Starting phenix.real_space_refine on Sun Apr 14 17:50:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls9_23506/04_2024/7ls9_23506.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls9_23506/04_2024/7ls9_23506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls9_23506/04_2024/7ls9_23506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls9_23506/04_2024/7ls9_23506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls9_23506/04_2024/7ls9_23506.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ls9_23506/04_2024/7ls9_23506.pdb" } resolution = 3.42 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= 0.003 sd= 0.021 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 144 5.16 5 C 20436 2.51 5 N 5304 2.21 5 O 6342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 848": "OD1" <-> "OD2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B ASP 936": "OD1" <-> "OD2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "D ASP 31": "OD1" <-> "OD2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1": "OE1" <-> "OE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 848": "OD1" <-> "OD2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1": "OE1" <-> "OE2" Residue "G TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32226 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "H" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8574 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 54, 'TRANS': 1042} Chain breaks: 5 Chain: "E" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.74, per 1000 atoms: 0.52 Number of scatterers: 32226 At special positions: 0 Unit cell: (140.17, 140.17, 206.51, 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 144 16.00 O 6342 8.00 N 5304 7.00 C 20436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100A" - pdb=" SG CYS H 100F" distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 100A" - pdb=" SG CYS D 100F" distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 100A" - pdb=" SG CYS E 100F" distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 17 " " NAG A1310 " - " ASN A 343 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 17 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 17 " " NAG C1310 " - " ASN C 343 " " NAG I 1 " - " ASN A 165 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN B 165 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN C 165 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN B 122 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN C 122 " " NAG Z 1 " - " ASN A 717 " " NAG a 1 " - " ASN A 801 " " NAG b 1 " - " ASN A1098 " " NAG c 1 " - " ASN A1134 " " NAG d 1 " - " ASN A 122 " Time building additional restraints: 11.95 Conformation dependent library (CDL) restraints added in 5.2 seconds 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7446 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 69 sheets defined 22.5% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.040A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.306A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 749 through 757 Processing helix chain 'A' and resid 757 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 832 through 838 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.929A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.970A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.254A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.713A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.846A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.215A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.871A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.766A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 31 removed outlier: 4.248A pdb=" N SER L 31 " --> pdb=" O VAL L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.090A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.050A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.300A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.650A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.626A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 749 through 757 Processing helix chain 'B' and resid 757 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 832 through 838 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.782A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 889 removed outlier: 3.702A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 889' Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.100A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.618A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.822A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.006A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.900A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 52A through 54 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.900A pdb=" N THR D 87 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 removed outlier: 3.906A pdb=" N SER F 31 " --> pdb=" O VAL F 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 31' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.077A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.882A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.296A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.737A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 630 through 636 removed outlier: 3.601A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 749 through 783 removed outlier: 6.415A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 832 through 838 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.810A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.236A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.174A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.642A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.806A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.287A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.801A pdb=" N THR E 87 " --> pdb=" O THR E 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 31 removed outlier: 4.202A pdb=" N SER G 31 " --> pdb=" O VAL G 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 31' Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.155A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.083A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.814A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.519A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.996A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.996A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.891A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.616A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.230A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.674A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.791A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.755A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP H 72 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.647A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.647A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 100 through 100B Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.511A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.511A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.124A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.806A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.819A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 141 through 144 Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.008A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.008A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.192A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.719A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.175A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.512A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.733A pdb=" N THR D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.733A pdb=" N THR D 107 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 100 through 100B removed outlier: 3.522A pdb=" N ILE D 100B" --> pdb=" O VAL D 100E" (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.587A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.608A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN F 37 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.608A pdb=" N ALA F 84 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.124A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.810A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.787A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 141 through 144 Processing sheet with id=AF7, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AF8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.038A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.038A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AG3, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.750A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.684A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.684A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.794A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 1094 through 1098 Processing sheet with id=AG9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AH1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.912A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.912A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 100 through 100B Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.593A pdb=" N SER G 22 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS G 23 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.674A pdb=" N GLN G 89 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 37 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.699A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 1303 hydrogen bonds defined for protein. 3528 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: 15.87 Time building geometry restraints manager: 13.