Starting phenix.real_space_refine on Mon Feb 19 11:38:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byr_30247/02_2024/7byr_30247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byr_30247/02_2024/7byr_30247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byr_30247/02_2024/7byr_30247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byr_30247/02_2024/7byr_30247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byr_30247/02_2024/7byr_30247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7byr_30247/02_2024/7byr_30247.pdb" } resolution = 3.84 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= 0.001 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 110 5.16 5 C 15644 2.51 5 N 4012 2.21 5 O 4796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A PHE 1042": "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 GLU 1072": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24562 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7311 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 46, 'TRANS': 912} Chain breaks: 13 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 7681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7681 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 49, 'TRANS': 948} Chain breaks: 9 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 7327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7327 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 13 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 209 Chain: "H" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 807 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.22, per 1000 atoms: 0.54 Number of scatterers: 24562 At special positions: 0 Unit cell: (136.095, 136.095, 198.34, 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 110 16.00 O 4796 8.00 N 4012 7.00 C 15644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.01 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN A 282 " " NAG A1314 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 282 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B1074 " " NAG B1314 " - " ASN B 343 " " NAG C1301 " - " ASN C1134 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 801 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 616 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 234 " " NAG C1313 " - " ASN C 282 " " NAG C1314 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN C1098 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 165 " Time building additional restraints: 9.88 Conformation dependent library (CDL) restraints added in 4.4 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 48 sheets defined 24.1% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.571A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.017A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.838A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.132A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 4.247A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.546A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.846A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.420A 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 983 removed outlier: 3.637A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.117A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.746A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.961A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.788A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 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 782 removed outlier: 3.576A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.931A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.379A 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 983 removed outlier: 3.795A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.565A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1120 removed outlier: 3.994A pdb=" N THR B1120 " --> pdb=" O THR B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.901A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.623A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.982A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 738 through 744 removed outlier: 3.662A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.611A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.924A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.545A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.541A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.727A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.658A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.260A 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: 5.822A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.683A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.864A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.974A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 327 removed outlier: 7.535A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.116A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.910A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.012A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.571A