_final: 0.7353 (t0) REVERT: I 367 ASP cc_start: 0.7682 (m-30) cc_final: 0.7317 (m-30) REVERT: J 116 LEU cc_start: 0.9208 (mm) cc_final: 0.9003 (mt) REVERT: J 142 ARG cc_start: 0.8293 (mtm180) cc_final: 0.7963 (mtm180) REVERT: J 271 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8731 (ttpp) REVERT: J 306 ILE cc_start: 0.9123 (mm) cc_final: 0.8847 (mm) REVERT: N 47 GLN cc_start: 0.6893 (mm110) cc_final: 0.5910 (mm110) REVERT: N 98 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: N 106 MET cc_start: 0.8145 (ptm) cc_final: 0.7921 (ptm) REVERT: O 90 ARG cc_start: 0.7773 (mtm110) cc_final: 0.7135 (mtm-85) REVERT: P 367 ASP cc_start: 0.7720 (m-30) cc_final: 0.7371 (m-30) REVERT: Q 116 LEU cc_start: 0.9154 (mm) cc_final: 0.8899 (mt) REVERT: Q 142 ARG cc_start: 0.8548 (mtm180) cc_final: 0.8059 (mtm180) REVERT: Q 143 MET cc_start: 0.8375 (tpp) cc_final: 0.8174 (ttt) REVERT: Q 168 ASP cc_start: 0.7940 (p0) cc_final: 0.7668 (p0) REVERT: Q 242 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7442 (tm-30) REVERT: Q 271 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8502 (ttpp) REVERT: R 68 THR cc_start: 0.8779 (p) cc_final: 0.8558 (t) REVERT: R 105 TRP cc_start: 0.8052 (p-90) cc_final: 0.7653 (p-90) REVERT: S 32 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7535 (p90) REVERT: S 118 GLU cc_start: 0.7059 (pt0) cc_final: 0.6852 (pt0) REVERT: T 45 SER cc_start: 0.9072 (p) cc_final: 0.8869 (p) REVERT: U 98 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7962 (t80) REVERT: U 102 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: W 110 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9147 (tt) REVERT: W 367 ASP cc_start: 0.7762 (m-30) cc_final: 0.7559 (m-30) REVERT: X 116 LEU cc_start: 0.9185 (mm) cc_final: 0.8943 (mt) REVERT: X 242 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7543 (tm-30) REVERT: X 271 LYS cc_start: 0.8863 (ttpp) cc_final: 0.8617 (ttpp) REVERT: Y 2 MET cc_start: 0.8034 (tpp) cc_final: 0.7805 (tmm) REVERT: Y 107 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7368 (tt) REVERT: Y 113 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7882 (ptt-90) REVERT: Y 165 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8464 (pp) REVERT: Z 32 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7987 (p90) REVERT: Z 46 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8364 (m) REVERT: 0 108 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7685 (tm-30) REVERT: 1 81 GLN cc_start: 0.8566 (tp40) cc_final: 0.8314 (tp40) REVERT: 3 108 GLU cc_start: 0.7671 (pt0) cc_final: 0.7329 (tt0) REVERT: 3 164 LYS cc_start: 0.8509 (mmtp) cc_final: 0.8180 (mmtm) REVERT: 3 216 ASP cc_start: 0.7687 (t70) cc_final: 0.7386 (t0) REVERT: 3 349 GLN cc_start: 0.8527 (tt0) cc_final: 0.8295 (mm-40) REVERT: 3 367 ASP cc_start: 0.7683 (m-30) cc_final: 0.7345 (m-30) REVERT: 4 116 LEU cc_start: 0.9209 (mm) cc_final: 0.8999 (mt) REVERT: 4 133 ARG cc_start: 0.8327 (mmp80) cc_final: 0.7859 (mmp-170) REVERT: 4 242 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7599 (tm-30) REVERT: 8 47 GLN cc_start: 0.6939 (mm110) cc_final: 0.5986 (mm110) REVERT: 8 98 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: 8 106 MET cc_start: 0.8139 (ptm) cc_final: 0.7930 (ptm) REVERT: 9 90 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7140 (mtm-85) REVERT: a 367 ASP cc_start: 0.7719 (m-30) cc_final: 0.7374 (m-30) REVERT: b 116 LEU cc_start: 0.9163 (mm) cc_final: 0.8916 (mt) REVERT: b 168 ASP cc_start: 0.7931 (p0) cc_final: 0.7638 (p0) REVERT: b 242 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7454 (tm-30) REVERT: c 105 TRP cc_start: 0.8033 (p-90) cc_final: 0.7787 (p-90) REVERT: c 107 LEU cc_start: 0.7553 (tt) cc_final: 0.7288 (tt) REVERT: d 32 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7525 (p90) REVERT: d 118 GLU cc_start: 0.7079 (pt0) cc_final: 0.6875 (pt0) REVERT: e 59 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: e 108 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7707 (tp30) REVERT: f 98 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7993 (t80) REVERT: f 102 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7874 (tm-30) outliers start: 344 outliers final: 272 residues processed: 1568 average time/residue: 0.6587 time to fit residues: 1754.0788 Evaluate side-chains 1610 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1317 time to evaluate : 5.