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5373 1.32 - 1.46: 11551 1.46 - 1.59: 15840 1.59 - 1.73: 2 1.73 - 1.86: 180 Bond restraints: 32946 Sorted by residual: bond pdb=" CG PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 1.503 1.244 0.259 3.40e-02 8.65e+02 5.79e+01 bond pdb=" CG PRO G 59 " pdb=" CD PRO G 59 " ideal model delta sigma weight residual 1.503 1.309 0.194 3.40e-02 8.65e+02 3.26e+01 bond pdb=" CA ALA D 99 " pdb=" CB ALA D 99 " ideal model delta sigma weight residual 1.530 1.463 0.066 1.48e-02 4.57e+03 2.01e+01 bond pdb=" CA ALA H 99 " pdb=" CB ALA H 99 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.66e-02 3.63e+03 1.61e+01 bond pdb=" C PHE E 100G" pdb=" O PHE E 100G" ideal model delta sigma weight residual 1.236 1.189 0.046 1.17e-02 7.31e+03 1.58e+01 ... (remaining 32941 not shown) Histogram of bond angle deviations from ideal: 87.93 - 97.23: 7 97.23 - 106.53: 892 106.53 - 115.83: 20702 115.83 - 125.12: 22773 125.12 - 134.42: 440 Bond angle restraints: 44814 Sorted by residual: angle pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 112.00 95.54 16.46 1.40e+00 5.10e-01 1.38e+02 angle pdb=" N PRO F 40 " pdb=" CD PRO F 40 " pdb=" CG PRO F 40 " ideal model delta sigma weight residual 103.20 87.93 15.27 1.50e+00 4.44e-01 1.04e+02 angle pdb=" CA GLY C 447 " pdb=" C GLY C 447 " pdb=" O GLY C 447 " ideal model delta sigma weight residual 121.88 114.92 6.96 7.80e-01 1.64e+00 7.97e+01 angle pdb=" N PRO G 59 " pdb=" CD PRO G 59 " pdb=" CG PRO G 59 " ideal model delta sigma weight residual 103.20 90.02 13.18 1.50e+00 4.44e-01 7.72e+01 angle pdb=" C PHE A 140 " pdb=" CA PHE A 140 " pdb=" CB PHE A 140 " ideal model delta sigma weight residual 111.17 95.96 15.21 1.96e+00 2.60e-01 6.02e+01 ... (remaining 44809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 19383 21.66 - 43.32: 1006 43.32 - 64.98: 116 64.98 - 86.64: 45 86.64 - 108.30: 15 Dihedral angle restraints: 20565 sinusoidal: 8949 harmonic: 11616 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.51 -80.49 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.81 -76.19 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -10.44 -75.56 1 1.00e+01 1.00e-02 7.21e+01 ... (remaining 20562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4792 0.096 - 0.192: 416 0.192 - 0.288: 44 0.288 - 0.384: 3 0.384 - 0.479: 4 Chirality restraints: 5259 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.33e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.10e+01 ... (remaining 5256 not shown) Planarity restraints: 5751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.244 2.00e-02 2.50e+03 2.07e-01 5.37e+02 pdb=" C7 NAG I 2 " 0.051 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.342 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.232 2.00e-02 2.50e+03 1.97e-01 4.86e+02 pdb=" C7 NAG K 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.323 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " -0.221 2.00e-02 2.50e+03 1.88e-01 4.42e+02 pdb=" C7 NAG P 2 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " 0.308 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " -0.171 2.00e-02 2.50e+03 ... (remaining 5748 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5085 2.77 - 3.30: 28806 3.30 - 3.83: 52493 3.83 - 4.37: 59924 4.37 - 4.90: 106489 Nonbonded interactions: 252797 Sorted by model distance: nonbonded pdb=" OG SER B 494 " pdb=" OH TYR F 32 " model vdw 2.232 2.440 nonbonded pdb=" OE1 GLN B 314 " pdb=" OG SER C 735 " model vdw 2.282 2.440 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.304 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.315 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.331 2.440 ... (remaining 252792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' 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: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 18.070 Check model and map are aligned: 0.440 Set scattering table: 0.290 Process input model: 84.630 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.470 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: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 32946 Z= 0.351 Angle : 0.888 16.459 44814 Z= 0.520 Chirality : 0.057 0.479 5259 Planarity : 0.008 0.207 5700 Dihedral : 12.843 108.299 12957 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 3954 helix: -0.05 (0.18), residues: 741 sheet: 0.48 (0.17), residues: 963 loop : -1.11 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 35 HIS 0.012 0.001 HIS B 519 PHE 0.043 0.002 PHE C 817 TYR 0.035 0.002 TYR B 741 ARG 0.017 0.001 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 3.442 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 725 GLU cc_start: 0.7602 (pp20) cc_final: 0.7284 (pp20) REVERT: A 864 LEU cc_start: 0.7503 (tp) cc_final: 0.7124 (tp) REVERT: H 4 LEU cc_start: 0.8613 (mm) cc_final: 0.8249 (mm) REVERT: H 57 THR cc_start: 0.8853 (p) cc_final: 0.8553 (m) REVERT: L 53 SER cc_start: 0.7978 (t) cc_final: 0.7589 (p) REVERT: B 406 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6757 (mm-30) REVERT: D 4 LEU cc_start: 0.8327 (mm) cc_final: 