pdb=" N ILE B 788 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.554A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1121 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 31 Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.031A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.847A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 103 through 104 removed outlier: 3.951A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.544A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.636A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 removed outlier: 4.056A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 3.732A pdb=" N ILE C 788 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.488A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.344A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 5.230A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.881A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.840A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.116A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.838A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.647A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE C 515 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N CYS C 432 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS C 378 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE C 434 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR C 376 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.587A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.898A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.007A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1096 removed outlier: 4.917A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.648A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 46 through 47 Processing sheet with id=AE9, first strand: chain 'H' and resid 46 through 47 Processing sheet with id=AF1, first strand: chain 'H' and resid 68 through 69 Processing sheet with id=AF2, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.841A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2583 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: 10.63 Time building geometry restraints manager: 10.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7809 1.35 - 1.48: 6689 1.48 - 1.61: 10446 1.61 - 1.74: 1 1.74 - 1.88: 137 Bond restraints: 25082 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N MET H 34 " pdb=" CA MET H 34 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.29e-02 6.01e+03 6.17e+00 bond pdb=" N ALA H 33 " pdb=" CA ALA H 33 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.09e-02 8.42e+03 6.07e+00 bond pdb=" N SER H 31 " pdb=" CA SER H 31 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.62e+00 bond pdb=" N TYR H 32 " pdb=" CA TYR H 32 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.36e-02 5.41e+03 5.40e+00 ... (remaining 25077 not shown) Histogram of bond angle deviations from ideal: 97.57 - 104.90: 447 104.90 - 112.24: 12700 112.24 - 119.58: 7946 119.58 - 126.91: 12836 126.91 - 134.25: 244 Bond angle restraints: 34173 Sorted by residual: angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 131.87 -17.47 2.30e+00 1.89e-01 5.77e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 125.96 -11.56 2.30e+00 1.89e-01 2.53e+01 angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 125.01 -10.61 2.30e+00 1.89e-01 2.13e+01 angle pdb=" N ASN B 542 " pdb=" CA ASN B 542 " pdb=" C ASN B 542 " ideal model delta sigma weight residual 110.80 101.18 9.62 2.13e+00 2.20e-01 2.04e+01 angle pdb=" C SER C1030 " pdb=" N GLU C1031 " pdb=" CA GLU C1031 " ideal model delta sigma weight residual 122.65 115.81 6.84 1.60e+00 3.91e-01 1.83e+01 ... (remaining 34168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.02: 14234 24.02 - 48.04: 1021 48.04 - 72.06: 149 72.06 - 96.08: 35 96.08 - 120.10: 7 Dihedral angle restraints: 15446 sinusoidal: 6333 harmonic: 9113 Sorted by residual: dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 3.50 89.50 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 5.64 87.36 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 13.22 79.78 1 1.00e+01 1.00e-02 7.90e+01 ... (remaining 15443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3419 0.073 - 0.145: 619 0.145 - 0.218: 37 0.218 - 0.290: 7 0.290 - 0.363: 4 Chirality restraints: 4086 Sorted by residual: chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 4083 not shown) Planarity restraints: 4383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.039 2.00e-02 2.50e+03 3.70e-02 1.71e+01 pdb=" CG ASN B 616 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " 0.041 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " -0.025 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP B 886 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 105 " -0.023 2.00e-02 2.50e+03 1.84e-02 8.50e+00 pdb=" CG TRP H 105 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP H 105 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP H 105 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 105 