Starting phenix.real_space_refine on Mon Mar 25 01:52:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z97_11119/03_2024/6z97_11119_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z97_11119/03_2024/6z97_11119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z97_11119/03_2024/6z97_11119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z97_11119/03_2024/6z97_11119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z97_11119/03_2024/6z97_11119_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z97_11119/03_2024/6z97_11119_trim.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 104 5.16 5 C 14973 2.51 5 N 3836 2.21 5 O 4554 1.98 5 H 21895 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C ARG 1019": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1127": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45362 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 14982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 14982 Classifications: {'peptide': 995} Link IDs: {'PTRANS': 49, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 14831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 14831 Classifications: {'peptide': 989} Link IDs: {'PTRANS': 49, 'TRANS': 939} Chain breaks: 9 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 10, 'ASN:plan1': 5, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 14863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 14863 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 99 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 19.44, per 1000 atoms: 0.43 Number of scatterers: 45362 At special positions: 0 Unit cell: (123.67, 136.95, 193.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 O 4554 8.00 N 3836 7.00 C 14973 6.00 H 21895 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1314 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1313 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1314 " - " ASN C1134 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " Time building additional restraints: 33.44 Conformation dependent library (CDL) restraints added in 5.6 seconds 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5576 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 46 sheets defined 27.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 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 383 through 388 removed outlier: 3.738A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.307A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.687A pdb=" N ASN A 856 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.871A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 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 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.793A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.291A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.923A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.691A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.342A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.559A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.502A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.084A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.324A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.383A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.411A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.123A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.718A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.748A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.696A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.419A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.531A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.513A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.848A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.716A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.898A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.471A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.058A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.566A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.110A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 327 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: 6.348A 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 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.895A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.474A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.863A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.910A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.489A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.268A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.257A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.766A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.199A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 319 removed outlier: 5.831A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.442A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.982A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.779A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.895A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.397A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.409A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2781 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: 22.66 Time building geometry restraints manager: 34.