0.7838 (mm) REVERT: F 2 ILE cc_start: 0.8290 (mp) cc_final: 0.8030 (mp) REVERT: F 27 GLN cc_start: 0.7368 (pt0) cc_final: 0.6528 (pp30) REVERT: F 53 SER cc_start: 0.8263 (t) cc_final: 0.7734 (p) REVERT: F 54 ARG cc_start: 0.7958 (mpt90) cc_final: 0.7534 (mtt90) REVERT: E 4 LEU cc_start: 0.8408 (mm) cc_final: 0.8157 (mm) REVERT: E 101 ASP cc_start: 0.8075 (t0) cc_final: 0.7806 (t0) REVERT: G 49 TYR cc_start: 0.8182 (p90) cc_final: 0.7799 (p90) REVERT: G 53 SER cc_start: 0.7441 (t) cc_final: 0.7027 (t) REVERT: G 79 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7196 (pm20) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.4538 time to fit residues: 321.0076 Evaluate side-chains 312 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 1.9990 chunk 297 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 159 optimal weight: 0.0060 chunk 308 optimal weight: 0.6980 chunk 119 optimal weight: 0.0770 chunk 187 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 498 GLN A 613 GLN A 644 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN B 207 HIS B 498 GLN B 644 GLN B1011 GLN D 100CASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 519 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 32946 Z= 0.159 Angle : 0.558 10.172 44814 Z= 0.289 Chirality : 0.043 0.174 5259 Planarity : 0.004 0.059 5700 Dihedral : 6.288 65.783 5895 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.67 % Allowed : 7.47 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 3954 helix: 0.82 (0.19), residues: 744 sheet: 0.74 (0.16), residues: 981 loop : -0.92 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 35 HIS 0.004 0.001 HIS D 32 PHE 0.018 0.001 PHE A 140 TYR 0.022 0.001 TYR B1067 ARG 0.004 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 355 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1005 GLN cc_start: 0.6786 (tm-30) cc_final: 0.6485 (tm-30) REVERT: B 869 MET cc_start: 0.7705 (mtm) cc_final: 0.7496 (ttm) REVERT: D 58 GLU cc_start: 0.7852 (mp0) cc_final: 0.7479 (mp0) REVERT: F 2 ILE cc_start: 0.8268 (mp) cc_final: 0.8062 (mp) REVERT: F 27 GLN cc_start: 0.7296 (pt0) cc_final: 0.6511 (pp30) REVERT: F 53 SER cc_start: 0.7486 (t) cc_final: 0.6962 (t) REVERT: C 389 ASP cc_start: 0.5980 (p0) cc_final: 0.5640 (p0) REVERT: G 35 TRP cc_start: 0.6068 (m100) cc_final: 0.5791 (m100) REVERT: G 48 ILE cc_start: 0.7714 (mt) cc_final: 0.7409 (mm) outliers start: 23 outliers final: 12 residues processed: 370 average time/residue: 0.4866 time to fit residues: 287.0829 Evaluate side-chains 306 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 294 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 chunk 386 optimal weight: 6.9990 chunk 318 optimal weight: 0.0670 chunk 354 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 286 optimal weight: 6.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 613 GLN C 901 GLN G 37 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 32946 Z= 0.353 Angle : 0.647 10.557 44814 Z= 0.330 Chirality : 0.046 0.177 5259 Planarity : 0.004 0.055 5700 Dihedral : 5.106 35.130 5895 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.77 % Allowed : 10.22 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 3954 helix: 0.48 (0.19), residues: 786 sheet: 0.72 (0.17), residues: 912 loop : -0.86 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 35 HIS 0.008 0.001 HIS B1058 PHE 0.026 0.002 PHE B 347 TYR 0.021 0.002 TYR B 453 ARG 0.005 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 325 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 864 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7145 (tp) REVERT: H 31 ASP cc_start: 0.8273 (t0) cc_final: 0.8049 (t0) REVERT: L 27 GLN cc_start: 0.7178 (pp30) cc_final: 0.6738 (pp30) REVERT: B 389 ASP cc_start: 0.5957 (p0) cc_final: 0.5525 (p0) REVERT: B 495 TYR cc_start: 0.8097 (m-10) cc_final: 0.7760 (m-10) REVERT: B 900 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7400 (mtm) REVERT: B 902 MET cc_start: 0.7589 (mmp) cc_final: 0.7193 (mmt) REVERT: B 1029 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7442 (tpp) REVERT: D 97 ARG cc_start: 0.8542 (ttt-90) cc_final: 0.8334 (ttt-90) REVERT: F 53 SER cc_start: 0.7682 (t) cc_final: 0.7211 (t) REVERT: C 389 ASP cc_start: 0.5896 (p0) cc_final: 0.5476 (p0) REVERT: C 1005 GLN cc_start: 0.7273 (tm-30) cc_final: 0.6775 (tm-30) REVERT: E 29 PHE cc_start: 0.7689 (t80) cc_final: 0.7438 (t80) REVERT: G 48 ILE cc_start: 0.7716 (mt) cc_final: 0.7314 (mm) outliers start: 61 outliers final: 42 residues processed: 370 average time/residue: 0.4552 time to fit residues: 270.4254 Evaluate side-chains 326 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 281 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 240 optimal weight: 10.0000 chunk 358 optimal weight: 2.9990 chunk 379 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 chunk 340 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 784 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 613 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 