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 105 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 105 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 105 " -0.004 2.00e-02 2.50e+03 ... (remaining 4380 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 18 2.20 - 2.88: 10138 2.88 - 3.55: 34047 3.55 - 4.23: 53005 4.23 - 4.90: 91511 Nonbonded interactions: 188719 Sorted by model distance: nonbonded pdb=" O GLN H 3 " pdb=" C SER H 25 " model vdw 1.529 3.270 nonbonded pdb=" N GLN H 3 " pdb=" O SER H 25 " model vdw 1.877 2.520 nonbonded pdb=" O CYS C1032 " pdb=" OG SER C1051 " model vdw 2.004 2.440 nonbonded pdb=" O CYS B1032 " pdb=" OG SER B1051 " model vdw 2.061 2.440 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.083 2.440 ... (remaining 188714 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 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 66 or resid 81 through 95 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 104 or (resid 105 and (name N or name CA or name C or name O \ or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA or n \ ame C or name O or name CB )) or resid 130 through 140 or (resid 157 through 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 1 \ 87 or (resid 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 through 194 or (resid 195 through 198 and (name N or name CA or name C or \ name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 209 or resid 217 through 236 or ( \ resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ or (resid 239 and (name N or name CA or name C or name O or name CB )) or resid \ 240 through 243 or resid 264 through 350 or (resid 351 through 352 and (name N o \ r name CA or name C or name O or name CB )) or resid 353 through 363 or (resid 3 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 365 through \ 368 or (resid 369 and (name N or name CA or name C or name O or name CB )) or r \ esid 370 through 373 or (resid 374 and (name N or name CA or name C or name O or \ name CB )) or resid 375 through 407 or (resid 408 and (name N or name CA or nam \ e C or name O or name CB )) or resid 409 through 441 or (resid 442 and (name N o \ r name CA or name C or name O or name CB )) or resid 443 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 496 or (res \ id 497 through 498 and (name N or name CA or name C or name O or name CB )) or r \ esid 503 through 508 or (resid 509 and (name N or name CA or name C or name O or \ name CB )) or resid 510 through 620 or resid 641 through 1146 or resid 1301 thr \ ough 1312)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 or (resid 239 and (n \ ame N or name CA or name C or name O or name CB )) or resid 240 through 289 or ( \ resid 290 and (name N or name CA or name C or name O or name CB )) or resid 291 \ through 328 or (resid 335 and (name N or name CA or name C or name O or name CB \ )) or resid 336 through 339 or (resid 340 and (name N or name CA or name C or na \ me O or name CB )) or resid 341 through 345 or (resid 346 and (name N or name CA \ or name C or name O or name CB )) or resid 347 through 348 or (resid 349 and (n \ ame N or name CA or name C or name O or name CB )) or resid 350 or (resid 351 th \ rough 352 and (name N or name CA or name C or name O or name CB )) or resid 353 \ through 363 or (resid 364 and (name N or name CA or name C or name O or name CB \ )) or resid 365 through 368 or (resid 369 and (name N or name CA or name C or na \ me O or name CB )) or resid 370 through 373 or (resid 374 and (name N or name CA \ or name C or name O or name CB )) or resid 375 through 397 or (resid 398 and (n \ ame N or name CA or name C or name O or name CB )) or resid 399 through 402 or ( \ resid 403 and (name N or name CA or name C or name O or name CB )) or resid 404 \ or (resid 405 through 408 and (name N or name CA or name C or name O or name CB \ )) or resid 409 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or resid 416 or (resid 417 and (name N or name CA \ or name C or name O or name CB )) or resid 418 through 419 or (resid 420 and (n \ ame N or name CA or name C or name O or name CB )) or resid 421 through 423 or ( \ resid 424 and (name N or name CA or name C or name O or name CB )) or resid 425 \ through 426 or (resid 427 through 428 and (name N or name CA or name C or name O \ or name CB )) or resid 429 through 440 or (resid 441 through 442 and (name N or \ name CA or name C or name O or name CB )) or resid 443 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 453 or (resi \ d 454 and (name N or name CA or name C or name O or name CB )) or resid 491 or ( \ resid 492 through 493 and (name N or name CA or name C or name O or name CB )) o \ r resid 494 through 496 or (resid 497 through 498 and (name N or name CA or name \ C or name O or name CB )) or resid 503 through 508 or (resid 509 and (name N or \ name CA or name C or name O or name CB )) or resid 510 through 515 or (resid 51 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 517 through \ 518 or (resid 519 through 520 and (name N or name CA or name C or name O or name \ CB )) or resid 521 through 527 or (resid 528 through 529 and (name N or name CA \ or