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 21893 1.04 - 1.23: 1342 1.23 - 1.43: 8931 1.43 - 1.63: 13583 1.63 - 1.83: 128 Bond restraints: 45877 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.90e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 NAG B1313 " pdb=" O5 NAG B1313 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 ... (remaining 45872 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.76: 812 106.76 - 113.56: 53011 113.56 - 120.37: 15192 120.37 - 127.17: 13026 127.17 - 133.97: 215 Bond angle restraints: 82256 Sorted by residual: angle pdb=" N SER B 813 " pdb=" CA SER B 813 " pdb=" C SER B 813 " ideal model delta sigma weight residual 110.80 117.40 -6.60 2.13e+00 2.20e-01 9.61e+00 angle pdb=" C PRO B 812 " pdb=" N SER B 813 " pdb=" CA SER B 813 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.00e+00 angle pdb=" C ASN C 122 " pdb=" N ALA C 123 " pdb=" CA ALA C 123 " ideal model delta sigma weight residual 121.54 126.49 -4.95 1.91e+00 2.74e-01 6.70e+00 angle pdb=" CG ASN A 343 " pdb=" ND2 ASN A 343 " pdb="HD21 ASN A 343 " ideal model delta sigma weight residual 120.00 127.55 -7.55 3.00e+00 1.11e-01 6.33e+00 angle pdb=" C ASN A 122 " pdb=" N ALA A 123 " pdb=" CA ALA A 123 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 ... (remaining 82251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 21147 17.81 - 35.63: 1202 35.63 - 53.44: 377 53.44 - 71.26: 93 71.26 - 89.07: 23 Dihedral angle restraints: 22842 sinusoidal: 12481 harmonic: 10361 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.88 79.88 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -163.69 77.69 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -160.88 74.88 1 1.00e+01 1.00e-02 7.10e+01 ... (remaining 22839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3844 0.119 - 0.238: 77 0.238 - 0.357: 3 0.357 - 0.476: 1 0.476 - 0.594: 2 Chirality restraints: 3927 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.84e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 3924 not shown) Planarity restraints: 6999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 122 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C ASN A 122 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN A 122 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 123 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.024 2.00e-02 2.50e+03 2.11e-02 6.70e+00 pdb=" CG ASN B 61 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.032 2.00e-02 2.50e+03 pdb="HD21 ASN B 61 " -0.006 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 122 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ASN C 122 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN C 122 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA C 123 " 0.014 2.00e-02 2.50e+03 ... (remaining 6996 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 775 2.09 - 2.72: 75654 2.72 - 3.35: 126457 3.35 - 3.97: 166633 3.97 - 4.60: 259870 Nonbonded interactions: 629389 Sorted by model distance: nonbonded pdb=" H THR C 716 " pdb=" O GLN C1071 " model vdw 1.468 1.850 nonbonded pdb=" O PRO C1053 " pdb="HE21 GLN C1054 " model vdw 1.487 1.850 nonbonded pdb=" O LYS B 811 " pdb=" H SER B 813 " model vdw 1.505 1.850 nonbonded pdb=" H THR A 716 " pdb=" O GLN A1071 " model vdw 1.516 1.850 nonbonded pdb="HD21 ASN C 334 " pdb=" O ASN C 360 " model vdw 1.560 1.850 ... (remaining 629384 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 name H or name HA )) or resid 42 through 45 or (resid \ 46 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 through 52 or (resid 53 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 54 through 60 or (resid 61 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 \ or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 62 through \ 66 or resid 82 through 87 or (resid 88 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 89 through 95 or (resid 96 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 111 or (resid 112 through 113 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 116 through 124 or (resid 125 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 126 through 131 or (resid 132 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 13 \ 3 or (resid 134 through 138 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 139 through 140 or resid 166 through 168 or ( \ resid 169 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 170 through 171 or (resid 172 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 188 through 196 or (resid \ 200 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ or name OH or name HA or name HB \ 2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HH )) or r \ esid 201 through 209 or (resid 210 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or (resid 215 and (name N or name CA or name C \ or name O or name CB or name HA )) or resid 216 through 217 or (resid 218 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 219 through 223 or (resid 224 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 225 through 263 or resid 265 through 308 o \ r (resid 309 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 310 through 323 or (resid 324 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 325 through 332 or (res \ id 333 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 334 through 457 or (resid 458 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 459 through 528 or (resid 529 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 530 through 536 or (resid 537 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 538 through 747 or (resid 748 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 749 through 793 or (resid 794 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 795 or (resid 796 