32946 Z= 0.296 Angle : 0.580 9.104 44814 Z= 0.298 Chirality : 0.044 0.169 5259 Planarity : 0.004 0.050 5700 Dihedral : 4.737 35.950 5895 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.17 % Allowed : 12.19 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 3954 helix: 0.90 (0.20), residues: 750 sheet: 0.62 (0.16), residues: 960 loop : -0.79 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 35 HIS 0.005 0.001 HIS C1058 PHE 0.021 0.002 PHE C 347 TYR 0.026 0.002 TYR E 102 ARG 0.006 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 300 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.6719 (p0) cc_final: 0.6480 (p0) REVERT: H 101 ASP cc_start: 0.8000 (t0) cc_final: 0.7761 (t0) REVERT: L 27 GLN cc_start: 0.7159 (pp30) cc_final: 0.6633 (pp30) REVERT: B 495 TYR cc_start: 0.8089 (m-10) cc_final: 0.7795 (m-10) REVERT: B 900 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7173 (mtm) REVERT: B 1029 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7438 (tpp) REVERT: F 48 ILE cc_start: 0.7500 (mt) cc_final: 0.7066 (mm) REVERT: F 53 SER cc_start: 0.7565 (t) cc_final: 0.7141 (t) REVERT: C 389 ASP cc_start: 0.6019 (p0) cc_final: 0.5641 (p0) REVERT: C 1005 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6718 (tm-30) REVERT: G 48 ILE cc_start: 0.7742 (mt) cc_final: 0.7439 (mm) outliers start: 75 outliers final: 59 residues processed: 351 average time/residue: 0.4570 time to fit residues: 257.5456 Evaluate side-chains 340 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 279 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 282 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 324 optimal weight: 0.7980 chunk 262 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 0.4980 chunk 340 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 207 HIS C 644 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32946 Z= 0.223 Angle : 0.548 8.045 44814 Z= 0.281 Chirality : 0.043 0.163 5259 Planarity : 0.004 0.050 5700 Dihedral : 4.489 35.284 5895 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.40 % Allowed : 13.55 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 3954 helix: 1.31 (0.20), residues: 726 sheet: 0.55 (0.16), residues: 981 loop : -0.80 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 35 HIS 0.004 0.001 HIS B1058 PHE 0.017 0.001 PHE E 29 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 305 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ASP cc_start: 0.8010 (t0) cc_final: 0.7738 (t0) REVERT: L 27 GLN cc_start: 0.7173 (pp30) cc_final: 0.6603 (pp30) REVERT: B 900 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7112 (mtm) REVERT: B 1029 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7379 (tpp) REVERT: F 48 ILE cc_start: 0.7569 (mt) cc_final: 0.7117 (mm) REVERT: F 53 SER cc_start: 0.7420 (t) cc_final: 0.7023 (t) REVERT: F 79 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7261 (mm-30) REVERT: C 389 ASP cc_start: 0.5934 (p0) cc_final: 0.5531 (p0) REVERT: C 1005 GLN cc_start: 0.6830 (tm-30) cc_final: 0.6463 (tm-30) REVERT: G 27 GLN cc_start: 0.6832 (pt0) cc_final: 0.6362 (pp30) REVERT: G 48 ILE cc_start: 0.7745 (mt) cc_final: 0.7363 (mm) outliers start: 83 outliers final: 65 residues processed: 366 average time/residue: 0.4611 time to fit residues: 270.9771 Evaluate side-chains 350 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 283 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 9.9990 chunk 342 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 380 optimal weight: 1.9990 chunk 315 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 644 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32946 Z= 0.304 Angle : 0.583 9.166 44814 Z= 0.298 Chirality : 0.044 0.184 5259 Planarity : 0.004 0.052 5700 Dihedral : 4.548 36.271 5895 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.75 % Allowed : 14.22 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 3954 helix: 1.04 (0.20), residues: 732 sheet: 0.47 (0.16), residues: 1011 loop : -0.77 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 35 HIS 0.003 0.001 HIS C1088 PHE 0.032 0.002 PHE E 29 TYR 0.020 0.002 TYR B1067 ARG 0.007 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 283 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.7116 (pp30) cc_final: 0.6573 (pp30) REVERT: B 900 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7191 (mtm) REVERT: B 1029 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7497 (tpp) REVERT: F 48 ILE cc_start: 0.7690 (mt) cc_final: 0.7190 (mm) REVERT: F 53 SER cc_start: 0.7469 (t) cc_final: 0.7102 (t) REVERT: C 389 ASP cc_start: 0.6045 (p0) cc_final: 0.5634 (p0) REVERT: C 740 MET cc_start: 0.7325 (tmm) cc_final: 0.6981 (tmm) REVERT: G 27 GLN cc_start: 0.6944 (pt0) cc_final: 0.6513 (pp30) REVERT: G 48 ILE cc_start: 0.7739 (mt) cc_final: 0.7438 (mm) outliers start: 95 outliers final: 81 residues processed: 346 average time/residue: 0.4650 time to fit residues: 259.4251 Evaluate side-chains 355 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 