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 ASN Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 292 GLU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 239 GLU Chi-restraints excluded: chain J residue 249 GLU Chi-restraints excluded: chain J residue 292 GLU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 115 SER Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 45 ASP Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 177 CYS Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain P residue 326 THR Chi-restraints excluded: chain P residue 346 LEU Chi-restraints excluded: chain P residue 349 GLN Chi-restraints excluded: chain P residue 386 VAL Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain Q residue 235 VAL Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain Q residue 373 ILE Chi-restraints excluded: chain R residue 31 ASP Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain U residue 47 GLN Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 102 GLN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 85 THR Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain V residue 137 THR Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain W residue 159 THR Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 177 CYS Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 346 LEU Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 235 VAL Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 75 MET Chi-restraints excluded: chain Y residue 107 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 113 ARG Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain Y residue 165 LEU Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 32 TYR Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 46 SER Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain 0 residue 38 GLU Chi-restraints excluded: chain 0 residue 57 VAL Chi-restraints excluded: chain 1 residue 12 LYS Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 102 GLN Chi-restraints excluded: chain 1 residue 111 ASP Chi-restraints excluded: chain 1 residue 115 SER Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 43 LEU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 123 LEU Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 3 residue 45 ASP Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 154 VAL Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 303 LEU Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 346 LEU Chi-restraints excluded: chain 3 residue 386 VAL Chi-restraints excluded: chain 4 residue 32 MET Chi-restraints excluded: chain 4 residue 77 ILE Chi-restraints excluded: chain 4 residue 159 THR Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 191 LEU Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 239 GLU Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 4 residue 292 GLU Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 5 residue 111 MET Chi-restraints excluded: chain 5 residue 137 THR Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 189 THR Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 6 residue 22 VAL Chi-restraints excluded: chain 6 residue 32 TYR Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 6 residue 51 ASP Chi-restraints excluded: chain 6 residue 70 SER Chi-restraints excluded: chain 6 residue 117 VAL Chi-restraints excluded: chain 6 residue 125 ILE Chi-restraints excluded: chain 7 residue 38 GLU Chi-restraints excluded: chain 7 residue 57 VAL Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 7 residue 103 SER Chi-restraints excluded: chain 8 residue 23 THR Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 98 PHE Chi-restraints excluded: chain 8 residue 111 ASP Chi-restraints excluded: chain 8 residue 115 SER Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 43 LEU Chi-restraints excluded: chain 9 residue 77 THR Chi-restraints excluded: chain 9 residue 101 VAL Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 123 LEU Chi-restraints excluded: chain 9 residue 135 ASP Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 108 GLU Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 177 CYS Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 303 LEU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 346 LEU Chi-restraints excluded: chain a residue 349 GLN Chi-restraints excluded: chain a residue 386 VAL Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain b residue 373 ILE Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 189 THR Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 32 TYR Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 59 THR Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 117 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain e residue 59 PHE Chi-restraints excluded: chain f residue 47 GLN Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 98 PHE Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 111 ASP Chi-restraints excluded: chain f residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 778 optimal weight: 0.9990 chunk 819 optimal weight: 4.9990 chunk 748 optimal weight: 4.9990 chunk 797 optimal weight: 7.9990 chunk 480 optimal weight: 0.9990 chunk 347 optimal weight: 4.9990 chunk 626 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 720 optimal weight: 0.7980 chunk 754 optimal weight: 0.3980 chunk 794 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 195 GLN B 257 ASN H 167 HIS I 119 ASN J 217 ASN O 167 HIS Q 195 GLN Q 217 ASN X 119 ASN X 195 GLN 2 167 HIS 3 119 ASN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 GLN b 217 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 69420 Z= 0.169 Angle : 0.639 13.933 94398 Z= 0.306 Chirality : 0.045 0.453 10512 Planarity : 0.005 0.064 12396 Dihedral : 4.904 47.801 9884 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 4.65 % Allowed : 17.55 % Favored : 77.80 % 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: -2.17 (0.09), residues: 8874 helix: 0.27 (0.10), residues: 2844 sheet: -1.75 (0.12), residues: 1476 loop : -2.53 (0.09), residues: 4554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 72 HIS 0.004 0.001 HIS W 178 PHE 0.014 0.001 PHE J 322 TYR 0.024 0.001 TYR f 122 ARG 0.016 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1705 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1394 time to evaluate : 5.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9137 (tt) REVERT: A 367 ASP cc_start: 0.7470 (m-30) cc_final: 0.7127 (m-30) REVERT: B 116 LEU cc_start: 0.9154 (mm) cc_final: 0.8901 (mt) REVERT: B 242 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 271 LYS cc_start: 0.8820 (ttpp) cc_final: 0.8603 (ttpp) REVERT: B 349 GLN cc_start: 0.7998 (tt0) cc_final: 0.7619 (tt0) REVERT: D 2 MET cc_start: 0.8014 (tpp) cc_final: 0.7782 (tmm) REVERT: D 107 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7542 (tt) REVERT: D 113 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7871 (ptt-90) REVERT: D 165 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8339 (pp) REVERT: F 32 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7956 (p90) REVERT: F 46 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8346 (m) REVERT: E 108 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7807 (tp30) REVERT: G 7 LYS cc_start: 0.9093 (ttmm) cc_final: 0.8763 (tttm) REVERT: G 85 ASP cc_start: 0.8338 (m-30) cc_final: 0.7874 (m-30) REVERT: H 75 MET cc_start: 0.7748 (mmt) cc_final: 0.7446 (mmt) REVERT: I 108 GLU cc_start: 0.7643 (pt0) cc_final: 0.7279 (tt0) REVERT: I 164 LYS cc_start: 0.8514 (mmtp) cc_final: 0.8172 (mmtm) REVERT: I 216 ASP cc_start: 0.7667 (t70) cc_final: 0.7335 (t0) REVERT: I 367 ASP cc_start: 0.7686 (m-30) cc_final: 0.7322 (m-30) REVERT: J 116 LEU cc_start: 0.9201 (mm) cc_final: 0.8996 (mt) REVERT: J 142 ARG cc_start: 0.8285 (mtm180) cc_final: 0.7963 (mtm180) REVERT: J 306 ILE cc_start: 0.9063 (mm) cc_final: 0.8808 (mm) REVERT: N 98 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: O 90 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7239 (mtm-85) REVERT: P 28 ARG cc_start: 0.7567 (ptm-80) cc_final: 0.7090 (mtp-110) REVERT: P 367 ASP cc_start: 0.7714 (m-30) cc_final: 0.7355 (m-30) REVERT: Q 116 LEU cc_start: 0.9094 (mm) cc_final: 0.8849 (mt) REVERT: Q 142 ARG cc_start: 0.8509 (mtm180) cc_final: 0.8042 (mtm180) REVERT: Q 168 ASP cc_start: 0.7898 (p0) cc_final: 0.7615 (p0) REVERT: Q 340 TRP cc_start: 0.8592 (t-100) cc_final: 0.8237 (t-100) REVERT: R 105 TRP cc_start: 0.7951 (p-90) cc_final: 0.7601 (p-90) REVERT: R 119 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6279 (mt) REVERT: S 32 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7392 (p90) REVERT: S 118 GLU cc_start: 0.7023 (pt0) cc_final: 0.6804 (pt0) REVERT: T 45 SER cc_start: 0.9046 (p) cc_final: 0.8817 (p) REVERT: U 98 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7966 (t80) REVERT: U 102 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: V 90 ARG cc_start: 0.7324 (mtp85) cc_final: 0.6878 (mtm180) REVERT: W 110 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9129 (tt) REVERT: W 353 LYS cc_start: 0.9120 (pttt) cc_final: 0.8782 (ptpp) REVERT: X 116 LEU cc_start: 0.9158 (mm) cc_final: 0.8918 (mt) REVERT: X 242 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7526 (tm-30) REVERT: X 