Starting phenix.real_space_refine on Thu Feb 22 08:28:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj3_22892/02_2024/7kj3_22892_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj3_22892/02_2024/7kj3_22892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj3_22892/02_2024/7kj3_22892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj3_22892/02_2024/7kj3_22892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj3_22892/02_2024/7kj3_22892_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kj3_22892/02_2024/7kj3_22892_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 161 5.16 5 C 21421 2.51 5 N 5472 2.21 5 O 6589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ASP 367": "OD1" <-> "OD2" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 198": "OD1" <-> "OD2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E GLU 457": "OE1" <-> "OE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E GLU 549": "OE1" <-> "OE2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E ARG 582": "NH1" <-> "NH2" Residue "E TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33643 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7661 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7665 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Chain: "C" Number of atoms: 7509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7509 Classifications: {'peptide': 961} Link IDs: {'PTRANS': 48, 'TRANS': 912} Chain breaks: 10 Chain: "D" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "F" 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: "G" 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: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: "K" 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: "L" 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: "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: "P" 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: "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: "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: "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: "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: "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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 17.37, per 1000 atoms: 0.52 Number of scatterers: 33643 At special positions: 0 Unit cell: (134.475, 167.475, 234.3, 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 161 16.00 O 6589 8.00 N 5472 7.00 C 21421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.45 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.54 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.26 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.49 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.25 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.67 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.99 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.05 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=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.84 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.83 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.49 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=2.88 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.32 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.22 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=1.99 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.01 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 Atom "HETATM33403 O5 NAG B1310 .*. O " rejected from bonding due to valence issues. Atom "HETATM33165 O5 NAG A1306 .*. O " rejected from bonding due to valence issues. Atom "HETATM33277 O5 NAG B1301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " 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 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 717 " " NAG A1312 " - " ASN A1074 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1074 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 122 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 343 " " NAG B1313 " - " ASN B 603 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C 165 " " NAG D 701 " - " ASN D 322 " " NAG E 701 " - " ASN E 322 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN D 53 " " NAG Q 1 " - " ASN D 90 " " NAG R 1 " - " ASN D 103 " " NAG S 1 " - " ASN D 432 " " NAG T 1 " - " ASN D 546 " " NAG U 1 " - " ASN E 53 " " NAG V 1 " - " ASN E 90 " " NAG W 1 " - " ASN E 103 " " NAG X 1 " - " ASN E 432 " " NAG Y 1 " - " ASN E 546 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.54 Conformation dependent library (CDL) restraints added in 5.8 seconds 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7730 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 49 sheets defined 40.