272 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 0.7980 chunk 42 optimal weight: 0.0470 chunk 216 optimal weight: 0.9990 chunk 277 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 320 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 378 optimal weight: 6.9990 chunk 237 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 856 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32946 Z= 0.179 Angle : 0.528 7.918 44814 Z= 0.272 Chirality : 0.042 0.159 5259 Planarity : 0.004 0.049 5700 Dihedral : 4.303 34.056 5895 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.17 % Allowed : 15.35 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 3954 helix: 1.37 (0.20), residues: 741 sheet: 0.53 (0.16), residues: 987 loop : -0.73 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 35 HIS 0.003 0.001 HIS A 207 PHE 0.020 0.001 PHE E 29 TYR 0.020 0.001 TYR B1067 ARG 0.007 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 302 time to evaluate : 3.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 GLU cc_start: 0.8018 (mp0) cc_final: 0.7494 (tt0) REVERT: H 101 ASP cc_start: 0.8032 (t0) cc_final: 0.7806 (t0) REVERT: H 105 GLN cc_start: 0.8421 (pm20) cc_final: 0.8123 (pm20) REVERT: L 27 GLN cc_start: 0.7092 (pp30) cc_final: 0.6519 (pp30) REVERT: L 54 ARG cc_start: 0.8255 (mtt90) cc_final: 0.8021 (mtt90) REVERT: B 740 MET cc_start: 0.7423 (mmm) cc_final: 0.7199 (tpp) REVERT: B 900 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7047 (mtm) REVERT: B 1029 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7394 (tpp) REVERT: F 48 ILE cc_start: 0.7859 (mt) cc_final: 0.7496 (mm) REVERT: C 389 ASP cc_start: 0.6056 (p0) cc_final: 0.5619 (p0) REVERT: C 740 MET cc_start: 0.7267 (mmm) cc_final: 0.7033 (tmm) REVERT: C 902 MET cc_start: 0.8400 (mmt) cc_final: 0.8047 (mmp) REVERT: E 79 TYR cc_start: 0.7544 (m-10) cc_final: 0.7343 (m-10) REVERT: G 27 GLN cc_start: 0.6898 (pt0) cc_final: 0.6404 (pp30) REVERT: G 48 ILE cc_start: 0.7718 (mt) cc_final: 0.7465 (mm) REVERT: G 54 ARG cc_start: 0.7954 (mpt180) cc_final: 0.7745 (mtt90) outliers start: 75 outliers final: 65 residues processed: 352 average time/residue: 0.4571 time to fit residues: 259.5817 Evaluate side-chains 344 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 277 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 226 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 73 optimal weight: 0.0970 chunk 240 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 32946 Z= 0.242 Angle : 0.561 9.096 44814 Z= 0.286 Chirality : 0.043 0.167 5259 Planarity : 0.004 0.050 5700 Dihedral : 4.322 34.686 5895 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.43 % Allowed : 15.61 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.13), residues: 3954 helix: 1.14 (0.20), residues: 747 sheet: 0.47 (0.16), residues: 1017 loop : -0.69 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 35 HIS 0.003 0.001 HIS C 207 PHE 0.015 0.001 PHE C 347 TYR 0.021 0.001 TYR E 102 ARG 0.008 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 282 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 101 ASP cc_start: 0.8023 (t0) cc_final: 0.7791 (t0) REVERT: H 105 GLN cc_start: 0.8378 (pm20) cc_final: 0.8096 (pm20) REVERT: L 27 GLN cc_start: 0.7166 (pp30) cc_final: 0.6596 (pp30) REVERT: L 62 PHE cc_start: 0.7874 (m-80) cc_final: 0.7593 (m-80) REVERT: B 900 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7143 (mtm) REVERT: B 980 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8131 (mt) REVERT: B 1029 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7466 (tpp) REVERT: F 27 GLN cc_start: 0.6878 (pt0) cc_final: 0.6506 (pp30) REVERT: F 48 ILE cc_start: 0.7865 (mt) cc_final: 0.7509 (mm) REVERT: C 389 ASP cc_start: 0.6129 (p0) cc_final: 0.5656 (p0) REVERT: G 27 GLN cc_start: 0.6937 (pt0) cc_final: 0.6498 (pp30) REVERT: G 48 ILE cc_start: 0.7620 (mt) cc_final: 0.7358 (mm) REVERT: G 54 ARG cc_start: 0.8001 (mpt180) cc_final: 0.7636 (mtt90) REVERT: G 103 LYS cc_start: 0.7978 (tptt) cc_final: 0.7741 (tptp) outliers start: 84 outliers final: 73 residues processed: 339 average time/residue: 0.4591 time to fit residues: 249.4396 Evaluate side-chains 349 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 273 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 1.9990 chunk 362 optimal weight: 0.5980 chunk 331 optimal weight: 0.9990 chunk 352 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 277 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 318 optimal weight: 6.9990 chunk 333 optimal weight: 3.9990 chunk 351 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32946 Z= 0.187 Angle : 0.539 8.257 44814 Z= 0.275 Chirality : 0.043 0.237 5259 Planarity : 0.004 0.051 5700 Dihedral : 4.255 33.011 5895 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.23 % Allowed : 15.75 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 3954 helix: 1.39 (0.19), residues: 759 sheet: 0.47 (0.16), residues: 1035 loop : -0.65 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 