271 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8597 (ttpp) REVERT: Y 107 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7568 (tt) REVERT: Y 113 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7864 (ptt-90) REVERT: Y 165 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8376 (pp) REVERT: Z 32 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.7936 (p90) REVERT: Z 46 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8354 (m) REVERT: 0 108 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7647 (tm-30) REVERT: 3 143 MET cc_start: 0.8671 (mmt) cc_final: 0.8418 (mmt) REVERT: 3 164 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8136 (mmtm) REVERT: 3 216 ASP cc_start: 0.7667 (t70) cc_final: 0.7336 (t0) REVERT: 3 349 GLN cc_start: 0.8507 (tt0) cc_final: 0.8305 (mm-40) REVERT: 3 367 ASP cc_start: 0.7689 (m-30) cc_final: 0.7359 (m-30) REVERT: 4 116 LEU cc_start: 0.9196 (mm) cc_final: 0.8963 (mt) REVERT: 4 133 ARG cc_start: 0.8305 (mmp80) cc_final: 0.7844 (mmp-170) REVERT: 4 142 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.7837 (mtm180) REVERT: 4 242 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7603 (tm-30) REVERT: 4 306 ILE cc_start: 0.9069 (mm) cc_final: 0.8783 (mm) REVERT: 6 122 MET cc_start: 0.8327 (mmm) cc_final: 0.8115 (mmm) REVERT: 8 98 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: 8 106 MET cc_start: 0.8128 (ptm) cc_final: 0.7914 (ptm) REVERT: 9 90 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7261 (mtm-85) REVERT: a 353 LYS cc_start: 0.9090 (pttt) cc_final: 0.8810 (pttt) REVERT: a 367 ASP cc_start: 0.7704 (m-30) cc_final: 0.7358 (m-30) REVERT: b 116 LEU cc_start: 0.9090 (mm) cc_final: 0.8843 (mt) REVERT: b 163 ARG cc_start: 0.6175 (mtt180) cc_final: 0.5881 (ptp-170) REVERT: b 168 ASP cc_start: 0.7880 (p0) cc_final: 0.7586 (p0) REVERT: b 242 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7428 (tm-30) REVERT: c 105 TRP cc_start: 0.7961 (p-90) cc_final: 0.7667 (p-90) REVERT: c 107 LEU cc_start: 0.6577 (tt) cc_final: 0.6085 (tt) REVERT: d 32 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7434 (p90) REVERT: d 118 GLU cc_start: 0.7041 (pt0) cc_final: 0.6838 (pt0) REVERT: e 108 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7713 (tp30) REVERT: f 98 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7955 (t80) REVERT: f 102 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7829 (tm-30) outliers start: 311 outliers final: 251 residues processed: 1573 average time/residue: 0.6509 time to fit residues: 1724.3886 Evaluate side-chains 1598 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1326 time to evaluate : 5.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 292 GLU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 239 GLU Chi-restraints excluded: chain J residue 249 GLU Chi-restraints excluded: chain J residue 292 GLU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 115 SER Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 45 ASP Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 177 CYS Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain P residue 326 THR Chi-restraints excluded: chain P residue 346 LEU Chi-restraints excluded: chain P residue 386 VAL Chi-restraints excluded: chain Q residue 159 THR Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain Q residue 235 VAL Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain Q residue 373 ILE Chi-restraints excluded: chain R residue 31 ASP Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain U residue 47 GLN Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 102 GLN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 137 THR Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain W residue 159 THR Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 177 CYS Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 346 LEU Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 235 VAL Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 75 MET Chi-restraints excluded: chain Y residue 107 LEU Chi-restraints excluded: chain Y residue 113 ARG Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain Y residue 165 LEU Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 32 TYR Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 46 SER Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain 0 residue 57 VAL Chi-restraints excluded: chain 1 residue 12 LYS Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 102 GLN Chi-restraints excluded: chain 1 residue 111 ASP Chi-restraints excluded: chain 1 residue 115 