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.248A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.740A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.727A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.555A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.583A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.850A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.221A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.168A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.562A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.832A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.732A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.153A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.683A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.200A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.593A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.602A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.757A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.848A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.568A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.654A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.596A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.819A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.204A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.075A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.549A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.598A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.576A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.520A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.516A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.708A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.431A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.154A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.635A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.070A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.076A 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 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.676A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.948A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.736A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.160A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.752A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.537A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.649A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.765A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.507A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.062A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.190A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 22 through 52 removed outlier: 4.137A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.629A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.622A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.541A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.648A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 removed outlier: 3.641A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.934A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.633A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.618A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.059A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.544A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 386 removed outlier: 3.602A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.583A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.589A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.010A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 removed outlier: 3.819A pdb=" N GLU D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 465 " --> pdb=" O TRP D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.703A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.346A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.739A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 4.176A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 removed outlier: 3.521A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Proline residue: D 590 - end of helix removed outlier: 4.278A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 53 removed outlier: 4.384A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 4.359A pdb=" N LEU E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.541A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 130 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.613A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 Processing helix chain 'E' and resid 172 through 194 Proline residue: E 178 - end of helix removed outlier: 4.105A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 252 removed outlier: 3.873A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.187A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.980A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.775A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 414 removed outlier: 4.634A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.617A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 465 removed outlier: 4.231A pdb=" N GLU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.291A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 528 " --> pdb=" O GLN E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 548 through 559 removed outlier: 4.088A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 4.390A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 599 Proline residue: E 590 - end of helix removed outlier: 