name C or name O or name CB )) or resid 530 through 620 or resid 641 through \ 1146 or resid 1301 through 1314)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 66 or resid 81 throug \ h 95 or (resid 99 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 104 or (resid 105 and (name N or name CA or name C o \ r name O or name CB )) or resid 106 through 187 or (resid 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 199 or (resid 200 an \ d (name N or name CA or name C or name O or name CB )) or resid 201 through 209 \ or resid 217 through 243 or resid 264 through 328 or resid 335 through 454 or re \ sid 491 through 1146 or resid 1301 through 1314)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' } 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: 3.490 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: 13.950 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 67.110 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 : 0.006 0.082 25082 Z= 0.407 Angle : 0.918 17.466 34173 Z= 0.498 Chirality : 0.054 0.363 4086 Planarity : 0.005 0.054 4345 Dihedral : 16.343 120.104 9448 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.27 % Allowed : 1.39 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.00 (0.14), residues: 3051 helix: 0.47 (0.21), residues: 629 sheet: -1.01 (0.19), residues: 675 loop : -2.24 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP B 886 HIS 0.011 0.002 HIS C 655 PHE 0.031 0.003 PHE A 168 TYR 0.041 0.003 TYR B1067 ARG 0.014 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 200 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6465 (t80) cc_final: 0.6090 (t80) REVERT: A 170 TYR cc_start: 0.6729 (m-80) cc_final: 0.6454 (m-80) REVERT: A 229 LEU cc_start: 0.7192 (mm) cc_final: 0.6953 (tp) REVERT: A 238 PHE cc_start: 0.6235 (p90) cc_final: 0.5806 (p90) REVERT: A 740 MET cc_start: 0.7051 (tmm) cc_final: 0.6410 (tpp) REVERT: H 50 TRP cc_start: 0.8045 (t60) cc_final: 0.7841 (t60) REVERT: L 24 ARG cc_start: 0.7281 (mtp180) cc_final: 0.6779 (mtm-85) outliers start: 7 outliers final: 2 residues processed: 205 average time/residue: 0.3316 time to fit residues: 113.2866 Evaluate side-chains 169 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 282 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 907 ASN B 394 ASN B 474 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 949 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25082 Z= 0.232 Angle : 0.700 10.734 34173 Z= 0.353 Chirality : 0.047 0.266 4086 Planarity : 0.004 0.050 4345 Dihedral : 9.008 107.337 4263 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.47 % Allowed : 11.96 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.67 (0.15), residues: 3051 helix: 1.11 (0.21), residues: 613 sheet: -0.85 (0.19), residues: 674 loop : -2.13 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 105 HIS 0.009 0.001 HIS C 655 PHE 0.020 0.002 PHE B 342 TYR 0.031 0.002 TYR B 904 ARG 0.005 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8930 (mm) cc_final: 0.8460 (pp) REVERT: A 92 PHE cc_start: 0.6467 (t80) cc_final: 0.6170 (t80) REVERT: A 170 TYR cc_start: 0.6731 (m-80) cc_final: 0.6461 (m-80) REVERT: A 238 PHE cc_start: 0.6086 (p90) cc_final: 0.5833 (p90) REVERT: A 365 TYR cc_start: 0.5015 (t80) cc_final: 0.4802 (t80) REVERT: A 740 MET cc_start: 0.7506 (tmm) cc_final: 0.6781 (tpp) REVERT: B 346 ARG cc_start: 0.7936 (tpp80) cc_final: 0.7716 (tpp80) REVERT: H 6 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.5973 (mt0) REVERT: H 50 TRP cc_start: 0.7963 (t60) cc_final: 0.7632 (t60) REVERT: H 100 GLN cc_start: 0.6137 (mt0) cc_final: 0.5594 (mp10) REVERT: H 104 SER cc_start: 0.9113 (t) cc_final: 0.8817 (p) REVERT: H 118 GLN cc_start: 0.7958 (mp10) cc_final: 0.7536 (pm20) outliers start: 38 outliers final: 23 residues processed: 206 average time/residue: 0.3100 time to fit residues: 108.4938 Evaluate side-chains 188 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 235 optimal weight: 5.9990 chunk 192 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 0.6980 chunk 305 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN A 563 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25082 Z= 0.237 Angle : 0.653 11.249 34173 Z= 0.328 Chirality : 0.046 0.277 4086 Planarity : 0.004 0.049 4345 Dihedral : 8.300 104.611 4261 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.28 % Allowed : 15.40 % Favored : 82.32 % 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: -1.48 (0.15), residues: 3051 helix: 1.28 (0.21), residues: 618 sheet: -0.76 (0.19), residues: 671 loop : -2.00 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 105 HIS 0.007 0.001 HIS B 519 PHE 0.016 0.001 PHE A 377 TYR 0.022 0.001 TYR H 111 ARG 0.003 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 179 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9032 (mm) cc_final: 0.8494 (pp) REVERT: A 92 PHE cc_start: 0.6433 (t80) cc_final: 0.6174 (t80) REVERT: A 740 MET cc_start: 0.7529 (tmm) cc_final: 0.6830 (tpp) REVERT: C 51 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8770 (p) REVERT: H 50 TRP cc_start: 0.7930 (t60) cc_final: 0.7625 (t60) REVERT: H 104 