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 797 through 827 \ or (resid 854 and (name N or name CA or name C or name O or name CB or name HA ) \ ) or (resid 855 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 856 through 867 or (resid 868 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 869 through 939 or ( \ resid 940 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 941 through 984 or (resid 985 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 986 through 987 or (resid \ 988 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 989 through 1141 or (resid 1142 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 1143 through 1144 or (resid 11 \ 45 through 1146 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 1147 or resid 1303 through 1314)) selection = (chain 'B' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 42 through 45 or (resid \ 46 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 through 66 or resid 82 through 87 or (resid 88 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 89 through 10 \ 9 or (resid 110 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 111 or (resid 112 through 113 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or (resid 116 and (name N or \ name CA or name C or name O or name CB or name OG or name HA or name HB2 or name \ HB3 or name HG )) or resid 117 through 128 or (resid 129 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 130 through 134 \ or (resid 135 through 138 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 139 through 140 or (resid 166 and (name N or n \ ame CA or name C or name O or name CB or name SG or name HA or name HB2 or name \ HB3)) or resid 167 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 192 through 195 or (resid 19 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 200 through 205 or (resid 206 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 207 through 236 or (resid 237 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 238 through 241 or (resid 242 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 263 or resid 265 through 280 or (resid 2 \ 81 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 282 through 297 or (resid 298 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 299 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 325 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 390 through 457 or (resid 458 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 45 \ 9 through 567 or (resid 568 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 569 through 570 or (resid 571 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 572 thro \ ugh 579 or (resid 580 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 581 or (resid 582 through 583 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 584 through 61 \ 3 or (resid 614 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 615 through 618 or (resid 619 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 620 through 676 or ( \ resid 690 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 or \ name HG3 or name HE21 or name HE22)) or resid 691 through 744 or (resid 745 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 746 through 827 or (resid 854 and (name N or name CA or name C or name O or n \ ame CB or name HA )) or (resid 855 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 856 through 867 or (resid 868 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 8 \ 69 through 939 or (resid 940 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 941 through 984 or (resid 985 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 986 thr \ ough 987 or (resid 988 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 989 through 1063 or (resid 1064 and (name N or nam \ e CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name C \ E1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name \ HD2 or name HE1)) or resid 1065 through 1143 or (resid 1144 through 1146 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 54 through 66 or resid 8 \ 2 through 95 or (resid 96 through 97 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 98 through 113 or (resid 116 and (na \ me N or name CA or name C or name O or name CB or name OG or name HA or name HB2 \ or name HB3 or name HG )) or resid 117 through 134 or (resid 135 through 138 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 139 through 140 or (resid 166 and (name N or name CA or name C or name O or \ name CB or name SG or name HA or name HB2 or name HB3)) or resid 167 through 17 \ 2 or (resid 188 and (name N or name CA or name C or name O or name CB or name HA \ )) or resid 189 through 195 or (resid 196 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or (resid 200 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or n \ ame CE2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or \ name HD2 or name HE1 or name HE2 or name HH )) or resid 201 through 205 or (resi \ d 206 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 207 through 209 or (resid 210 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or (resid 215 and (name N or name CA or \ name C or name O or name CB or name HA )) or resid 216 through 217 or (resid 21 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 219 through 223 or (resid 224 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 225 through 233 or (resid 234 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 235 th \ rough 236 or (resid 237 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 238 through 297 or (resid 298 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 299 