3.714A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.627A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.855A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.646A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.616A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.045A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.671A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (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 654 through 655 removed outlier: 6.069A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.672A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.313A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.255A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.840A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.795A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 7.271A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 7.271A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.692A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.477A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.980A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.864A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.403A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.472A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.874A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.938A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 334 through 335 removed outlier: 6.524A pdb=" N ASN C 334 " --> pdb=" O VAL C 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.746A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.182A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AE9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.108A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AF2, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF3, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.106A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'E' and resid 347 through 350 1492 hydrogen bonds defined for protein. 4158 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: 15.38 Time building geometry restraints manager: 15.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7041 1.33 - 1.45: 8181 1.45 - 1.58: 18932 1.58 - 1.70: 38 1.70 - 1.82: 227 Bond restraints: 34419 Sorted by residual: bond pdb=" C1 NAG B1311 " pdb=" C2 NAG B1311 " ideal model delta sigma weight residual 1.532 1.633 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" CA ASN B 282 " pdb=" CB ASN B 282 " ideal model delta sigma weight residual 1.527 1.584 -0.058 1.15e-02 7.56e+03 2.52e+01 bond pdb=" N CYS A 488 " pdb=" CA CYS A 488 " ideal model delta sigma weight residual 1.457 1.511 -0.054 1.24e-02 6.50e+03 1.93e+01 bond pdb=" C5 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.413 1.493 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C5 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 34414 not shown) Histogram of bond angle deviations from ideal: 96.05 - 103.95: 401 103.95 - 111.86: 13775 111.86 - 119.76: 15524 119.76 - 127.67: 16873 127.67 - 135.57: 223 Bond angle restraints: 46796 Sorted by residual: angle pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " pdb=" CG PHE B 377 " ideal model delta sigma weight residual 113.80 121.24 -7.44 1.00e+00 1.00e+00 5.53e+01 angle pdb=" C ARG C 403 " pdb=" N GLY C 404 " pdb=" CA GLY C 404 " ideal model delta sigma weight residual 119.98 127.94 -7.96 1.11e+00 8.12e-01 5.15e+01 angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 120.95 -7.15 1.00e+00 1.00e+00 5.11e+01 angle pdb=" N ASN B 331 " pdb=" CA ASN B 331 " pdb=" C ASN B 331 " ideal model delta sigma weight residual 110.19 118.78 -8.59 1.24e+00 6.50e-01 4.80e+01 angle pdb=" N CYS C 361 " pdb=" CA CYS C 361 " pdb=" C CYS C 361 " ideal model delta sigma weight residual 108.38 117.24 -8.86 1.35e+00 5.49e-01 4.30e+01 ... (remaining 46791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 19754 18.09 - 36.19: 1318 36.19 - 54.28: 281 54.28 - 72.37: 101 72.37 - 90.47: 40 Dihedral angle restraints: 21494 sinusoidal: 9507 harmonic: 11987 Sorted by residual: dihedral pdb=" CB CYS E 344 " pdb=" SG CYS E 344 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual -86.00 -173.89 87.89 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -5.20 -80.80 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 13.44 79.56 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 21491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.867: 5414 0.867 - 1.735: 14 1.735 - 2.602: 6 2.602 - 3.470: 1 3.470 - 4.337: 1 Chirality restraints: 5436 Sorted by residual: chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 1.94 -4.34 2.00e-01 2.50e+01 4.70e+02 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 0.80 -3.20 2.00e-01 2.50e+01 2.56e+02 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.02 -2.38 2.00e-01 2.50e+01 1.42e+02 ... (remaining 5433 not shown) Planarity restraints: 6000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG R 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG W 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 546 " -0.189 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" CG ASN E 546 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN E 546 " -0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN E 546 " 0.530 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.371 2.00e-02 2.50e+03 ... (remaining 5997 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 7 2.13 - 2.82: 7044 2.82 - 3.51: 46106 3.51 - 4.21: 80645 4.21 - 4.90: 138147 Nonbonded interactions: 271949 Sorted by model distance: nonbonded pdb=" ND2 ASN C 125 " pdb=" C8 NAG C1302 " model vdw 1.436 3.540 nonbonded pdb=" NH2 ARG A1107 " pdb=" CE1 TYR B 904 " model vdw 1.888 3.420 nonbonded pdb=" O GLY A 485 " pdb=" OH TYR A 489 " model vdw 1.934 2.440 nonbonded pdb=" OH TYR B 380 " pdb=" O ILE B 410 " model vdw 1.979 2.440 nonbonded pdb=" OD1 ASN C 282 " pdb=" C1 NAG C1304 " model vdw 2.067 2.776 ... (remaining 271944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 140 or resid 165 through 263 or resid 265 throu \ gh 444 or resid 448 through 454 or resid 462 through 470 or resid 491 through 67 \ 6 or resid 690 through 827 or resid 856 through 1147 or resid 1301 through 1312) \ ) selection = (chain 'B' and (resid 27 through 140 or resid 165 through 263 or resid 265 throu \ gh 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 444 or resid 448 through 454 or resid 462 through 470 or resi \ d 491 through 676 or resid 690 through 827 or resid 856 through 1147 or resid 13 \ 01 through 1312)) selection = (chain 'C' and (resid 27 through 140 or resid 165 through 196 or resid 200 throu \ gh 211 or resid 215 through 308 or (resid 309 and (name N or name CA or name C o \ r name O or name CB )) or resid 310 through 515 or resid 522 through 1147 or res \ id 1301 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.930 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: 0.030 Extract box with map and model: 24.830 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 93.640 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 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 : 0.014 0.101 34419 Z= 0.878 Angle : 1.768 12.614 46796 Z= 1.184 Chirality : 0.157 4.337 5436 Planarity : 0.014 0.305 5943 Dihedral : 13.634 90.465 13632 Min Nonbonded Distance : 1.436 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.46 % Favored : 92.84 % Rotamer: Outliers : 1.58 % Allowed : 4.04 % Favored : 94.38 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.12), residues: 4039 helix: -2.04 (0.11), residues: 1366 sheet: 0.22 (0.21), residues: 503 loop : -1.50 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.181 0.027 TRP E 48 HIS 0.012 0.004 HIS D 374 PHE 0.095 0.014 PHE B 429 TYR 0.117 0.020 TYR B 453 ARG 0.017 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 768 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6321 (t80) cc_final: 0.6038 (t80) REVERT: A 584 ILE cc_start: 0.8602 (mm) cc_final: 0.8369 (mt) REVERT: A 881 THR cc_start: 0.8499 (m) cc_final: 0.8243 (m) REVERT: A 973 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8676 (tp) REVERT: B 333 THR cc_start: 0.5776 (OUTLIER) cc_final: 0.5553 (m) REVERT: B 973 ILE cc_start: 0.6991 (pp) cc_final: 0.6782 (tt) REVERT: C 875 SER cc_start: 0.9080 (t) cc_final: 0.8848 (m) REVERT: C 965 GLN cc_start: 0.8027 (mm110) cc_final: 0.7815 (mm-40) REVERT: C 984 LEU cc_start: 0.6633 (mt) cc_final: 0.6250 (mp) REVERT: C 1135 ASN cc_start: 0.7850 (t0) cc_final: 0.7583 (t0) REVERT: D 249 MET cc_start: 0.2927 (mtp) cc_final: 0.2707 (ptp) REVERT: D 376 MET cc_start: 0.5006 (ttm) cc_final: 0.4651 (ttm) REVERT: D 549 GLU cc_start: 0.7057 (tp30) cc_final: 0.6167 (mp0) REVERT: D 585 LEU cc_start: 0.3498 (mt) cc_final: 0.3011 (mt) REVERT: E 210 ASN cc_start: 0.4760 (OUTLIER) cc_final: 0.2578 (p0) REVERT: E 221 GLN cc_start: 0.3606 (tt0) cc_final: 0.2667 (mm-40) REVERT: E 297 MET cc_start: 0.0483 (mtp) cc_final: 0.0192 (ttm) REVERT: E 369 PHE cc_start: 0.1988 (t80) cc_final: 0.1732 (t80) REVERT: E 579 MET cc_start: 0.4490 (ptt) cc_final: 0.3001 (ttp) outliers start: 57 outliers final: 12 residues processed: 812 average time/residue: 0.5262 time to fit residues: 675.1632 Evaluate side-chains 384 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 369 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 371 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 195 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 372 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 164 ASN A 207 HIS A 218 GLN A 564 GLN A 762 GLN A1048 HIS B 125 ASN B 211 ASN B 450 ASN B 493 GLN B 613 GLN B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 965 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 762 GLN C 787 GLN C 804 GLN C 960 ASN C1048 HIS D 58 ASN D 81 GLN D 175 GLN D 330 ASN D 442 GLN D 505 HIS ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN D 599 ASN E 63 ASN E 117 ASN ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34419 Z= 0.263 Angle : 0.741 13.165 46796 Z= 0.386 Chirality : 0.052 0.627 5436 Planarity : 0.004 0.052 5943 Dihedral : 7.733 59.532 6090 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 2.38 % Allowed : 10.30 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.12), residues: 4039 helix: -0.26 (0.13), residues: 1389 sheet: 0.15 (0.18), residues: 630 loop : -1.27 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B1102 HIS 0.012 0.002 HIS A 49 PHE 0.028 0.002 PHE C 559 TYR 0.023 0.002 TYR A1138 ARG 0.005 0.001 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 429 time to evaluate : 4.