35 HIS 0.003 0.001 HIS C 207 PHE 0.013 0.001 PHE A 133 TYR 0.020 0.001 TYR B1067 ARG 0.009 0.000 ARG L 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 287 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.6919 (ttt90) cc_final: 0.6108 (tpt170) REVERT: H 58 GLU cc_start: 0.7990 (mp0) cc_final: 0.7685 (tt0) REVERT: H 101 ASP cc_start: 0.7995 (t0) cc_final: 0.7747 (t0) REVERT: H 105 GLN cc_start: 0.8360 (pm20) cc_final: 0.8107 (pm20) REVERT: L 27 GLN cc_start: 0.7165 (pp30) cc_final: 0.6580 (pp30) REVERT: L 62 PHE cc_start: 0.7835 (m-80) cc_final: 0.7561 (m-80) REVERT: B 900 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7080 (mtm) REVERT: B 980 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8126 (mt) REVERT: B 1029 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7429 (tpp) REVERT: F 27 GLN cc_start: 0.6944 (pt0) cc_final: 0.6602 (pp30) REVERT: C 389 ASP cc_start: 0.6089 (p0) cc_final: 0.5609 (p0) REVERT: C 740 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6821 (tmm) REVERT: C 902 MET cc_start: 0.8369 (mmt) cc_final: 0.8005 (mmp) REVERT: E 79 TYR cc_start: 0.7499 (m-10) cc_final: 0.7207 (m-10) REVERT: G 27 GLN cc_start: 0.6855 (pt0) cc_final: 0.6354 (pp30) REVERT: G 48 ILE cc_start: 0.7595 (mt) cc_final: 0.7340 (mm) REVERT: G 54 ARG cc_start: 0.8055 (mpt180) cc_final: 0.7696 (mtt90) outliers start: 77 outliers final: 70 residues processed: 341 average time/residue: 0.4733 time to fit residues: 260.8744 Evaluate side-chains 354 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 280 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 0.7980 chunk 373 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 177 optimal weight: 0.0010 chunk 259 optimal weight: 0.9990 chunk 391 optimal weight: 5.9990 chunk 360 optimal weight: 0.9980 chunk 311 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 69 HIS C 207 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32946 Z= 0.243 Angle : 0.562 8.763 44814 Z= 0.287 Chirality : 0.043 0.163 5259 Planarity : 0.004 0.054 5700 Dihedral : 4.317 34.378 5895 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.37 % Allowed : 15.84 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 3954 helix: 1.28 (0.19), residues: 759 sheet: 0.50 (0.16), residues: 1029 loop : -0.68 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 35 HIS 0.003 0.001 HIS E 32 PHE 0.014 0.001 PHE C 347 TYR 0.021 0.001 TYR F 49 ARG 0.009 0.000 ARG L 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 287 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 52 LYS cc_start: 0.8027 (mppt) cc_final: 0.7824 (mppt) REVERT: H 58 GLU cc_start: 0.7992 (mp0) cc_final: 0.7640 (tt0) REVERT: H 101 ASP cc_start: 0.8035 (t0) cc_final: 0.7795 (t0) REVERT: H 105 GLN cc_start: 0.8357 (pm20) cc_final: 0.8113 (pm20) REVERT: L 27 GLN cc_start: 0.7195 (pp30) cc_final: 0.6586 (pp30) REVERT: L 62 PHE cc_start: 0.7931 (m-80) cc_final: 0.7629 (m-80) REVERT: B 900 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7164 (mtm) REVERT: B 980 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8145 (mt) REVERT: B 1029 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7508 (tpp) REVERT: F 27 GLN cc_start: 0.6949 (pt0) cc_final: 0.6617 (pp30) REVERT: F 54 ARG cc_start: 0.7572 (mpt180) cc_final: 0.7016 (mpt180) REVERT: C 389 ASP cc_start: 0.6207 (p0) cc_final: 0.5736 (p0) REVERT: C 740 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6734 (tmm) REVERT: E 79 TYR cc_start: 0.7535 (m-10) cc_final: 0.7243 (m-10) REVERT: G 27 GLN cc_start: 0.6882 (pt0) cc_final: 0.6365 (pp30) REVERT: G 48 ILE cc_start: 0.7583 (mt) cc_final: 0.7317 (mm) REVERT: G 54 ARG cc_start: 0.8071 (mpt180) cc_final: 0.7828 (mtt90) outliers start: 82 outliers final: 71 residues processed: 347 average time/residue: 0.4801 time to fit residues: 267.3916 Evaluate side-chains 354 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 279 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 312 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 320 optimal weight: 0.0070 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 625 HIS ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.129416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.098643 restraints weight = 70191.459| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.79 r_work: 0.3427 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32946 Z= 0.215 Angle : 0.555 8.350 44814 Z= 0.283 Chirality : 0.043 0.161 5259 Planarity : 0.004 0.056 5700 Dihedral : 4.282 33.744 5895 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.35 % Allowed : 16.02 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 3954 helix: 1.31 (0.19), residues: 762 sheet: 0.43 (0.16), residues: 1053 loop : -0.61 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 35 HIS 0.003 0.001 HIS C 207 PHE 0.013 0.001 PHE A 133 TYR 0.020 0.001 TYR B1067 ARG 0.010 0.000 ARG L 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6893.69 seconds wall clock time: 128 minutes 36.17 seconds (7716.17 seconds total)