SER cc_start: 0.9185 (t) cc_final: 0.8943 (p) REVERT: H 105 TRP cc_start: 0.8428 (OUTLIER) cc_final: 0.7744 (p-90) outliers start: 59 outliers final: 42 residues processed: 215 average time/residue: 0.3148 time to fit residues: 113.7876 Evaluate side-chains 201 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 157 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 55 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 269 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25082 Z= 0.237 Angle : 0.632 10.098 34173 Z= 0.316 Chirality : 0.046 0.274 4086 Planarity : 0.004 0.051 4345 Dihedral : 7.812 101.447 4261 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.86 % Allowed : 17.37 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 3051 helix: 1.46 (0.21), residues: 612 sheet: -0.72 (0.19), residues: 666 loop : -1.89 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 886 HIS 0.007 0.001 HIS B 519 PHE 0.018 0.001 PHE A 377 TYR 0.019 0.001 TYR A 365 ARG 0.005 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 170 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8987 (mm) cc_final: 0.8376 (pp) REVERT: A 92 PHE cc_start: 0.6457 (t80) cc_final: 0.6126 (t80) REVERT: A 229 LEU cc_start: 0.7034 (mm) cc_final: 0.6780 (tp) REVERT: A 740 MET cc_start: 0.7562 (tmm) cc_final: 0.6903 (tpp) REVERT: B 324 GLU cc_start: 0.7688 (tp30) cc_final: 0.7355 (tp30) REVERT: B 346 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7645 (tpp80) REVERT: B 515 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: B 873 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8433 (m-10) REVERT: C 51 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8804 (p) REVERT: C 1031 GLU cc_start: 0.7963 (pt0) cc_final: 0.7732 (pt0) REVERT: H 50 TRP cc_start: 0.7876 (t60) cc_final: 0.7598 (t60) REVERT: H 104 SER cc_start: 0.9174 (t) cc_final: 0.8921 (p) REVERT: H 105 TRP cc_start: 0.8494 (OUTLIER) cc_final: 0.7921 (p-90) REVERT: H 118 GLN cc_start: 0.8200 (mp10) cc_final: 0.7580 (pm20) REVERT: L 36 TYR cc_start: 0.6254 (m-80) cc_final: 0.5940 (m-80) REVERT: L 49 TYR cc_start: 0.8213 (p90) cc_final: 0.7767 (p90) outliers start: 74 outliers final: 55 residues processed: 221 average time/residue: 0.3141 time to fit residues: 117.8000 Evaluate side-chains 212 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 153 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 55 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 1.9990 chunk 170 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 256 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS L 3 GLN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25082 Z= 0.283 Angle : 0.645 11.608 34173 Z= 0.321 Chirality : 0.046 0.274 4086 Planarity : 0.004 0.054 4345 Dihedral : 7.589 97.282 4261 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.13 % Allowed : 18.91 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 3051 helix: 1.46 (0.21), residues: 604 sheet: -0.71 (0.19), residues: 664 loop : -1.86 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 886 HIS 0.008 0.001 HIS B 519 PHE 0.015 0.001 PHE A 970 TYR 0.031 0.001 TYR C 904 ARG 0.005 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 171 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6552 (t80) cc_final: 0.6182 (t80) REVERT: A 324 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7123 (pp20) REVERT: A 740 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7132 (tpp) REVERT: B 324 GLU cc_start: 0.7649 (tp30) cc_final: 0.7365 (tp30) REVERT: B 409 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.8948 (mt0) REVERT: B 515 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: B 873 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8438 (m-10) REVERT: C 51 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8832 (p) REVERT: C 1029 MET cc_start: 0.9053 (tpp) cc_final: 0.8547 (ttm) REVERT: C 1031 GLU cc_start: 0.7784 (pt0) cc_final: 0.7465 (pt0) REVERT: H 50 TRP cc_start: 0.7904 (t60) cc_final: 0.7664 (t60) REVERT: H 100 GLN cc_start: 0.6645 (mp10) cc_final: 0.6291 (mp10) REVERT: H 104 SER cc_start: 0.9227 (t) cc_final: 0.8977 (p) REVERT: H 105 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.7989 (p-90) REVERT: H 118 GLN cc_start: 0.8131 (mp10) cc_final: 0.7527 (pm20) REVERT: L 36 TYR cc_start: 0.6501 (m-80) cc_final: 0.6000 (m-80) REVERT: L 49 TYR cc_start: 0.8332 (p90) cc_final: 0.7837 (p90) outliers start: 107 outliers final: 81 residues processed: 252 average time/residue: 0.2994 time to fit residues: 129.0693 Evaluate side-chains 244 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 156 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 300 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25082 Z= 0.245 Angle : 0.631 10.994 34173 Z= 0.313 Chirality : 0.046 0.268 4086 Planarity : 0.004 0.052 4345 Dihedral : 7.324 94.448 4261 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.01 % Allowed : 20.15 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 3051 helix: 1.49 (0.21), residues: 616 sheet: -0.69 (0.19), residues: 663 loop : -1.78 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 886 HIS 0.007 0.001 HIS