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 310 through 332 or (resid 333 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 334 through 342 or \ (resid 343 and (name N or name CA or name C or name O or name CB or name CG or \ name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) \ or resid 344 through 388 or (resid 389 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 390 through 527 or (resid 528 thr \ ough 529 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 530 through 536 or (resid 537 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 538 through 553 or (resid 5 \ 54 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 555 through 557 or (resid 558 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 559 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 569 through 570 or (resid 571 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 572 through 579 or (resid 580 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 58 \ 1 or (resid 582 through 583 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 584 through 602 or (resid 603 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or nam \ e H or name HA or name HB2 or name HB3 or name HD21)) or resid 604 through 618 o \ r (resid 619 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 620 through 645 or (resid 646 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 647 through 795 or (res \ id 796 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 797 through 1063 or (resid 1064 and (name N or name CA or name C o \ r name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 o \ r name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1) \ ) or resid 1065 through 1141 or (resid 1142 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 1143 or (resid 1144 through 1 \ 146 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 1147 or resid 1301 through 1314)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.860 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: 0.670 Extract box with map and model: 34.210 Check model and map are aligned: 0.620 Set scattering table: 0.360 Process input model: 141.040 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.300 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 191.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23982 Z= 0.278 Angle : 0.612 6.603 32699 Z= 0.325 Chirality : 0.049 0.594 3927 Planarity : 0.004 0.047 4159 Dihedral : 12.078 89.072 9156 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.73 % Allowed : 5.28 % Favored : 93.99 % 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: -0.75 (0.15), residues: 2921 helix: 0.41 (0.20), residues: 698 sheet: -0.22 (0.19), residues: 662 loop : -1.02 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1102 HIS 0.004 0.001 HIS B1083 PHE 0.016 0.001 PHE B 86 TYR 0.018 0.001 TYR A 369 ARG 0.005 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 352 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1111 GLU cc_start: 0.7350 (tt0) cc_final: 0.7120 (tt0) REVERT: B 92 PHE cc_start: 0.8036 (t80) cc_final: 0.7800 (t80) REVERT: B 878 LEU cc_start: 0.8965 (tp) cc_final: 0.8560 (mt) REVERT: C 269 TYR cc_start: 0.7028 (m-80) cc_final: 0.6663 (m-80) REVERT: C 389 ASP cc_start: 0.7134 (m-30) cc_final: 0.6820 (t0) REVERT: C 515 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7941 (p90) REVERT: C 983 ARG cc_start: 0.7435 (ttp-170) cc_final: 0.7121 (ttp-110) outliers start: 18 outliers final: 8 residues processed: 366 average time/residue: 0.8945 time to fit residues: 498.9636 Evaluate side-chains 226 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 141 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23982 Z= 0.253 Angle : 0.560 7.439 32699 Z= 0.296 Chirality : 0.045 0.367 3927 Planarity : 0.004 0.048 4159 Dihedral : 6.329 58.122 4209 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.25 % Allowed : 9.07 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.56 (0.15), residues: 2921 helix: 1.04 (0.20), residues: 680 sheet: -0.30 (0.19), residues: 665 loop : -1.03 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.005 0.001 HIS A1048 PHE 0.021 0.001 PHE C 238 TYR 0.014 0.001 TYR B 369 ARG 0.003 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 878 LEU cc_start: 0.9014 (tp) cc_final: 0.8557 (mt) REVERT: C 269 TYR cc_start: 0.7110 (m-80) cc_final: 0.6709 (m-80) REVERT: C 374 PHE cc_start: 0.6416 (m-80) cc_final: 0.6214 (m-10) REVERT: C 378 LYS cc_start: 0.7193 (ttmm) cc_final: 0.6970 (ttpt) REVERT: C 515 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.7984 (p90) outliers start: 31 outliers final: 17 residues processed: 266 average time/residue: 0.7706 time to fit residues: 326.2537 Evaluate side-chains 227 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 209 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 290 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 267 optimal weight: 0.0020 chunk 91 optimal weight: 0.7980 chunk 216 optimal weight: 0.7980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23982 Z= 0.215 Angle : 0.528 8.476 32699 Z= 0.278 Chirality : 0.044 0.262 3927 Planarity : 0.004 0.055 4159 Dihedral : 5.865 59.073 4209 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.33 % Allowed : 9.31 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.43 (0.15), residues: 2921 helix: 1.32 (0.21), residues: 675 sheet: -0.27 (0.19), residues: 659 loop : -0.99 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS C 519 PHE 0.020 0.001 PHE C 238 TYR 0.014 0.001 TYR B 369 ARG 0.006 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 878 LEU cc_start: 