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 THR cc_start: 0.5537 (OUTLIER) cc_final: 0.5245 (m) REVERT: B 365 TYR cc_start: 0.4202 (m-80) cc_final: 0.3995 (m-80) REVERT: C 752 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8013 (mt) REVERT: C 754 LEU cc_start: 0.8248 (mt) cc_final: 0.7992 (mm) REVERT: D 322 ASN cc_start: 0.4183 (p0) cc_final: 0.3772 (p0) REVERT: D 360 MET cc_start: 0.3956 (ptp) cc_final: 0.3725 (ptp) REVERT: D 578 ASN cc_start: 0.2067 (OUTLIER) cc_final: 0.1422 (t0) REVERT: D 585 LEU cc_start: 0.3028 (mt) cc_final: 0.2514 (mt) REVERT: D 609 ASP cc_start: 0.4784 (OUTLIER) cc_final: 0.3970 (t0) REVERT: E 221 GLN cc_start: 0.3630 (tt0) cc_final: 0.3203 (mm-40) REVERT: E 297 MET cc_start: 0.0579 (mtp) cc_final: 0.0263 (ttm) REVERT: E 338 ASN cc_start: 0.3175 (t0) cc_final: 0.2455 (t0) REVERT: E 474 MET cc_start: 0.2553 (tpp) cc_final: -0.0347 (ttt) REVERT: E 579 MET cc_start: 0.4556 (ptt) cc_final: 0.2966 (ttp) outliers start: 86 outliers final: 47 residues processed: 489 average time/residue: 0.4830 time to fit residues: 379.3999 Evaluate side-chains 367 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 316 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 554 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 206 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 309 optimal weight: 20.0000 chunk 253 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 372 optimal weight: 9.9990 chunk 402 optimal weight: 0.1980 chunk 332 optimal weight: 30.0000 chunk 369 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 299 optimal weight: 7.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 188 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 675 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS E 175 GLN E 508 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34419 Z= 0.289 Angle : 0.679 11.219 46796 Z= 0.351 Chirality : 0.048 0.520 5436 Planarity : 0.004 0.053 5943 Dihedral : 7.627 105.197 6075 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 2.82 % Allowed : 12.32 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.03 % 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: -0.76 (0.12), residues: 4039 helix: 0.29 (0.14), residues: 1385 sheet: 0.04 (0.18), residues: 632 loop : -1.24 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 353 HIS 0.013 0.001 HIS A 49 PHE 0.024 0.002 PHE B 58 TYR 0.026 0.002 TYR C1138 ARG 0.009 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 353 time to evaluate : 3.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6572 (t-90) cc_final: 0.6296 (p90) REVERT: C 436 TRP cc_start: 0.5589 (p90) cc_final: 0.5369 (p90) REVERT: C 732 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8740 (p) REVERT: D 34 HIS cc_start: 0.6946 (m-70) cc_final: 0.6536 (m170) REVERT: D 111 ASP cc_start: 0.6447 (t0) cc_final: 0.6045 (t0) REVERT: D 115 ARG cc_start: 0.6317 (ptm-80) cc_final: 0.5882 (ttp-110) REVERT: D 322 ASN cc_start: 0.4034 (p0) cc_final: 0.3700 (p0) REVERT: D 585 LEU cc_start: 0.2830 (mt) cc_final: 0.2180 (mt) REVERT: D 609 ASP cc_start: 0.4924 (OUTLIER) cc_final: 0.4264 (t0) REVERT: E 221 GLN cc_start: 0.3330 (tt0) cc_final: 0.3066 (mm-40) REVERT: E 297 MET cc_start: 0.0772 (mtp) cc_final: 0.0390 (ttm) REVERT: E 338 ASN cc_start: 0.2856 (t0) cc_final: 0.2155 (t0) REVERT: E 579 MET cc_start: 0.4462 (ptt) cc_final: 0.3050 (ttp) REVERT: E 603 PHE cc_start: 0.0510 (t80) cc_final: 0.0259 (t80) outliers start: 102 outliers final: 69 residues processed: 426 average time/residue: 0.4463 time to fit residues: 312.3705 Evaluate side-chains 374 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 303 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 368 optimal weight: 9.9990 chunk 280 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 374 optimal weight: 8.9990 chunk 396 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 354 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 935 GLN D 76 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN D 572 ASN E 540 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 34419 Z= 0.215 Angle : 0.616 11.235 46796 Z= 0.316 Chirality : 0.046 0.536 5436 Planarity : 0.004 0.051 5943 Dihedral : 7.238 108.824 6072 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 2.71 % Allowed : 13.71 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.13), residues: 4039 helix: 0.62 (0.14), residues: 1397 sheet: -0.04 (0.18), residues: 631 loop : -1.10 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 353 HIS 0.005 0.001 HIS A 49 PHE 0.024 0.002 PHE B 347 TYR 0.031 0.002 TYR C1110 ARG 0.010 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 354 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8235 (mm) REVERT: B 474 GLN cc_start: 0.5299 (OUTLIER) cc_final: 0.4144 (pp30) REVERT: B 973 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6682 (tt) REVERT: C 1027 THR cc_start: 0.9618 (m) cc_final: 0.9292 (p) REVERT: D 111 ASP cc_start: 0.6504 (t0) cc_final: 0.6075 (t0) REVERT: D 115 ARG cc_start: 0.6209 (ptm-80) cc_final: 0.5824 (ttp-110) REVERT: D 360 MET cc_start: 0.5238 (tmm) cc_final: 0.4437 (ptp) REVERT: D 455 MET cc_start: 