SER Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 43 LEU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 123 LEU Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 3 residue 45 ASP Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 154 VAL Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 303 LEU Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 346 LEU Chi-restraints excluded: chain 4 residue 32 MET Chi-restraints excluded: chain 4 residue 77 ILE Chi-restraints excluded: chain 4 residue 159 THR Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 191 LEU Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 239 GLU Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 4 residue 292 GLU Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 5 residue 91 LEU Chi-restraints excluded: chain 5 residue 137 THR Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 6 residue 22 VAL Chi-restraints excluded: chain 6 residue 51 ASP Chi-restraints excluded: chain 6 residue 70 SER Chi-restraints excluded: chain 6 residue 100 SER Chi-restraints excluded: chain 6 residue 117 VAL Chi-restraints excluded: chain 6 residue 125 ILE Chi-restraints excluded: chain 7 residue 38 GLU Chi-restraints excluded: chain 7 residue 57 VAL Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 7 residue 103 SER Chi-restraints excluded: chain 8 residue 23 THR Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 98 PHE Chi-restraints excluded: chain 8 residue 111 ASP Chi-restraints excluded: chain 8 residue 115 SER Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 43 LEU Chi-restraints excluded: chain 9 residue 77 THR Chi-restraints excluded: chain 9 residue 123 LEU Chi-restraints excluded: chain 9 residue 135 ASP Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 108 GLU Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 177 CYS Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 303 LEU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 346 LEU Chi-restraints excluded: chain a residue 386 VAL Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain b residue 373 ILE Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 41 SER Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 161 GLN Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 32 TYR Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 59 THR Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 117 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain e residue 59 PHE Chi-restraints excluded: chain f residue 47 GLN Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 98 PHE Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 111 ASP Chi-restraints excluded: chain f residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 523 optimal weight: 0.0000 chunk 843 optimal weight: 0.7980 chunk 514 optimal weight: 10.0000 chunk 400 optimal weight: 5.9990 chunk 586 optimal weight: 3.9990 chunk 884 optimal weight: 8.9990 chunk 814 optimal weight: 2.9990 chunk 704 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 544 optimal weight: 0.0770 chunk 431 optimal weight: 9.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 195 GLN I 79 GLN I 119 ASN J 217 ASN ** Q 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 195 GLN Q 217 ASN X 195 GLN ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 GLN b 217 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 69420 Z= 0.182 Angle : 0.651 13.797 94398 Z= 0.310 Chirality : 0.045 0.452 10512 Planarity : 0.005 0.065 12396 Dihedral : 4.875 48.312 9884 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.07 % Rotamer: Outliers : 4.50 % Allowed : 18.12 % Favored : 77.38 % 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: -2.08 (0.09), residues: 8874 helix: 0.34 (0.10), residues: 2856 sheet: -1.71 (0.12), residues: 1476 loop : -2.48 (0.09), residues: 4542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 72 HIS 0.004 0.001 HIS A 178 PHE 0.014 0.001 PHE Q 107 TYR 0.024 0.001 TYR U 122 ARG 0.015 0.000 ARG R 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1639 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1338 time to evaluate : 5.726 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: A 110 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9134 (tt) REVERT: A 216 ASP cc_start: 0.7637 (t70) cc_final: 0.7315 (t0) REVERT: A 367 ASP cc_start: 0.7369 (m-30) cc_final: 0.7029 (m-30) REVERT: B 57 ASN cc_start: 0.8522 (p0) cc_final: 0.8201 (p0) REVERT: B 96 ARG cc_start: 0.8417 (tpm170) cc_final: 0.8040 (tpm170) REVERT: B 116 LEU cc_start: 0.9142 (mm) cc_final: 