B 519 PHE 0.015 0.001 PHE A 970 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 167 time to evaluate : 2.633 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6502 (t80) cc_final: 0.6108 (t80) REVERT: A 324 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7129 (pp20) REVERT: A 740 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7047 (tpp) REVERT: B 515 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: B 543 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7536 (t80) REVERT: B 873 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8466 (m-10) REVERT: C 51 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8818 (p) REVERT: C 1031 GLU cc_start: 0.7750 (pt0) cc_final: 0.7385 (pt0) REVERT: H 60 TYR cc_start: 0.3315 (m-80) cc_final: 0.2092 (m-80) REVERT: H 62 GLN cc_start: 0.8479 (pp30) cc_final: 0.8274 (pp30) REVERT: H 100 GLN cc_start: 0.6477 (mp10) cc_final: 0.6272 (mp10) REVERT: H 105 TRP cc_start: 0.8620 (OUTLIER) cc_final: 0.8061 (p-90) REVERT: H 118 GLN cc_start: 0.8025 (mp10) cc_final: 0.7535 (pm20) REVERT: L 36 TYR cc_start: 0.6598 (m-80) cc_final: 0.6057 (m-80) outliers start: 104 outliers final: 82 residues processed: 249 average time/residue: 0.2889 time to fit residues: 123.3241 Evaluate side-chains 240 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 151 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 chunk 170 optimal weight: 0.6980 chunk 253 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 299 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25082 Z= 0.230 Angle : 0.626 11.862 34173 Z= 0.310 Chirality : 0.045 0.268 4086 Planarity : 0.004 0.054 4345 Dihedral : 7.089 91.541 4261 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.21 % Allowed : 20.96 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3051 helix: 1.53 (0.21), residues: 617 sheet: -0.63 (0.19), residues: 668 loop : -1.73 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 104 HIS 0.007 0.001 HIS B 519 PHE 0.016 0.001 PHE A 238 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 164 time to evaluate : 2.871 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8945 (mm) cc_final: 0.8326 (pp) REVERT: A 92 PHE cc_start: 0.6459 (t80) cc_final: 0.6053 (t80) REVERT: A 324 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7112 (pp20) REVERT: A 740 MET cc_start: 0.7644 (tmm) cc_final: 0.7050 (tpp) REVERT: A 990 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8591 (tm-30) REVERT: B 515 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: B 543 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7537 (t80) REVERT: B 873 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8542 (m-10) REVERT: C 34 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7119 (mmp80) REVERT: C 51 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8807 (p) REVERT: C 1029 MET cc_start: 0.9065 (tpp) cc_final: 0.8547 (ttm) REVERT: H 60 TYR cc_start: 0.3248 (m-80) cc_final: 0.2156 (m-80) REVERT: H 105 TRP cc_start: 0.8581 (OUTLIER) cc_final: 0.8118 (p-90) REVERT: H 118 GLN cc_start: 0.8055 (mp10) cc_final: 0.7532 (pm20) outliers start: 109 outliers final: 87 residues processed: 252 average time/residue: 0.3162 time to fit residues: 134.6511 Evaluate side-chains 243 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 149 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 204 optimal weight: 0.0370 chunk 148 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 272 optimal weight: 2.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25082 Z= 0.223 Angle : 0.618 9.755 34173 Z= 0.307 Chirality : 0.045 0.309 4086 Planarity : 0.004 0.054 4345 Dihedral : 6.943 88.910 4261 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.01 % Allowed : 21.69 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 3051 helix: 1.56 (0.21), residues: 617 sheet: -0.61 (0.19), residues: 667 loop : -1.71 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 886 HIS 0.006 0.001 HIS B 519 PHE 0.013 0.001 PHE A 238 TYR 0.018 0.001 TYR C1067 ARG 0.006 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 162 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6452 (t80) cc_final: 0.6115 (t80) REVERT: A 324 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7072 (pp20) REVERT: A 739 THR cc_start: 0.7722 (m) cc_final: 0.7453 (m) REVERT: A 740 MET cc_start: 0.7674 (tmm) cc_final: 0.7078 (tpp) REVERT: A 990 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8575 (tm-30) REVERT: B 318 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7762 (p90) REVERT: B 515 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: B 543 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7543 (t80) REVERT: B 873 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8451 (m-10) REVERT: C 34 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7141 (mmp80) REVERT: C 51 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8805 (p) REVERT: H 105 TRP cc_start: 0.8573 (OUTLIER) cc_final: 0.8115 (p-90) REVERT: H 118 GLN cc_start: 0.8024 (mp10) cc_final: 0.7512 (pm20) REVERT: L 46 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7749 (tt) outliers start: 104 outliers final: 85 residues