0.9071 (tp) cc_final: 0.8542 (mt) REVERT: C 269 TYR cc_start: 0.7110 (m-80) cc_final: 0.6668 (m-80) REVERT: C 389 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6751 (t0) outliers start: 33 outliers final: 22 residues processed: 246 average time/residue: 0.7526 time to fit residues: 299.2448 Evaluate side-chains 229 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 286 optimal weight: 0.9990 chunk 141 optimal weight: 0.0470 chunk 256 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23982 Z= 0.240 Angle : 0.517 7.339 32699 Z= 0.272 Chirality : 0.044 0.293 3927 Planarity : 0.003 0.044 4159 Dihedral : 5.675 59.166 4207 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.49 % Allowed : 10.12 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.39 (0.15), residues: 2921 helix: 1.45 (0.21), residues: 676 sheet: -0.29 (0.19), residues: 678 loop : -1.01 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 353 HIS 0.003 0.001 HIS C 519 PHE 0.022 0.001 PHE C 238 TYR 0.013 0.001 TYR B 369 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 CYS cc_start: 0.3501 (OUTLIER) cc_final: 0.3256 (t) REVERT: B 878 LEU cc_start: 0.9107 (tp) cc_final: 0.8531 (mt) REVERT: C 269 TYR cc_start: 0.7078 (m-80) cc_final: 0.6625 (m-80) REVERT: C 389 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6811 (t0) outliers start: 37 outliers final: 30 residues processed: 239 average time/residue: 0.7227 time to fit residues: 277.2449 Evaluate side-chains 232 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 0.4980 chunk 256 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23982 Z= 0.258 Angle : 0.512 5.638 32699 Z= 0.271 Chirality : 0.044 0.181 3927 Planarity : 0.003 0.042 4159 Dihedral : 5.568 58.164 4207 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 1.49 % Allowed : 10.73 % Favored : 87.78 % 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: -0.38 (0.15), residues: 2921 helix: 1.41 (0.21), residues: 680 sheet: -0.27 (0.19), residues: 671 loop : -0.99 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1102 HIS 0.003 0.001 HIS A1048 PHE 0.023 0.001 PHE C 238 TYR 0.013 0.001 TYR B 369 ARG 0.003 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: B 878 LEU cc_start: 0.9128 (tp) cc_final: 0.8527 (mt) REVERT: C 269 TYR cc_start: 0.7012 (m-80) cc_final: 0.6571 (m-80) REVERT: C 374 PHE cc_start: 0.6884 (m-80) cc_final: 0.6603 (m-80) REVERT: C 389 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6876 (t0) outliers start: 37 outliers final: 30 residues processed: 242 average time/residue: 0.7387 time to fit residues: 283.3498 Evaluate side-chains 237 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 0.1980 chunk 257 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 237 optimal weight: 0.5980 chunk 132 optimal weight: 30.0000 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23982 Z= 0.202 Angle : 0.489 5.093 32699 Z= 0.257 Chirality : 0.043 0.172 3927 Planarity : 0.003 0.043 4159 Dihedral : 5.387 58.496 4207 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 1.33 % Allowed : 10.69 % Favored : 87.98 % 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: -0.24 (0.15), residues: 2921 helix: 1.60 (0.21), residues: 677 sheet: -0.24 (0.19), residues: 680 loop : -0.91 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS C1088 PHE 0.025 0.001 PHE C 238 TYR 0.013 0.001 TYR B 369 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 209 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: B 878 LEU cc_start: 0.9110 (tp) cc_final: 0.8498 (mt) REVERT: C 269 TYR cc_start: 0.6963 (m-80) cc_final: 0.6530 (m-80) REVERT: C 389 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6942 (t0) REVERT: C 572 THR cc_start: 0.7963 (p) cc_final: 0.7614 (t) outliers start: 33 outliers final: 29 residues processed: 233 average time/residue: 0.7348 time to fit residues: 273.3246 Evaluate side-chains 232 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 201 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 285 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23982 Z= 0.277 Angle : 0.513 9.013 32699 Z= 0.272 Chirality : 0.044 0.190 3927 Planarity : 0.004 0.043 4159 Dihedral : 5.386 59.765 4206 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.04 % Rotamer: Outliers : 1.33 % Allowed : 10.97 % Favored : 87.70 % 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: -0.28 (0.15), residues: 2921 helix: 1.52 (0.21), residues: 677 sheet: -0.19 (0.19), residues: 669 loop : -0.95 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.003 0.001 HIS A1048 PHE 0.026 0.001 PHE C 238 TYR 0.014 0.001 TYR A 265 ARG 0.003 0.000 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 209 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.6566 (mt0) cc_final: 0.6270 (mt0) REVERT: A 957 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: B 878 LEU cc_start: 0.9142 (tp) cc_final: 0.8531 (mt) REVERT: C 269 TYR cc_start: 0.6918 (m-80) cc_final: 0.6506 (m-80) REVERT: C 389 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6942 (t0) REVERT: C 572 THR cc_start: 0.7973 (p) cc_final: 0.7632 (t) outliers start: 33 outliers final: 29 residues processed: 234 average time/residue: 0.7421 time to fit residues: 279.3795 Evaluate side-chains 233 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 23982 Z= 0.234 Angle : 0.505 11.169 32699 Z= 0.266 Chirality : 0.044 0.192 3927 Planarity : 0.003 0.044 4159 Dihedral : 5.285 59.690 4206 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 1.33 % Allowed : 11.17 % Favored : 87.50 % 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: -0.25 (0.15), residues: 2921 