0.8888 (mt) REVERT: B 242 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 271 LYS cc_start: 0.8810 (ttpp) cc_final: 0.8598 (ttpp) REVERT: B 349 GLN cc_start: 0.7999 (tt0) cc_final: 0.7631 (tt0) REVERT: B 353 LYS cc_start: 0.7441 (pttt) cc_final: 0.7045 (ptpp) REVERT: D 107 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7320 (tt) REVERT: D 113 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7884 (ptt-90) REVERT: D 165 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8291 (pp) REVERT: F 32 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7934 (p90) REVERT: F 46 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8357 (m) REVERT: E 108 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7824 (tp30) REVERT: G 7 LYS cc_start: 0.9105 (ttmm) cc_final: 0.8785 (tttm) REVERT: H 75 MET cc_start: 0.7676 (mmt) cc_final: 0.7447 (mmt) REVERT: I 108 GLU cc_start: 0.7650 (pt0) cc_final: 0.7277 (tt0) REVERT: I 143 MET cc_start: 0.8691 (mmt) cc_final: 0.8387 (mmt) REVERT: I 164 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8180 (mmtm) REVERT: I 216 ASP cc_start: 0.7658 (t70) cc_final: 0.7331 (t0) REVERT: I 367 ASP cc_start: 0.7719 (m-30) cc_final: 0.7371 (m-30) REVERT: J 306 ILE cc_start: 0.9062 (mm) cc_final: 0.8784 (mm) REVERT: L 46 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8332 (m) REVERT: N 13 LEU cc_start: 0.9082 (mm) cc_final: 0.8808 (mt) REVERT: N 98 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: O 90 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7235 (mtm-85) REVERT: P 28 ARG cc_start: 0.7550 (ptm-80) cc_final: 0.7186 (mtp-110) REVERT: P 367 ASP cc_start: 0.7717 (m-30) cc_final: 0.7367 (m-30) REVERT: Q 116 LEU cc_start: 0.9091 (mm) cc_final: 0.8856 (mt) REVERT: Q 168 ASP cc_start: 0.7913 (p0) cc_final: 0.7653 (p0) REVERT: Q 340 TRP cc_start: 0.8569 (t-100) cc_final: 0.8249 (t-100) REVERT: R 105 TRP cc_start: 0.8006 (p-90) cc_final: 0.7628 (p-90) REVERT: R 119 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6295 (mt) REVERT: S 32 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7469 (p90) REVERT: T 45 SER cc_start: 0.9034 (p) cc_final: 0.8800 (p) REVERT: T 108 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7456 (tm-30) REVERT: U 98 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7956 (t80) REVERT: U 102 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: V 90 ARG cc_start: 0.7269 (mtp85) cc_final: 0.6909 (mtm180) REVERT: W 110 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9137 (tt) REVERT: W 164 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8395 (mttm) REVERT: W 353 LYS cc_start: 0.9131 (pttt) cc_final: 0.8806 (ptpp) REVERT: X 57 ASN cc_start: 0.8518 (p0) cc_final: 0.8201 (p0) REVERT: X 116 LEU cc_start: 0.9140 (mm) cc_final: 0.8893 (mt) REVERT: X 242 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7527 (tm-30) REVERT: X 271 LYS cc_start: 0.8824 (ttpp) cc_final: 0.8592 (ttpp) REVERT: Y 107 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7353 (tt) REVERT: Y 113 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7877 (ptt-90) REVERT: Y 165 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8317 (pp) REVERT: Z 32 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7965 (p90) REVERT: Z 46 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8341 (m) REVERT: 0 108 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7646 (tm-30) REVERT: 1 7 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8779 (tttm) REVERT: 3 28 ARG cc_start: 0.7289 (ptm-80) cc_final: 0.6761 (mtp-110) REVERT: 3 143 MET cc_start: 0.8676 (mmt) cc_final: 0.8415 (mmt) REVERT: 3 156 TYR cc_start: 0.9271 (m-80) cc_final: 0.9043 (m-80) REVERT: 3 164 LYS cc_start: 0.8506 (mmtp) cc_final: 0.8156 (mmtm) REVERT: 3 216 ASP cc_start: 0.7659 (t70) cc_final: 0.7338 (t0) REVERT: 3 367 ASP cc_start: 0.7700 (m-30) cc_final: 0.7340 (m-30) REVERT: 4 116 LEU cc_start: 0.9190 (mm) cc_final: 0.8965 (mt) REVERT: 4 133 ARG cc_start: 0.8334 (mmp80) cc_final: 0.7860 (mmp-170) REVERT: 4 242 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7616 (tm-30) REVERT: 4 273 MET cc_start: 0.8951 (mmt) cc_final: 0.8206 (mmt) REVERT: 4 306 ILE cc_start: 0.9068 (mm) cc_final: 0.8770 (mm) REVERT: 6 122 MET cc_start: 0.8332 (mmm) cc_final: 0.8119 (mmm) REVERT: 8 98 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: 8 106 MET cc_start: 0.8103 (ptm) cc_final: 0.7894 (ptm) REVERT: 9 90 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7283 (mtm-85) REVERT: a 32 MET cc_start: 0.7441 (ptp) cc_final: 0.7181 (ptp) REVERT: a 367 ASP