processed: 245 average time/residue: 0.3110 time to fit residues: 130.6714 Evaluate side-chains 246 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 152 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 219 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 252 optimal weight: 0.1980 chunk 264 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25082 Z= 0.212 Angle : 0.610 9.922 34173 Z= 0.302 Chirality : 0.045 0.265 4086 Planarity : 0.004 0.054 4345 Dihedral : 6.762 85.014 4261 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.98 % Allowed : 21.96 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.15), residues: 3051 helix: 1.55 (0.21), residues: 624 sheet: -0.52 (0.19), residues: 656 loop : -1.70 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.007 0.001 HIS B 519 PHE 0.014 0.001 PHE A 238 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 162 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6395 (t80) cc_final: 0.6046 (t80) REVERT: A 324 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7051 (pp20) REVERT: A 740 MET cc_start: 0.7756 (tmm) cc_final: 0.7159 (tpp) REVERT: A 990 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8562 (tm-30) REVERT: B 318 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.7893 (p90) REVERT: B 515 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: B 543 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7538 (t80) REVERT: B 873 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8460 (m-10) REVERT: C 34 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7115 (mmp80) REVERT: C 51 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8795 (p) REVERT: H 105 TRP cc_start: 0.8498 (OUTLIER) cc_final: 0.8011 (p-90) REVERT: H 118 GLN cc_start: 0.8014 (mp10) cc_final: 0.7519 (pm20) outliers start: 103 outliers final: 82 residues processed: 244 average time/residue: 0.3007 time to fit residues: 125.7559 Evaluate side-chains 243 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 153 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 140 optimal weight: 0.3980 chunk 205 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25082 Z= 0.198 Angle : 0.621 10.110 34173 Z= 0.305 Chirality : 0.045 0.267 4086 Planarity : 0.004 0.053 4345 Dihedral : 6.633 81.531 4261 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.74 % Allowed : 22.19 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3051 helix: 1.63 (0.21), residues: 624 sheet: -0.53 (0.19), residues: 676 loop : -1.67 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 886 HIS 0.007 0.001 HIS B 519 PHE 0.014 0.001 PHE A 377 TYR 0.025 0.001 TYR A 365 ARG 0.006 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 160 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6390 (t80) cc_final: 0.6036 (t80) REVERT: A 324 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7033 (pp20) REVERT: A 740 MET cc_start: 0.7960 (tmm) cc_final: 0.7322 (tpp) REVERT: A 990 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8551 (tm-30) REVERT: B 318 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7874 (p90) REVERT: B 515 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: B 543 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7518 (t80) REVERT: B 873 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8457 (m-10) REVERT: C 34 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7128 (mmp80) REVERT: C 51 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8792 (p) REVERT: C 697 MET cc_start: 0.7766 (mtt) cc_final: 0.7523 (mtt) REVERT: H 105 TRP cc_start: 0.8495 (OUTLIER) cc_final: 0.7957 (p-90) REVERT: H 118 GLN cc_start: 0.7980 (mp10) cc_final: 0.7494 (pm20) outliers start: 97 outliers final: 82 residues processed: 238 average time/residue: 0.3033 time to fit residues: 121.8666 Evaluate side-chains 245 residues out of total 2738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 155 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 227 optimal weight: 0.0170 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 0.3980 chunk 103 optimal weight: 10.0000 chunk 253 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 216 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.100476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078330 restraints weight = 69210.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078383 restraints weight = 43513.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078922 restraints weight = 33168.520| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25082 Z= 0.177 Angle : 0.616 10.100 34173 Z= 0.303 Chirality : 0.045 0.264 4086 Planarity : 0.004 0.054 4345 Dihedral : 6.478 77.521 4259 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.55 % Allowed : 22.39 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 3051 helix: 1.76 (0.22), residues: 620 sheet: -0.51 (0.19), residues: 681 loop : -1.63 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 886 HIS 0.007 0.001 HIS B 519 PHE 0.015 0.001 PHE A 238 TYR 0.020 0.001 TYR A 365 ARG 0.004 0.000 ARG B 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4014.56 seconds wall clock time: 75 minutes 7.28 seconds (4507.28 seconds total)