helix: 1.47 (0.21), residues: 684 sheet: -0.12 (0.20), residues: 668 loop : -0.93 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.003 0.001 HIS A1048 PHE 0.025 0.001 PHE C 238 TYR 0.013 0.001 TYR B 369 ARG 0.002 0.000 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.6618 (mt0) cc_final: 0.6328 (mt0) REVERT: A 723 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 957 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: B 878 LEU cc_start: 0.9123 (tp) cc_final: 0.8507 (mt) REVERT: C 269 TYR cc_start: 0.6898 (m-80) cc_final: 0.6481 (m-80) REVERT: C 389 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6945 (t0) REVERT: C 572 THR cc_start: 0.7959 (p) cc_final: 0.7627 (t) outliers start: 33 outliers final: 29 residues processed: 228 average time/residue: 0.7367 time to fit residues: 270.3319 Evaluate side-chains 233 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 251 optimal weight: 0.7980 chunk 264 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 23982 Z= 0.261 Angle : 0.508 9.834 32699 Z= 0.267 Chirality : 0.044 0.161 3927 Planarity : 0.004 0.043 4159 Dihedral : 5.196 57.979 4206 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 1.57 % Allowed : 11.21 % Favored : 87.22 % 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: -0.28 (0.15), residues: 2921 helix: 1.45 (0.21), residues: 683 sheet: -0.19 (0.20), residues: 664 loop : -0.92 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 PHE 0.018 0.001 PHE C 238 TYR 0.013 0.001 TYR A 265 ARG 0.002 0.000 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 213 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.6663 (mt0) cc_final: 0.6393 (mt0) REVERT: A 723 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8291 (p) REVERT: A 957 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: B 878 LEU cc_start: 0.9130 (tp) cc_final: 0.8523 (mt) REVERT: C 269 TYR cc_start: 0.6859 (m-80) cc_final: 0.6447 (m-80) REVERT: C 572 THR cc_start: 0.7964 (p) cc_final: 0.7641 (t) outliers start: 39 outliers final: 32 residues processed: 241 average time/residue: 0.7297 time to fit residues: 281.4163 Evaluate side-chains 241 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.3980 chunk 281 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 195 optimal weight: 0.9990 chunk 294 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 chunk 234 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 181 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23982 Z= 0.209 Angle : 0.495 8.359 32699 Z= 0.261 Chirality : 0.043 0.203 3927 Planarity : 0.003 0.044 4159 Dihedral : 5.052 55.797 4206 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.58 % Rotamer: Outliers : 1.41 % Allowed : 11.65 % Favored : 86.94 % 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: -0.18 (0.16), residues: 2921 helix: 1.55 (0.21), residues: 684 sheet: -0.14 (0.20), residues: 658 loop : -0.85 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS C1088 PHE 0.028 0.001 PHE C 238 TYR 0.012 0.001 TYR B 369 ARG 0.002 0.000 ARG C 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 206 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LEU 582 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue ILE 210 is missing expected H atoms. Skipping. Residue THR 333 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue LYS 558 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Residue LEU 1145 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue LEU 242 is missing expected H atoms. Skipping. Residue LYS 458 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue ILE 794 is missing expected H atoms. Skipping. Residue LYS 811 is missing expected H atoms. Skipping. Residue LYS 814 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue SER 940 is missing expected H atoms. Skipping. Residue LYS 1045 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 4.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 563 GLN cc_start: 0.6670 (mt0) cc_final: 0.6413 (mt0) REVERT: A 723 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8280 (p) REVERT: A 878 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8793 (mm) REVERT: B 878 LEU cc_start: 0.9118 (tp) cc_final: 0.8496 (mt) REVERT: B 985 ASP cc_start: 0.7200 (p0) cc_final: 0.6902 (p0) REVERT: C 269 TYR cc_start: 0.6837 (m-80) cc_final: 0.6413 (m-80) REVERT: C 572 THR cc_start: 0.7943 (p) cc_final: 0.7636 (t) outliers start: 35 outliers final: 28 residues processed: 234 average time/residue: 0.7453 time to fit residues: 281.8153 Evaluate side-chains 235 residues out of total 2603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 216 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 98 optimal weight: 0.0040 chunk 241 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130371 restraints weight = 89618.281| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.02 r_work: 0.3273 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23982 Z= 0.176 Angle : 0.482 7.628 32699 Z= 0.252 Chirality : 0.043 0.166 3927 Planarity : 0.003 0.048 4159 Dihedral : 4.890 53.477 4206 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 1.21 % Allowed : 12.02 % Favored : 86.77 % 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: -0.10 (0.16), residues: 2921 helix: 1.62 (0.21), residues: 693 sheet: -0.14 (0.20), residues: 674 loop : -0.80 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.002 0.001 HIS C1088 PHE 0.020 0.001 PHE B 92 TYR 0.012 0.001 TYR B 369 ARG 0.002 0.000 ARG C 577 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9653.30 seconds wall clock time: 171 minutes 47.01 seconds (10307.01 seconds total)