cc_start: 0.7709 (m-30) cc_final: 0.7370 (m-30) REVERT: b 116 LEU cc_start: 0.9094 (mm) cc_final: 0.8853 (mt) REVERT: b 163 ARG cc_start: 0.6231 (mtt180) cc_final: 0.5874 (ptp-170) REVERT: b 168 ASP cc_start: 0.7831 (p0) cc_final: 0.7534 (p0) REVERT: b 242 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7438 (tm-30) REVERT: c 105 TRP cc_start: 0.7948 (p-90) cc_final: 0.7680 (p-90) REVERT: d 32 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7456 (p90) REVERT: d 101 ARG cc_start: 0.8633 (ptm160) cc_final: 0.8415 (ptm160) REVERT: e 108 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7678 (tp30) REVERT: f 98 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7949 (t80) REVERT: f 102 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7790 (tm-30) outliers start: 301 outliers final: 259 residues processed: 1518 average time/residue: 0.6575 time to fit residues: 1694.2976 Evaluate side-chains 1584 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1303 time to evaluate : 5.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 292 GLU Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 326 THR Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 239 GLU Chi-restraints excluded: chain J residue 249 GLU Chi-restraints excluded: chain J residue 292 GLU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 75 MET Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 115 SER Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain O residue 29 PHE Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain O residue 135 ASP Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain P residue 45 ASP Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 177 CYS Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 303 LEU Chi-restraints excluded: chain P residue 326 THR Chi-restraints excluded: chain P residue 346 LEU Chi-restraints excluded: chain P residue 386 VAL Chi-restraints excluded: chain Q residue 159 THR Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain Q residue 222 SER Chi-restraints excluded: chain Q residue 225 ILE Chi-restraints excluded: chain Q residue 235 VAL Chi-restraints excluded: chain Q residue 356 LEU Chi-restraints excluded: chain Q residue 373 ILE Chi-restraints excluded: chain R residue 31 ASP Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 GLN Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 PHE Chi-restraints excluded: chain U residue 47 GLN Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 102 GLN Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 29 PHE Chi-restraints excluded: chain V residue 43 LEU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 137 THR Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 154 VAL Chi-restraints excluded: chain W residue 159 THR Chi-restraints excluded: chain W residue 160 VAL Chi-restraints excluded: chain W residue 187 ASP Chi-restraints excluded: chain W residue 231 ASP Chi-restraints excluded: chain W residue 326 THR Chi-restraints excluded: chain W residue 346 LEU Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 163 ARG Chi-restraints excluded: chain X residue 235 VAL Chi-restraints excluded: chain X residue 239 GLU Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain Y residue 75 MET Chi-restraints excluded: chain Y residue 107 LEU Chi-restraints excluded: chain Y residue 113 ARG Chi-restraints excluded: chain Y residue 149 VAL Chi-restraints excluded: chain Y residue 165 LEU Chi-restraints excluded: chain Y residue 189 THR Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 32 TYR Chi-restraints excluded: chain Z residue 46 SER Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain 0 residue 57 VAL Chi-restraints excluded: chain 1 residue 12 LYS Chi-restraints excluded: chain 1 residue 94 ILE Chi-restraints excluded: chain 1 residue 98 PHE Chi-restraints excluded: chain 1 residue 102 GLN Chi-restraints excluded: chain 1 residue 111 ASP Chi-restraints excluded: chain 1 residue 115 SER Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 2 residue 29 PHE Chi-restraints excluded: chain 2 residue 43 LEU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 123 LEU Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 193 LEU Chi-restraints excluded: chain 3 residue 45 ASP Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 160 VAL Chi-restraints excluded: chain 3 residue 187 ASP Chi-restraints excluded: chain 3 residue 303 LEU Chi-restraints excluded: chain 3 residue 326 THR Chi-restraints excluded: chain 3 residue 346 LEU Chi-restraints excluded: chain 3 residue 386 