0.4577 (ttt) cc_final: 0.3832 (tpt) REVERT: D 609 ASP cc_start: 0.4987 (OUTLIER) cc_final: 0.4574 (t0) REVERT: E 297 MET cc_start: 0.0739 (mtp) cc_final: 0.0419 (ttm) REVERT: E 338 ASN cc_start: 0.2985 (t0) cc_final: 0.1897 (t0) REVERT: E 574 VAL cc_start: 0.1394 (OUTLIER) cc_final: 0.0950 (p) REVERT: E 579 MET cc_start: 0.4422 (ptt) cc_final: 0.2924 (ttp) outliers start: 98 outliers final: 62 residues processed: 425 average time/residue: 0.4625 time to fit residues: 324.2464 Evaluate side-chains 365 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 298 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 330 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 295 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 273 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 355 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34419 Z= 0.330 Angle : 0.679 11.552 46796 Z= 0.345 Chirality : 0.050 1.198 5436 Planarity : 0.004 0.050 5943 Dihedral : 7.525 109.657 6072 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 4.13 % Allowed : 13.27 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.58 (0.13), residues: 4039 helix: 0.55 (0.14), residues: 1399 sheet: -0.11 (0.19), residues: 632 loop : -1.13 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 353 HIS 0.007 0.001 HIS C 207 PHE 0.024 0.002 PHE E 314 TYR 0.025 0.002 TYR C1110 ARG 0.005 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 315 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8322 (mm) REVERT: A 1050 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7452 (ptm) REVERT: B 425 LEU cc_start: 0.4669 (OUTLIER) cc_final: 0.4026 (mp) REVERT: B 474 GLN cc_start: 0.5207 (OUTLIER) cc_final: 0.4198 (pp30) REVERT: B 854 LYS cc_start: 0.5450 (tttt) cc_final: 0.5183 (mmtt) REVERT: B 973 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6698 (tt) REVERT: B 1067 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8821 (t80) REVERT: C 1027 THR cc_start: 0.9618 (m) cc_final: 0.9287 (p) REVERT: D 360 MET cc_start: 0.5173 (tmm) cc_final: 0.4964 (tpt) REVERT: D 578 ASN cc_start: 0.1777 (OUTLIER) cc_final: 0.1219 (t0) REVERT: D 585 LEU cc_start: 0.2713 (OUTLIER) cc_final: 0.2260 (tt) REVERT: E 297 MET cc_start: 0.0483 (mtp) cc_final: 0.0145 (ttm) REVERT: E 338 ASN cc_start: 0.3404 (t0) cc_final: 0.2280 (t0) REVERT: E 574 VAL cc_start: 0.1123 (OUTLIER) cc_final: 0.0677 (p) outliers start: 149 outliers final: 110 residues processed: 430 average time/residue: 0.4429 time to fit residues: 314.6421 Evaluate side-chains 406 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 287 time to evaluate : 4.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 586 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 232 optimal weight: 0.0170 chunk 97 optimal weight: 4.9990 chunk 396 optimal weight: 0.9980 chunk 329 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 overall best weight: 1.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34419 Z= 0.212 Angle : 0.601 13.380 46796 Z= 0.306 Chirality : 0.045 0.465 5436 Planarity : 0.004 0.048 5943 Dihedral : 7.105 112.808 6072 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.06 % Favored : 95.87 % Rotamer: Outliers : 2.96 % Allowed : 14.95 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 4039 helix: 0.79 (0.14), residues: 1391 sheet: -0.15 (0.18), residues: 636 loop : -1.04 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 275 HIS 0.005 0.001 HIS D 241 PHE 0.016 0.001 PHE E 314 TYR 0.020 0.001 TYR B1067 ARG 0.006 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 324 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8203 (mm) REVERT: B 474 GLN cc_start: 0.4968 (OUTLIER) cc_final: 0.4026 (pp30) REVERT: B 854 LYS cc_start: 0.5356 (tttt) cc_final: 0.5070 (mmtt) REVERT: B 1067 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8711 (t80) REVERT: C 221 SER cc_start: 0.8498 (t) cc_final: 0.8198 (p) REVERT: C 436 TRP cc_start: 0.5625 (p90) cc_final: 0.4831 (p90) REVERT: C 732 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8704 (p) REVERT: C 1027 THR cc_start: 0.9619 (m) cc_final: 0.9293 (p) REVERT: C 1138 TYR cc_start: 0.7307 (t80) cc_final: 0.7069 (t80) REVERT: D 297 MET cc_start: 0.1077 (mpp) cc_final: 0.0839 (mpp) REVERT: D 419 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6225 (pttp) REVERT: D 455 MET cc_start: 0.4727 (ttt) cc_final: 0.3614 (tpt) REVERT: D 609 ASP cc_start: 0.4868 (OUTLIER) cc_final: 0.4420 (t0) REVERT: E 297 MET cc_start: 0.0557 (mtp) cc_final: 0.0232 (ttm) REVERT: E 338 ASN cc_start: 0.3428 (t0) cc_final: 0.2309 (t0) REVERT: E 546 ASN cc_start: 0.1863 (OUTLIER) cc_final: 0.1619 (m-40) REVERT: E 574 VAL cc_start: 0.1649 (OUTLIER) cc_final: 0.1121 (p) REVERT: E 579 MET cc_start: 0.1939 (ptm) cc_final: 0.1527 (ttp) outliers start: 107 outliers final: 82 residues processed: 405 average time/residue: 0.4330 time to fit residues: 291.4577 Evaluate side-chains 381 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 291 time to evaluate : 3.