VAL Chi-restraints excluded: chain 4 residue 32 MET Chi-restraints excluded: chain 4 residue 77 ILE Chi-restraints excluded: chain 4 residue 159 THR Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 4 residue 191 LEU Chi-restraints excluded: chain 4 residue 235 VAL Chi-restraints excluded: chain 4 residue 239 GLU Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 4 residue 292 GLU Chi-restraints excluded: chain 4 residue 356 LEU Chi-restraints excluded: chain 5 residue 91 LEU Chi-restraints excluded: chain 5 residue 111 MET Chi-restraints excluded: chain 5 residue 137 THR Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 161 GLN Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 6 residue 22 VAL Chi-restraints excluded: chain 6 residue 45 VAL Chi-restraints excluded: chain 6 residue 51 ASP Chi-restraints excluded: chain 6 residue 70 SER Chi-restraints excluded: chain 6 residue 117 VAL Chi-restraints excluded: chain 6 residue 125 ILE Chi-restraints excluded: chain 7 residue 38 GLU Chi-restraints excluded: chain 7 residue 57 VAL Chi-restraints excluded: chain 7 residue 60 THR Chi-restraints excluded: chain 7 residue 103 SER Chi-restraints excluded: chain 8 residue 23 THR Chi-restraints excluded: chain 8 residue 53 LEU Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 98 PHE Chi-restraints excluded: chain 8 residue 111 ASP Chi-restraints excluded: chain 8 residue 115 SER Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 43 LEU Chi-restraints excluded: chain 9 residue 77 THR Chi-restraints excluded: chain 9 residue 123 LEU Chi-restraints excluded: chain 9 residue 135 ASP Chi-restraints excluded: chain 9 residue 193 LEU Chi-restraints excluded: chain a residue 45 ASP Chi-restraints excluded: chain a residue 108 GLU Chi-restraints excluded: chain a residue 160 VAL Chi-restraints excluded: chain a residue 177 CYS Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 303 LEU Chi-restraints excluded: chain a residue 326 THR Chi-restraints excluded: chain a residue 346 LEU Chi-restraints excluded: chain a residue 386 VAL Chi-restraints excluded: chain b residue 145 VAL Chi-restraints excluded: chain b residue 159 THR Chi-restraints excluded: chain b residue 160 VAL Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 356 LEU Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 161 GLN Chi-restraints excluded: chain c residue 189 THR Chi-restraints excluded: chain c residue 193 LEU Chi-restraints excluded: chain d residue 32 TYR Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 59 THR Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 96 ASP Chi-restraints excluded: chain d residue 117 VAL Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain e residue 59 PHE Chi-restraints excluded: chain f residue 47 GLN Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 94 ILE Chi-restraints excluded: chain f residue 98 PHE Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 111 ASP Chi-restraints excluded: chain f residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 559 optimal weight: 6.9990 chunk 750 optimal weight: 4.9990 chunk 215 optimal weight: 0.3980 chunk 649 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 195 optimal weight: 0.0070 chunk 705 optimal weight: 0.0270 chunk 295 optimal weight: 8.9990 chunk 724 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.8258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 HIS B 195 GLN ** H 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 ASN J 217 ASN Q 195 GLN Q 217 ASN V 167 HIS X 195 GLN ** 2 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 217 ASN b 195 GLN b 217 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.098721 restraints weight = 93685.644| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.88 r_work: 0.2842 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 69420 Z= 0.172 Angle : 0.648 13.548 94398 Z= 0.308 Chirality : 0.045 0.461 10512 Planarity : 0.005 0.065 12396 Dihedral : 4.787 48.458 9884 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 4.54 % Allowed : 18.34 % Favored : 77.12 % 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: -1.96 (0.09), residues: 8874 helix: 0.48 (0.10), residues: 2832 sheet: -1.65 (0.12), residues: 1476 loop : -2.42 (0.09), residues: 4566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 72 HIS 0.004 0.001 HIS A 178 PHE 0.012 0.001 PHE J 322 TYR 0.026 0.001 TYR N 122 ARG 0.014 0.000 ARG R 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24299.37 seconds wall clock time: 421 minutes 20.52 seconds (25280.52 seconds total)