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 586 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 382 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 289 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 395 optimal weight: 20.0000 chunk 247 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A1135 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34419 Z= 0.275 Angle : 0.625 10.842 46796 Z= 0.318 Chirality : 0.046 0.468 5436 Planarity : 0.004 0.048 5943 Dihedral : 7.223 112.171 6071 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 3.60 % Allowed : 15.09 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 4039 helix: 0.75 (0.14), residues: 1390 sheet: -0.18 (0.18), residues: 638 loop : -1.09 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.004 0.001 HIS C 207 PHE 0.023 0.002 PHE A 192 TYR 0.030 0.002 TYR C1110 ARG 0.007 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 305 time to evaluate : 4.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8353 (mm) cc_final: 0.8153 (mt) REVERT: A 822 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8275 (mm) REVERT: A 1050 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7784 (ptp) REVERT: B 474 GLN cc_start: 0.5024 (OUTLIER) cc_final: 0.4073 (pp30) REVERT: B 492 LEU cc_start: 0.3778 (OUTLIER) cc_final: 0.3335 (tp) REVERT: B 854 LYS cc_start: 0.5411 (tttt) cc_final: 0.5051 (mmtt) REVERT: B 1067 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8746 (t80) REVERT: C 221 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8244 (p) REVERT: C 436 TRP cc_start: 0.5709 (p90) cc_final: 0.4820 (p90) REVERT: C 732 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8722 (p) REVERT: C 1027 THR cc_start: 0.9630 (m) cc_final: 0.9295 (p) REVERT: D 297 MET cc_start: 0.1247 (mpp) cc_final: 0.0717 (mpp) REVERT: D 360 MET cc_start: 0.5365 (OUTLIER) cc_final: 0.4956 (tpt) REVERT: D 455 MET cc_start: 0.4873 (ttt) cc_final: 0.3772 (tpt) REVERT: D 480 MET cc_start: 0.5476 (mtt) cc_final: 0.4727 (mtt) REVERT: D 609 ASP cc_start: 0.4878 (OUTLIER) cc_final: 0.4388 (t0) REVERT: E 297 MET cc_start: 0.0653 (mtp) cc_final: 0.0272 (ttm) REVERT: E 338 ASN cc_start: 0.3489 (t0) cc_final: 0.2444 (t0) REVERT: E 546 ASN cc_start: 0.1483 (OUTLIER) cc_final: 0.1246 (m-40) REVERT: E 574 VAL cc_start: 0.1624 (OUTLIER) cc_final: 0.1107 (p) REVERT: E 579 MET cc_start: 0.2092 (ptm) cc_final: 0.1619 (ttp) outliers start: 130 outliers final: 100 residues processed: 405 average time/residue: 0.4304 time to fit residues: 292.7522 Evaluate side-chains 399 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 288 time to evaluate : 4.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain D residue 609 ASP Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 244 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 251 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 chunk 36 optimal weight: 0.0060 chunk 310 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34419 Z= 0.169 Angle : 0.582 12.397 46796 Z= 0.295 Chirality : 0.045 0.417 5436 Planarity : 0.004 0.062 5943 Dihedral : 6.816 114.620 6071 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.06 % Rotamer: Outliers : 2.63 % Allowed : 16.23 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.26 (0.13), residues: 4039 helix: 0.98 (0.14), residues: 1389 sheet: -0.04 (0.19), residues: 622 loop : -1.02 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 436 HIS 0.004 0.001 HIS C 207 PHE 0.020 0.001 PHE A 192 TYR 0.038 0.001 TYR C 904 ARG 0.009 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 316 time to evaluate : 3.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8171 (mm) REVERT: B 425 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.4041 (mp) REVERT: B 474 GLN cc_start: 0.5043 (OUTLIER) cc_final: 0.4081 (pp30) REVERT: B 492 LEU cc_start: 0.3715 (OUTLIER) cc_final: 0.3286 (tp) REVERT: B 854 LYS cc_start: 0.5119 (tttt) cc_final: 0.4823 (mmtt) REVERT: C 221 SER cc_start: 0.8478 (t) cc_final: 0.8232 (p) REVERT: C 436 TRP cc_start: 0.5570 (p90) cc_final: 0.4859 (p90) REVERT: C 732 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8680 (p) REVERT: C 1027 THR cc_start: 0.9610 (m) cc_final: 0.9285 (p) REVERT: D 419 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6330 (pttp) REVERT: D 455 MET cc_start: 0.4858 (ttt) cc_final: 0.4412 (ttt) REVERT: E 297 MET cc_start: 0.0618 (mtp) cc_final: 0.0244 (ttm) REVERT: E 338 ASN cc_start: 0.3310 (t0) cc_final: 0.2172 (m-40) REVERT: E 546 ASN cc_start: 0.1472 (OUTLIER) cc_final: 0.1252 (m-40) REVERT: E 579 MET cc_start: 0.1987 (ptm) cc_final: 0.1601 (ttp) outliers start: 95 outliers final: 72 residues processed: 390 average time/residue: 0.4335 time to fit residues: 282.1805 Evaluate side-chains 358 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 279 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain E residue 586 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 359 optimal weight: 7.9990 chunk 378 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 chunk 368 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 289 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 332 optimal weight: 8.9990 chunk 348 optimal weight: 1.9990 chunk 366 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C1113 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 HIS D 572 ASN ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 34419 Z= 0.360 Angle : 0.683 12.812 46796 Z= 0.347 Chirality : 0.048 0.460 5436 Planarity : 0.004 0.054 5943 Dihedral : 7.233 112.274 6070 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 3.16 % Allowed : 16.31 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 4039 helix: 0.66 (0.14), residues: 1405 sheet: -0.23 (0.19), residues: 625 loop : -1.13 (0.14), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 610 HIS 0.009 0.001 HIS E 378 PHE 0.033 0.002 PHE C 970 TYR 0.036 0.002 TYR C 904 ARG 0.007 0.001 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 280 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8348 (mm) REVERT: A 973 ILE cc_start: 0.9011 (pt) cc_final: 0.8754 (mt) REVERT: B 131 CYS cc_start: 0.5599 (OUTLIER) cc_final: 0.4715 (m) REVERT: B 425 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.3918 (mp) REVERT: B 854 LYS cc_start: 0.5328 (tttt) cc_final: 0.5038 (mmtt) REVERT: B 1067 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8772 (t80) REVERT: C 221 SER cc_start: 0.8623 (t) cc_final: 0.8341 (p) REVERT: D 34 HIS cc_start: 0.6974 (m170) cc_final: 0.6767 (m170) REVERT: D 297 MET cc_start: 0.0935 (mpp) cc_final: 0.0564 (mpp) REVERT: D 419 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6296 (pttp) REVERT: D 455 MET cc_start: 0.4832 (ttt) cc_final: 0.4472 (ttt) REVERT: E 270 MET cc_start: 0.2019 (mmm) cc_final: 0.1552 (mmm) REVERT: E 297 MET cc_start: 0.0440 (mtp) cc_final: 0.0081 (ttm) REVERT: E 338 ASN cc_start: 0.3292 (t0) cc_final: 0.2259 (m-40) outliers start: 114 outliers final: 91 residues processed: 368 average time/residue: 0.4341 time to fit residues: 267.8510 Evaluate side-chains 369 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 273 time to evaluate : 3.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 586 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 241 optimal weight: 2.9990 chunk 389 optimal weight: 8.9990 chunk 237 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 270 optimal weight: 1.9990 chunk 408 optimal weight: 0.4980 chunk 375 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 251 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 HIS ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34419 Z= 0.172 Angle : 0.592 12.399 46796 Z= 0.301 Chirality : 0.045 0.399 5436 Planarity : 0.004 0.047 5943 Dihedral : 6.709 114.992 6068 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.94 % Rotamer: Outliers : 2.30 % Allowed : 17.31 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 4039 helix: 0.92 (0.14), residues: 1403 sheet: -0.11 (0.19), residues: 635 loop : -1.06 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 436 HIS 0.011 0.001 HIS E 378 PHE 0.021 0.001 PHE B 565 TYR 0.028 0.001 TYR A 904 ARG 0.007 0.000 ARG D 582 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 296 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8193 (mm) REVERT: B 131 CYS cc_start: 0.5465 (OUTLIER) cc_final: 0.4549 (m) REVERT: B 492 LEU cc_start: 0.4060 (OUTLIER) cc_final: 0.3675 (tp) REVERT: B 854 LYS cc_start: 0.4870 (tttt) cc_final: 0.4561 (mmtt) REVERT: C 221 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8298 (p) REVERT: C 732 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8690 (p) REVERT: C 1027 THR cc_start: 0.9606 (m) cc_final: 0.9265 (p) REVERT: D 297 MET cc_start: 0.1447 (mpp) cc_final: 0.1112 (mpp) REVERT: D 419 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6394 (pttp) REVERT: D 455 MET cc_start: 0.4782 (ttt) cc_final: 0.4403 (ttt) REVERT: E 270 MET cc_start: 0.2178 (mmm) cc_final: 0.1820 (mtp) REVERT: E 297 MET cc_start: 0.0607 (mtp) cc_final: 0.0198 (ttm) REVERT: E 338 ASN cc_start: 0.3418 (t0) cc_final: 0.2478 (m-40) outliers start: 83 outliers final: 69 residues processed: 360 average time/residue: 0.4397 time to fit residues: 264.8749 Evaluate side-chains 354 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 279 time to evaluate : 3.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 554 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 258 optimal weight: 5.9990 chunk 346 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 325 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 chunk 334 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 HIS ** D 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.162981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.142591 restraints weight = 78085.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.140226 restraints weight = 136747.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.137604 restraints weight = 108624.611| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 34419 Z= 0.226 Angle : 0.611 11.883 46796 Z= 0.309 Chirality : 0.045 0.401 5436 Planarity : 0.004 0.047 5943 Dihedral : 6.728 113.417 6068 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.57 % Rotamer: Outliers : 2.52 % Allowed : 17.17 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.33 (0.13), residues: 4039 helix: 0.90 (0.14), residues: 1414 sheet: -0.19 (0.19), residues: 629 loop : -1.03 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 69 HIS 0.011 0.001 HIS E 378 PHE 0.030 0.001 PHE C 970 TYR 0.029 0.001 TYR A 904 ARG 0.008 0.000 ARG B 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7403.22 seconds wall clock time: 136 minutes 7.29 seconds (8167.29 seconds total)